Syntrophobacter fumaroxidans oxidizes propionate to acetate via the methylmalonyl-CoA pathway, using protons as the electron acceptor and producing H2 and formate as electron sink products. This propionate oxidation is thermodynamically unfavorable under standard conditions and only proceeds when H2 and formate partial pressures are kept extremely low by a syntrophic partner. Formate dehydrogenase Fdh1 and hydrogenase Hox are the main confurcating enzymes used for energy conservation, while periplasmic Fdh2 and hydrogenase Hyn play an important role in reverse electron transport. -
+S. fumaroxidans oxidizes propionate in syntrophy with M. formicicum, releasing reducing equivalents through hydrogen and/or formate. The methylmalonyl-CoA pathway produces acetate and inorganic carbon. Partner consumption maintains low hydrogen partial pressure and formate concentration; these are different physical quantities. This is the tested methanogenic growth context, not universal partner dependence: sulfate or fumarate can support axenic growth. PARTIAL: comparative protein abundance and homology support proposed Fdh1/Hox confurcation and Fdh2/Hyn reverse-electron-transport roles, not direct demonstration of every enzyme assignment or the fraction of electrons carried by each route in this pair.
Source Taxon: Syntrophobacter fumaroxidans
@@ -650,7 +654,7 @@H2 and formate produced by S. fumaroxidans are consumed by M. formicicum for methanogenesis
+DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M. formicicum through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate fluxes in this pair.
Methanobacterium formicicum consumes the H2 and formate produced by S. fumaroxidans, combining them with CO2 to produce methane via hydrogenotrophic methanogenesis. This H2/formate removal maintains low partial pressures, making the thermodynamically unfavorable propionate oxidation by S. fumaroxidans energetically feasible. This interspecies electron transfer via both H2 and formate is a classic example of syntrophic metabolism in anaerobic environments critical for biogeochemical cycling. -
+M. formicicum acts as the hydrogen/formate-using methanogenic partner of S. fumaroxidans. Carrier consumption supports methane formation and relieves the thermodynamic constraint on propionate oxidation. Low hydrogen partial pressure and low formate concentration are distinct constraints; formate is not a gas pressure. The comparative proteome suggests an important formate route but does not independently quantify exact-pair carrier partitioning.
Source Taxon: Methanobacterium formicicum
@@ -769,13 +785,12 @@H2/formate scavenging by M. formicicum keeps both carriers at low partial pressure, which is what makes the thermodynamically unfavourable propionate oxidation by S. fumaroxidans feasible. S. fumaroxidans oxidizes propionate either in syntrophy with an H2/formate-utilizing methanogen or, axenically, only with an external electron acceptor (sulfate or fumarate). Reciprocal arm of the syntrophic loop; DIRECTLY IMPLIED by the axenic-vs-syntrophic contrast rather than demonstrated by a partner-removal or carrier-inhibition perturbation in this exact pair.
+DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. formicicum lowers hydrogen partial pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective carrier-removal assay in this exact pair.
Reciprocal formate and H2 exchange links S. fumaroxidans propionate oxidation to M. formicicum hydrogenotrophic methanogenesis. -
+Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen, not bidirectional donation.
S. fumaroxidans grows syntrophically on propionate with the H2/formate-consuming methanogen M. formicicum, combining bacterial propionate oxidation, interspecies carrier transfer, and hydrogenotrophic methanogenesis into a coupled anaerobic conversion. -
+The S. fumaroxidans-M. formicicum coculture joins propionate oxidation to methanogenesis. This community conversion is the outcome of the two existing partner processes, not a third pairwise exchange. Acetate remains a bacterial product, so this does not assert complete mineralization of propionate carbon to methane.
@@ -926,7 +939,7 @@Several evidence items on this record quote doi:10.1099/00207713-48-4-1383 (Harmsen et al. 1998), whose syntrophic coculture passage names *Methanospirillum hungateii*, not this record's partner *Methanobacterium formicicum*. Two of those items previously carried explanations asserting that the passage established M. formicicum as the partner; they have been corrected and downgraded to PARTIAL, and exact-pair support has been added from PMID:29611893 (Sedano-Nunez et al. 2018), which explicitly grew S. fumaroxidans in syntrophy with M. formicicum. The residual gap: the frequently cited biochemical formate-transfer and FDH/hydrogenase transcription results for this system were obtained with M. hungatei, so carrier apportionment ("formate is the dominant carrier") must NOT be curated as an exact-pair finding. PARTLY RESOLVED: the 2024 exact-pair perturbation study (Li et al., Water 16:3551, doi:10.3390/w16243551) is now ingested - its full text was supplied by a curator from the publisher PDF, since the journal is absent from PubMed and Europe PMC and MDPI blocks programmatic download. Its graded-formate results for the exact S. fumaroxidans-M. formicicum coculture are curated under the Exogenous Formate Dosage environmental factor, and its FDH downregulation result on the Propionate Oxidation interaction. Two cautions came out of that ingestion: (a) the paper runs an anaerobic-sludge system ALONGSIDE the coculture, and sludge-only results (e.g. Acetobacterium homoacetogenesis rising with formate dose) must not be attributed to this two-member consortium; (b) the dose response is non-monotonic - 30 mM recovers in the later stage - so it is NOT a simple ">=30 mM inhibits" threshold. Still open: carrier apportionment between H2 and formate for the M. formicicum pair specifically, which no retrieved study resolves with an isotope or selective-inhibition experiment. -
+ Batch112: the graph now uses exact-pair proteomic cultivation evidence rather than the 1998 M. hungatei passage as full support. Main-text Fdh1/Hox assignments are qualified mechanistic interpretations; no exact-pair hydrogen/formate flux ratio is inferred. The 2024 transcription passages were rechecked in the existing curator-supplied text; fresh publisher retrieval was unavailable. Hydrogen partial pressure is distinguished from formate concentration.Attaches to: ecological_interactions#Propionate Oxidation and H2/Formate Production, ecological_interactions#Interspecies Electron Transfer and Methanogenesis
Syntrophobacter fumaroxidans oxidizes propionate to acetate via the methylmalonyl-CoA pathway, using protons as the electron acceptor and producing H2 and formate as electron sink products. This propionate oxidation is thermodynamically unfavorable under standard conditions and only proceeds when H2 and formate partial pressures are kept extremely low by a syntrophic partner. Formate dehydrogenase Fdh1 and hydrogenase Hox are the main confurcating enzymes used for energy conservation, while periplasmic Fdh2 and hydrogenase Hyn play an important role in reverse electron transport. -
+S. fumaroxidans oxidizes propionate in syntrophy with M. hungatei, releasing reducing equivalents through hydrogen and/or formate. The methylmalonyl-CoA pathway produces acetate and inorganic carbon. Partner consumption maintains low hydrogen partial pressure and formate concentration; these are different physical quantities. This is the tested methanogenic growth context, not universal partner dependence: sulfate or fumarate can support axenic growth. PARTIAL: comparative protein abundance and homology support proposed Fdh1/Hox confurcation and Fdh2/Hyn reverse-electron-transport roles, not direct demonstration of every enzyme assignment or the fraction of electrons carried by each route in this pair.
Source Taxon: Syntrophobacter fumaroxidans
@@ -639,7 +643,7 @@H2 and formate produced by S. fumaroxidans are consumed by M. hungatei for methanogenesis
+DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M. hungatei through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate fluxes in this pair.
Methanospirillum hungatei consumes the H2 and formate produced by S. fumaroxidans, combining them with CO2 to produce methane via hydrogenotrophic methanogenesis. This H2/formate removal maintains low partial pressures, making the thermodynamically unfavorable propionate oxidation by S. fumaroxidans energetically feasible. This interspecies electron transfer via both H2 and formate is a classic example of syntrophic metabolism in anaerobic environments critical for biogeochemical cycling. -
+M. hungatei acts as the hydrogen/formate-using methanogenic partner of S. fumaroxidans. Carrier consumption supports methane formation and relieves the thermodynamic constraint on propionate oxidation. Low hydrogen partial pressure and low formate concentration are distinct constraints; formate is not a gas pressure. The comparative proteome suggests an important formate route but does not independently quantify exact-pair carrier partitioning.
Source Taxon: Methanospirillum hungatei
@@ -732,13 +748,12 @@H2/formate scavenging by M. hungatei keeps the partial pressures of both carriers low enough for propionate oxidation to remain thermodynamically feasible. S. fumaroxidans oxidizes propionate either syntrophically with an H2/formate-utilizing partner or, in pure culture, only when supplied with an external electron acceptor (sulfate or fumarate) — establishing the partner-dependence that this feedback edge encodes. Reciprocal arm of the syntrophic loop.
+DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. hungatei lowers hydrogen partial pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective carrier-removal assay in this exact pair.
Reciprocal formate and H2 exchange links S. fumaroxidans propionate oxidation to M. hungatei hydrogenotrophic methanogenesis. -
+Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen, not bidirectional donation.
S. fumaroxidans oxidizes propionate syntrophically with the H2/formate-utilizing methanogen M. hungatei, forming a coupled anaerobic conversion that joins propionate catabolism with hydrogenotrophic methanogenesis. -
+The S. fumaroxidans-M. hungatei coculture joins propionate oxidation to methanogenesis. This community conversion is the outcome of the two existing partner processes, not a third pairwise exchange. Acetate remains a bacterial product, so this does not assert complete mineralization of propionate carbon to methane.
@@ -844,13 +870,13 @@Comparative proteomics supports candidate energy-conservation and electron-transfer roles. It does not resolve exact carrier fractions or selectively demonstrate all enzyme assignments. Existing metabolic feedback is retained with that boundary.
+ +Attaches to: ecological_interactions#Propionate Oxidation and H2/Formate Production, ecological_interactions#Interspecies Electron Transfer and Methanogenesis
It has long been speculated that formate plays a more important role than hydrogen as an electron carrier
+The main text explicitly frames relative carrier importance as a mechanistic interpretation rather than a measured exact-pair flux.
+S. wolfei and M. maripaludis form a thermodynamically required syntrophic partnership in which fatty acid oxidation is coupled to methanogenesis under anoxic conditions. -
+S. wolfei and M. maripaludis grow syntrophically on butyrate, coupling bacterial oxidation to hydrogenotrophic methanogenesis. The dependence is for the tested butyrate medium; S. wolfei was separately maintained in pure culture on crotonate.
Source Taxon: Syntrophomonas wolfei
@@ -665,8 +659,7 @@The thermodynamically required syntrophic coupling of butyrate oxidation to hydrogenotrophic methanogenesis drives coordinated partner growth — cultures inoculated at different initial cell ratios converge to a relatively constant Syntrophomonas:Methanococcus ratio over time. -
+DIRECTLY IMPLIED/PARTIAL: syntrophic metabolism supports growth of both partners during the observed convergence of their population ratio. Different starting ratios alter relative growth and lag, but the study does not isolate a molecular feedback controller that enforces the endpoint ratio.
When the two members were inoculated at different initial ratios, the initially lower-abundance organism grew faster and the population ratio converged, indicating growth synchronization between partners. -
+In the mesophilic S. wolfei-M. maripaludis cultures, different starting population ratios converged to around one during growth. This is a community population outcome, not a second directional mutualism interaction or proof that the converged ratio itself accelerates metabolism.
-Source Taxon: Syntrophomonas wolfei
+Participating Taxa: -
Target Taxon: Methanococcus maripaludis
+ Syntrophomonas wolfei, + + Methanococcus maripaludis + + @@ -738,17 +733,6 @@Cell aggregation and attraction keep butyrate-oxidizing and hydrogenotrophic partners close enough for efficient H2 transfer during syntrophic methanogenesis. -
-FISH, SEM, and microfluidic experiments showed aggregate formation and directional attraction between Syntrophomonas and Methanococcus cells, supporting spatial organization as part of syntrophic cooperation. -
+FISH and SEM showed development of mixed aggregates, while microfluidic loading in either order showed preferential movement toward the other partner. A same-organism control lacked that preference. This supports reciprocal spatial association, not a uniquely directed colonization effect. Ultrasound and shaking reduced methane-production activity without a detectable change in aggregation tendency; causal mediation by aggregation remains unresolved.
-Source Taxon: Syntrophomonas wolfei
+Participating Taxa: -
Target Taxon: Methanococcus maripaludis
+ Syntrophomonas wolfei, + + Methanococcus maripaludis + + @@ -830,7 +803,7 @@Aggregation and disturbance-resistant cell-to-cell attraction are observed, but no experiment demonstrates that aggregation increases butyrate oxidation or methane production in this exact coculture, so no aggregation→enhancement `downstream` edge was added. Likewise, carbon-nanotube acceleration of methane production is reported, but DIET "does not always explain the enhancement of methane production" and was not directly proven here, so a DIET mechanism is not asserted. -
+The former population-ratio-to-metabolism arrow described aggregation rather than its source node and is removed. Initial ratios were experimentally varied; the converged endpoint is not an independently manipulated cause. Reciprocal attraction is supported, but ultrasound and shaking change activity without changing aggregation tendency. The separate nanomaterial study reports acceleration and proposes DIET without a decisive demonstration. No new aggregation-to-metabolism direction is added.
-Attaches to: ecological_interactions#Syntrophic Aggregation and Cell-to-Cell Attraction
Attaches to: ecological_interactions#Population Ratio Convergence During Growth, ecological_interactions#Syntrophic Aggregation and Cell-to-Cell Attraction
suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus
-Attraction/aggregation is observed, but its causal contribution to metabolic performance is untested — the basis for the knowledge gap.
+the tendency of microbial aggregation was not
+Aggregation tendency was unchanged despite the disturbance-associated activity change.
+Though decisive conclusion can not be made, our study tends to support the possibility of DIET in syntrophic oxidation of butyrate.
+The nanomaterial study explicitly qualifies DIET; it is not proof of the carrier mechanism in the unamended coordination assay.
Syntrophomonas wolfei β-oxidizes butyrate (C4) to acetate, using protons as the electron acceptor and producing H2 as the electron sink product. This fatty acid β-oxidation is thermodynamically unfavorable under standard conditions and only proceeds when H2 partial pressure is kept extremely low by a syntrophic partner. The organism cannot utilize common electron acceptors (nitrate, sulfate, etc.) and is therefore obligately dependent on syntrophic H2 removal. -
+S. wolfei oxidizes butyrate to acetate with hydrogen as an electron-sink product in the studied syntrophic cultures. Common electron acceptors did not support the tested butyrate metabolism. This is substrate- and assay-bounded dependence on a hydrogen-using partner, not a claim that every substrate requires coculture.
Source Taxon: Syntrophomonas wolfei
@@ -654,7 +658,7 @@Methanospirillum hungatei consumes the H2 produced by S. wolfei, combining it with CO2 to produce methane via hydrogenotrophic methanogenesis. This H2 removal maintains a low H2 partial pressure (<10^-4 atm), making the thermodynamically unfavorable butyrate oxidation by S. wolfei energetically feasible. This interspecies hydrogen transfer (IHT) is the classic example of syntrophic metabolism in anaerobic environments. -
+M. hungatei is a documented hydrogen-using partner of S. wolfei. Hydrogen removal supports bacterial butyrate oxidation and methanogenesis. The abstract reports inhibition of growth and butyrate degradation by added hydrogen, but does not provide an exact permissive partial-pressure threshold or quantify competing carrier contributions.
Source Taxon: Methanospirillum hungatei
@@ -724,7 +727,7 @@H2 scavenging by M. hungatei keeps the H2 partial pressure low enough for butyrate β-oxidation to remain thermodynamically feasible; S. wolfei grows and degrades butyrate only in association with an H2-using partner, and adding H2 back to the medium stops both. Reciprocal (feedback) arm of the syntrophic loop.
+DIRECTLY IMPLIED feedback: removal of hydrogen by the methanogenic partner relieves a constraint on S. wolfei butyrate oxidation. The 1981 abstract reports that added hydrogen stops growth and butyrate degradation; it does not specify a numerical permissive threshold or isolate hydrogen from all alternative carrier routes in this exact pairing.
S. wolfei oxidizes butyrate only when a hydrogen-consuming partner such as M. hungatei removes the produced H2, coupling fatty-acid beta-oxidation to hydrogenotrophic methanogenesis in the two-member consortium. -
+S. wolfei butyrate oxidation is coupled to hydrogen-consuming M. hungatei methanogenesis in the documented coculture. This is a community conversion endpoint, not an additional pairwise exchange; acetate is retained as an organic product.
@@ -859,6 +834,19 @@The accessible primary abstract supports the named partner and hydrogen-addition inhibition, but not the former less-than-10^-4-atm threshold. The existing feedback remains directly implied; no carrier-exclusive mechanism or universal obligacy is asserted. The older full-text XML endpoint failed, so detailed perturbation conditions remain unverified here.
+ +Attaches to: ecological_interactions#Butyrate Oxidation and H2 Production, ecological_interactions#Interspecies Hydrogen Transfer and Methanogenesis
The addition of H(2) to the medium stopped growth and butyrate degradation by S. wolfei.
+The reported hydrogen perturbation supports product-inhibition feedback; the abstract does not specify every assay condition or a numerical threshold.
+S. aciditrophicus strain SB metabolizes benzoate in coculture with hydrogen-using partners and transiently produces cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate during growth on benzoate. These Syntrophus reactions initiate the methanogenic coculture conversion of benzoate to acetate and methane. -
+S. aciditrophicus strain SB metabolizes benzoate in the M. hungatei coculture, with transient alicyclic and dicarboxylate intermediates. This is the syntrophic route; the separate pure-culture experiment also demonstrates benzoate fermentation with a different product balance. Enzyme activities measured with Desulfovibrio or crotonate-grown pure cultures are not attributed as exact-pair assays here.
Source Taxon: Syntrophus aciditrophicus SB
@@ -596,8 +600,8 @@Metabolites:
benzoate
- (CHEBI:30746),
+ (CHEBI:16150),
acetate
(Syntrophus Benzoate Metabolism
Downstream Effects:
S. aciditrophicus benzoate metabolism supplies reduced products to the methanogenic partner and enables methane-producing benzoate mineralization by the coculture. Bacterial benzoate metabolism supplies reducing equivalents for the methanogenic partner and generates acetate, enabling the coupled coculture conversion rather than complete carbon mineralization. M. hungatei functions as the hydrogen-using methanogen in the S. aciditrophicus coculture. Hydrogen consumption keeps the concentration of hydrogen produced during benzoate oxidation low, a thermodynamic requirement for anaerobic benzoate degradation through interspecies hydrogen transfer.
- M. hungatei is the hydrogen-using methanogen in the benzoate coculture. Hydrogen consumption provides an electron sink for the syntrophic conversion to acetate and methane. This does not mean benzoate metabolism is impossible without a partner: S. aciditrophicus pure cultures ferment benzoate with cyclohexane carboxylate accumulation and a different acetate yield. Source Taxon: Methanospirillum hungatei Methanogenic hydrogen removal closes the syntrophic electron sink that lets benzoate oxidation continue to methane production. Methanogenic hydrogen consumption supplies the electron sink that couples benzoate oxidation to methane production and the coculture product balance; a different benzoate fermentation remains possible without this partner. The two-member S. aciditrophicus-M. hungatei coculture consumes benzoate and completes the methanogenic community outcome by producing acetate and methane at the stoichiometry predicted for syntrophic benzoate degradation.
- The two-member benzoate coculture produced approximately three mol acetate and 0.75 mol methane per mol benzoate, as summarized in the primary abstract. This is substrate conversion, not complete mineralization: acetate remains organic carbon. The reported pure-culture product balance differs, including cyclohexane carboxylate accumulation. Metabolites:
benzoate
- (CHEBI:30746),
+ (CHEBI:16150),
acetate
(Evidence
- SUPPORT (IN_VITRO)
Metabolites:
benzoate
- (CHEBI:30746),
+ (CHEBI:16150),
acetate
(Evidence
During growth on benzoate, the free energy available to S. gentianae was near the lower limit for energy conservation, showing why syntrophic partner activity and product concentrations constrain the community. During growth of the methanogenic coculture, calculated free energy available to S. gentianae was -50 to -55 kJ per mol benzoate. The authors inferred an approximate -45 kJ/mol requirement for growth and energy conservation. This is a condition-dependent energetic constraint of the fermenter, not a second partner-directed syntrophy event or an invariant value for every suspension or perturbation. Source Taxon: Syntrophus gentianae Target Taxon: Methanospirillum hungatei Metabolites:
benzoate
- (CHEBI:30746)
+ (CHEBI:16150)
Accumulated acetate and hydrogen thermodynamically inhibit the syntrophic reaction, lowering benzoate-degradation rates when products build up. DIRECTLY IMPLIED: the fermenter must conserve sufficient energy to sustain growth-associated benzoate conversion. The observed endpoint correlates with residual substrate and calculated free energy; the inferred approximate growth threshold is not an independently manipulated universal constant. Acetate and hydrogen inhibited benzoate degradation thermodynamically, while acetate and propionate additions lowered the degradation rate, linking product accumulation to community performance. Accumulated hydrogen and acetate constrain methanogenic benzoate degradation thermodynamically. Acetate and separately added propionate also lower degradation rate; propionate is not identified as a benzoate product here. These are metabolite and energetic constraints on the coculture, not competition between S. gentianae and M. hungatei. Rescue with added sulfate reducers or Methanosaeta changes community composition and is not an unmodified two-member outcome. Source Taxon: Syntrophus gentianae Participating Taxa:
- Target Taxon: Methanospirillum hungatei Hydrogen and acetate product accumulation constrain the free energy remaining to the benzoate-fermenting Syntrophus partner. Product accumulation changes the free energy available to the fermenter, bringing growth-associated benzoate conversion toward its energetic limit. Acetate also partly uncouples substrate degradation from energy conservation, so this does not assert that product addition changes a fixed intrinsic threshold. The primary abstract distinguishes growing cocultures from cell suspensions and inhibitor or added-partner treatments. Its approximate -45 kJ/mol growth requirement is not a universal endpoint. The graph preserves product-inhibition constraints without encoding interspecies competition or treating expanded-community rescue as the original pair. Attaches to: acetate also partly uncouples substrate degradation from energy conservation This is an energetic constraint rather than a competition phenotype. Addition of T. flocculiformis ES5 stimulated the S. wolfei and M. hungatei syntrophic coculture, increasing butyrate consumption and volumetric methane production.
- Adding T. flocculiformis ES5 stimulated the S. wolfei-M. hungatei culture, most clearly by shortening the lag before conversion. In the exact-pair comparison, Table 1 marks the methane lag difference significant, not the fitted maximum production-rate or final-concentration differences. The Discussion reports similar butyrate-consumption slopes with and without ES5. Abstract-wide 120%/150% wording is not an exact-triculture increase estimate. This is a three-member outcome, not an ES5-to-S. wolfei syntrophic exchange. Source Taxon: Trichococcus flocculiformis strain ES5 Participating Taxa:
- Target Taxon: Syntrophomonas wolfei Scanning electron microscopy showed a tendency for T. flocculiformis ES5 to aggregate with S. wolfei and M. hungatei in the most positively affected coculture, consistent with spatial facilitation of the syntrophic partners.
- SEM of the exact three-member culture showed ES5 in close spatial association with both syntrophic partners and altered aggregation relative to the biculture. This is a community morphology observation, not an isolated directional colonization benefit or proof of conductive bridging. Source Taxon: Trichococcus flocculiformis strain ES5 Participating Taxa:
+ Trichococcus flocculiformis strain ES5,
- Target Taxon: Methanospirillum hungatei HYPOTHESIZED — ES5 co-aggregation with S. wolfei and M. hungatei may spatially facilitate the improved butyrate oxidation and methane production, but the aggregation is an observed correlate of the ES5 effect and was NOT demonstrated to causally mediate the rate increases.
- HYPOTHESIZED/PARTIAL: ES5-associated aggregation could contribute to the shorter conversion lag, but morphology was not selectively manipulated to show mediation. Conductive bridging and DIET remain proposed explanations, not demonstrated routes. Proteome analysis linked ES5 addition to signal-transducing systems in M. hungatei and activation of additional butyryl coenzyme A dehydrogenase and electron transfer flavoprotein in S. wolfei.
- Comparative proteomics of the two syntrophic partners with and without ES5 detected differential protein abundance. Additional S. wolfei butyryl-CoA dehydrogenase and electron-transfer flavoprotein were more abundant in the triculture; many candidate M. hungatei signaling proteins were instead more abundant in the biculture. These observations do not directly measure enzyme activation, prove a signaling mechanism or establish a second syntrophic exchange. ES5 is the added member; the assayed proteomes belong to S. wolfei and M. hungatei. Source Taxon: Trichococcus flocculiformis strain ES5 Participating Taxa:
+ Trichococcus flocculiformis strain ES5,
- Target Taxon: Syntrophomonas wolfei HYPOTHESIZED — the ES5-associated proteomic changes (activation of additional butyryl-CoA dehydrogenase and electron-transfer flavoprotein in S. wolfei; signal-transducing systems in M. hungatei) may underlie the improved butyrate oxidation, but the proteome response is correlative and was NOT shown to be the causal mediator of the improved performance.
- HYPOTHESIZED/PARTIAL: changes in partner protein abundance may contribute to the shorter lag associated with ES5 addition. The comparison does not selectively establish enzymatic or signaling mediation, and protein abundance is not a direct activity assay. The ES5-driven increase in butyrate consumption (120%) and methane (150%) is perturbation-supported, but the mediating mechanism is unresolved: aggregation and the partner proteome response are observed correlates, not demonstrated causal mediators (the two `downstream` edges here are flagged HYPOTHESIZED accordingly). Direct interspecies electron transfer was not experimentally demonstrated for this tri-culture, and the exact ES5 bridging role remains an open question per the source.
- The exact-pair Results and Table 1 support a shorter lag; the Discussion reports similar butyrate-consumption slopes. The former abstract-wide 120%/150% increase attribution is therefore removed from this discussion and graph. Aggregation and differential protein abundance are measured correlates, while causal mediation, conductive bridging and DIET remain unresolved. Both existing explanatory arrows stay hypothetical. No direct enzyme activation or uniformly enhanced methanogen signaling is inferred. Attaches to: Attaches to: T. flocculiformis ES5 to aggregate with the syntrophic partners Aggregation is reported as an association accompanying the ES5 effect, without a demonstrated causal-mediation or DIET mechanism — the basis for the knowledge gap. it is not clear whether the presence of T. flocculiformis ES5 alone was activating production of this enzyme. The source explicitly withholds direct enzyme-activation attribution.Evidence
- SUPPORT (IN_VITRO)
- Evidence
- SUPPORT (IN_VITRO)
- Evidence
Interspecies Hydrogen Transfer and Methanogenesis
SYNTROPHY
- Interspecies Hydrogen Transfer and Methanogenesis
Downstream Effects:
Evidence
- SUPPORT (IN_VITRO)
- Evidence
- SUPPORT (IN_VITRO)
- Evidence
Community Benzoate Mineralization to Acetate and Methane
- SYNTROPHY
+ Community Benzoate Conversion to Acetate and Methane
Community Benzoate Mineralization to Acetate and Methane
Evidence
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1233,7 +1234,7 @@ Evidence
nodes.push({
id: intId,
- label: "Community Benzoate Mineralization to Acetate and Methane",
+ label: "Community Benzoate Conversion to Acetate and Methane",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html b/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html
index 28bbdd17f..e40a65ba7 100644
--- a/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html
+++ b/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html
@@ -585,7 +585,7 @@ Ecological Interactions
Ecological Interactions
Methanogenic Benzoate Degradation
Minimum Energy Threshold for Syntrophic Growth
- SYNTROPHY
Minimum Energy Threshold for Syntrophic Growth
Evidence
- SUPPORT (IN_VITRO)
- Evidence
Product Inhibition of Benzoate Degradation
- COMPETITION
Product Inhibition of Benzoate Degradation
Associated Datasets
+ Knowledge gaps & discussions (1)
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How do energetic limits vary with growth, dense suspensions and added partners?
+
+ ecological_interactions#Minimum Energy Threshold for Syntrophic Growth, ecological_interactions#Product Inhibition of Benzoate Degradation1 evidence item(s)
+
+ Evidence
(function() {
var intId = "interaction:1";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1437,16 +1476,11 @@ Evidence
- var tgtKey = "Methanospirillum hungatei";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
-
})();
(function() {
var intId = "interaction:2";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1474,17 +1508,20 @@ Evidence
});
- var srcKey = "Syntrophus gentianae";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Methanospirillum hungatei";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Syntrophus gentianae",
+
+ "Methanospirillum hungatei"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html b/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html
index c3f7e3972..c74e12348 100644
--- a/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html
+++ b/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html
@@ -640,7 +640,7 @@ Ecological Interactions
Ecological Interactions
Ecological Interactions
Fermenter-Stimulated Butyrate Oxidation and Methane Production
- SYNTROPHY
Evidence
- SUPPORT (IN_VITRO)
Evidence
- SUPPORT (IN_VITRO)
- Evidence
Aggregation With Syntrophic Partners
- COLONIZATION_FACILITATION
Aggregation With Syntrophic Partners
Evidence
- SUPPORT (IN_VITRO)
- Evidence
Proteome Response in the Syntrophic Partners
- SYNTROPHY
Proteome Response in the Syntrophic Partners
Evidence
- SUPPORT (IN_VITRO)
- Evidence
PMID:35699440
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
- Knowledge gaps & discussions (1)
KNOWLEDGE_GAP
OPEN
- Does T. flocculiformis ES5 improve the S. wolfei / M. hungatei syntrophy via co-aggregation-based spatial bridging (possible DIET) or via the observed proteomic changes, and is either mechanism causal rather than correlative?
-
+ Which ES5-associated processes mediate the shorter lag in this exact triculture?
- ecological_interactions#Aggregation With Syntrophic Partners, ecological_interactions#Proteome Response in the Syntrophic Partnersecological_interactions#Fermenter-Stimulated Butyrate Oxidation and Methane Production, ecological_interactions#Aggregation With Syntrophic Partners, ecological_interactions#Proteome Response in the Syntrophic Partners
-
Evidence
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1461,23 +1451,28 @@ Evidence
});
- var srcKey = "Trichococcus flocculiformis strain ES5";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Syntrophomonas wolfei";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Trichococcus flocculiformis strain ES5",
+
+ "Syntrophomonas wolfei",
+
+ "Methanospirillum hungatei"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1486,7 +1481,7 @@ Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 1;
nodes.push({
id: intId,
@@ -1499,23 +1494,28 @@ Evidence
});
- var srcKey = "Trichococcus flocculiformis strain ES5";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Methanospirillum hungatei";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Trichococcus flocculiformis strain ES5",
+
+ "Syntrophomonas wolfei",
+
+ "Methanospirillum hungatei"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1537,17 +1537,22 @@ Evidence
});
- var srcKey = "Trichococcus flocculiformis strain ES5";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Syntrophomonas wolfei";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Trichococcus flocculiformis strain ES5",
+
+ "Syntrophomonas wolfei",
+
+ "Methanospirillum hungatei"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/history/records/Syntrophobacter_Methanobacterium_Syntrophy/2026-10-08T071057Z-codex-d473fc.yaml b/history/records/Syntrophobacter_Methanobacterium_Syntrophy/2026-10-08T071057Z-codex-d473fc.yaml
new file mode 100644
index 000000000..b736ccb66
--- /dev/null
+++ b/history/records/Syntrophobacter_Methanobacterium_Syntrophy/2026-10-08T071057Z-codex-d473fc.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml
+ slug: Syntrophobacter_Methanobacterium_Syntrophy
+session:
+ id: 2026-10-08T071057Z-codex-d473fc
+ timestamp: '2026-10-08T07:10:57Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1871
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain
+ carrier-removal feedback with physical units and flux uncertainty explicit.; Retain coupled
+ community conversion without duplicate exchange typing.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/history/records/Syntrophobacter_Methanospirillum_Syntrophy/2026-10-08T071057Z-codex-fb396b.yaml b/history/records/Syntrophobacter_Methanospirillum_Syntrophy/2026-10-08T071057Z-codex-fb396b.yaml
new file mode 100644
index 000000000..11af0d269
--- /dev/null
+++ b/history/records/Syntrophobacter_Methanospirillum_Syntrophy/2026-10-08T071057Z-codex-fb396b.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml
+ slug: Syntrophobacter_Methanospirillum_Syntrophy
+session:
+ id: 2026-10-08T071057Z-codex-fb396b
+ timestamp: '2026-10-08T07:10:57Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1871
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain
+ carrier-removal feedback with physical units and flux uncertainty explicit.; Retain coupled
+ community conversion without duplicate exchange typing.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/history/records/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture/2026-10-08T071057Z-codex-28253a.yaml b/history/records/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture/2026-10-08T071057Z-codex-28253a.yaml
new file mode 100644
index 000000000..0ef5b1653
--- /dev/null
+++ b/history/records/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture/2026-10-08T071057Z-codex-28253a.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
+ slug: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+session:
+ id: 2026-10-08T071057Z-codex-28253a
+ timestamp: '2026-10-08T07:10:57Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1872
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain substrate-bounded syntrophic growth and qualify the existing growth-to-ratio
+ inference.; Retain population convergence as an outcome and remove misplaced reverse causality.;
+ Retain reciprocal attraction and aggregation without one-way colonization or proven metabolic
+ mediation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/history/records/Syntrophomonas_Methanospirillum_Syntrophy/2026-10-08T071058Z-codex-a2e51d.yaml b/history/records/Syntrophomonas_Methanospirillum_Syntrophy/2026-10-08T071058Z-codex-a2e51d.yaml
new file mode 100644
index 000000000..d3eed99bc
--- /dev/null
+++ b/history/records/Syntrophomonas_Methanospirillum_Syntrophy/2026-10-08T071058Z-codex-a2e51d.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml
+ slug: Syntrophomonas_Methanospirillum_Syntrophy
+session:
+ id: 2026-10-08T071058Z-codex-a2e51d
+ timestamp: '2026-10-08T07:10:58Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1873
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain butyrate oxidation with substrate-bounded dependence.; Retain hydrogen feedback
+ without an uncited pressure threshold or duplicate evidence.; Retain the conversion endpoint
+ without an additional exchange claim.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/history/records/Syntrophus_Benzoate_Degrader/2026-10-08T071058Z-codex-9e1dfe.yaml b/history/records/Syntrophus_Benzoate_Degrader/2026-10-08T071058Z-codex-9e1dfe.yaml
new file mode 100644
index 000000000..43f6084a9
--- /dev/null
+++ b/history/records/Syntrophus_Benzoate_Degrader/2026-10-08T071058Z-codex-9e1dfe.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophus_Benzoate_Degrader.yaml
+ slug: Syntrophus_Benzoate_Degrader
+session:
+ id: 2026-10-08T071058Z-codex-9e1dfe
+ timestamp: '2026-10-08T07:10:58Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1874
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain coculture benzoate metabolism without importing other-partner enzyme assays.;
+ Bound hydrogen-user dependence to the syntrophic product route.; Rename mineralization
+ as conversion and correct graph benzoate grounding.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml b/history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml
new file mode 100644
index 000000000..985d2f522
--- /dev/null
+++ b/history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophus_Benzoate_Degrader.yaml
+ slug: Syntrophus_Benzoate_Degrader
+session:
+ id: 2026-10-08T072502Z-codex-a76868
+ timestamp: '2026-10-08T07:25:02Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1874
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ summary: 'Use a shorter contiguous benzoate-intermediate quote after bracket-stripping failure
+ #622; retain the compound-or-CoA qualification and original failed validation log.'
+ details: Append-only correction after initial batch112 reference validation; original history
+ and failed log retained.
diff --git a/history/records/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture/2026-10-08T071058Z-codex-4e26a3.yaml b/history/records/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture/2026-10-08T071058Z-codex-4e26a3.yaml
new file mode 100644
index 000000000..6e013bbd5
--- /dev/null
+++ b/history/records/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture/2026-10-08T071058Z-codex-4e26a3.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
+ slug: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+session:
+ id: 2026-10-08T071058Z-codex-4e26a3
+ timestamp: '2026-10-08T07:10:58Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1875
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain exact-pair benzoate conversion and correct benzoate grounding.; Assign inferred
+ energy availability to the fermenter without a spurious recipient.; Retain product inhibition
+ without competition typing or treatment-system conflation.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/history/records/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture/2026-10-08T071059Z-codex-12f831.yaml b/history/records/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture/2026-10-08T071059Z-codex-12f831.yaml
new file mode 100644
index 000000000..5174c81d9
--- /dev/null
+++ b/history/records/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture/2026-10-08T071059Z-codex-12f831.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
+ slug: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+session:
+ id: 2026-10-08T071059Z-codex-12f831
+ timestamp: '2026-10-08T07:10:59Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1876
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Bound stimulation to exact-pair lag and statistical comparisons at community scope.;
+ Retain three-member spatial association without directed colonization or DIET proof.;
+ Retain differential proteomics without enzyme-activation or signaling-causality overstatement.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
diff --git a/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml b/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml
index 4809146bf..8ee026e35 100644
--- a/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml
+++ b/kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml
@@ -103,14 +103,13 @@ taxonomy:
the partner IDENTITY. See discussion kg-syntrophobacter-methanobacterium-partner-attribution.
ecological_interactions:
- name: Propionate Oxidation and H2/Formate Production
- description: 'Syntrophobacter fumaroxidans oxidizes propionate to acetate via the methylmalonyl-CoA
- pathway, using protons as the electron acceptor and producing H2 and formate as electron sink products.
- This propionate oxidation is thermodynamically unfavorable under standard conditions and only proceeds
- when H2 and formate partial pressures are kept extremely low by a syntrophic partner. Formate dehydrogenase
- Fdh1 and hydrogenase Hox are the main confurcating enzymes used for energy conservation, while periplasmic
- Fdh2 and hydrogenase Hyn play an important role in reverse electron transport.
-
- '
+ description: 'S. fumaroxidans oxidizes propionate in syntrophy with M. formicicum, releasing reducing equivalents
+ through hydrogen and/or formate. The methylmalonyl-CoA pathway produces acetate and inorganic carbon. Partner
+ consumption maintains low hydrogen partial pressure and formate concentration; these are different physical
+ quantities. This is the tested methanogenic growth context, not universal partner dependence: sulfate or fumarate
+ can support axenic growth. PARTIAL: comparative protein abundance and homology support proposed Fdh1/Hox confurcation
+ and Fdh2/Hyn reverse-electron-transport roles, not direct demonstration of every enzyme assignment or the fraction
+ of electrons carried by each route in this pair.'
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -128,22 +127,22 @@ ecological_interactions:
term:
id: CHEBI:17272
label: propionate
- concentration: Substrate for oxidation
+ notes: Substrate for oxidation
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
- concentration: Product of propionate oxidation
+ notes: Product of propionate oxidation
- preferred_term: dihydrogen
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Electron sink product - must be maintained at low levels
+ notes: Electron sink product - must be maintained at low levels
- preferred_term: formate
term:
id: CHEBI:15740
label: formate
- concentration: Electron sink product - must be maintained at low levels
+ notes: Electron sink product - must be maintained at low levels
biological_processes:
- preferred_term: propionate metabolic process
term:
@@ -155,48 +154,47 @@ ecological_interactions:
label: propionate catabolic process
downstream:
- target: Interspecies Electron Transfer and Methanogenesis
- description: H2 and formate produced by S. fumaroxidans are consumed by M. formicicum for methanogenesis
+ description: 'DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M.
+ formicicum through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate
+ fluxes in this pair.'
evidence:
- - reference: doi:10.1099/00207713-48-4-1383
+ - reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing
- Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure
- culture with sulfate or fumarate as the electron acceptor
- explanation: Demonstrates the core metabolic activity of S. fumaroxidans in propionate degradation
- with H2/formate transfer
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: The proteomic study cultivated both named methanogenic pairings; this supports the exact partner,
+ not carrier apportionment.
+ - reference: PMID:29611893
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: a very plausible candidate for a confurcating-type of formate dehydrogenase
+ explanation: The main Discussion qualifies the Fdh1 assignment; abundance and homology are not an enzyme-specific
+ intervention.
+ - reference: PMID:29611893
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Hox is most probably a confurcating hydrogenase involved in energy conservation
+ explanation: The source explicitly qualifies the Hox mechanism.
- reference: doi:10.3390/w16243551
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: of all four formate dehydrogenases (FDH1, FDH2, FDH3, FDH4) was down-regulated under
- formate stress
- explanation: Exact-pair transcriptional response - S. fumaroxidans FDH genes are downregulated
- under formate stress (5 mM vs 50 mM), the regulatory arm of the formate dose response curated
- under the Exogenous Formate Dosage environmental factor.
+ snippet: of all four formate dehydrogenases (FDH1, FDH2, FDH3, FDH4) was down-regulated under formate stress
+ explanation: Existing curator-supplied publisher text reports the exact-pair transcriptional response under
+ 50 mM formate stress. RNA abundance is not enzyme activity or selective causal mediation.
- reference: doi:10.3390/w16243551
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: the downregulation of RNA transcription of formate dehydrogenase (FDH) and hydrogenase
- (Hyd) related to MMC pathway may be the main reason for the inhibition of syntrophic propionate
- oxidation
- explanation: The authors' mechanistic link from FDH/Hyd downregulation to inhibited propionate
- oxidation. PARTIAL - stated as "may be the main reason", i.e. transcript-and-phenotype
- association, not knockout-proven, so it is not curated as a demonstrated causal edge.
- - reference: PMID:29611893
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Formate dehydrogenase Fdh1 and hydrogenase Hox were the main confurcating enzymes used for
- energy conservation
- explanation: Demonstrates the enzymatic mechanism of H2 and formate production during syntrophic propionate
- oxidation
+ snippet: the downregulation of RNA transcription of formate dehydrogenase (FDH) and hydrogenase (Hyd) related
+ to MMC pathway may be the main reason for the inhibition of syntrophic propionate oxidation
+ explanation: The authors propose mediation; no new causal edge is inferred from transcript-and-phenotype association.
- name: Interspecies Electron Transfer and Methanogenesis
- description: 'Methanobacterium formicicum consumes the H2 and formate produced by S. fumaroxidans, combining
- them with CO2 to produce methane via hydrogenotrophic methanogenesis. This H2/formate removal maintains
- low partial pressures, making the thermodynamically unfavorable propionate oxidation by S. fumaroxidans
- energetically feasible. This interspecies electron transfer via both H2 and formate is a classic example
- of syntrophic metabolism in anaerobic environments critical for biogeochemical cycling.
-
- '
+ description: M. formicicum acts as the hydrogen/formate-using methanogenic partner of S. fumaroxidans. Carrier
+ consumption supports methane formation and relieves the thermodynamic constraint on propionate oxidation. Low
+ hydrogen partial pressure and low formate concentration are distinct constraints; formate is not a gas pressure.
+ The comparative proteome suggests an important formate route but does not independently quantify exact-pair
+ carrier partitioning.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -214,17 +212,17 @@ ecological_interactions:
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Consumed from environment - must be maintained at low levels
+ notes: Consumed from environment - must be maintained at low levels
- preferred_term: formate
term:
id: CHEBI:15740
label: formate
- concentration: Consumed from environment - must be maintained at low levels
+ notes: Consumed from environment - must be maintained at low levels
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- concentration: End product of methanogenesis
+ notes: End product of methanogenesis
biological_processes:
- preferred_term: methanogenesis
term:
@@ -232,47 +230,39 @@ ecological_interactions:
label: methanogenesis
downstream:
- target: Propionate Oxidation and H2/Formate Production
- description: H2/formate scavenging by M. formicicum keeps both carriers at low partial
- pressure, which is what makes the thermodynamically unfavourable propionate oxidation by
- S. fumaroxidans feasible. S. fumaroxidans oxidizes propionate either in syntrophy with an
- H2/formate-utilizing methanogen or, axenically, only with an external electron acceptor
- (sulfate or fumarate). Reciprocal arm of the syntrophic loop; DIRECTLY IMPLIED by the
- axenic-vs-syntrophic contrast rather than demonstrated by a partner-removal or
- carrier-inhibition perturbation in this exact pair.
+ description: 'DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. formicicum lowers hydrogen partial
+ pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic
+ cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective
+ carrier-removal assay in this exact pair.'
- target: Syntrophic Propionate-to-Methane Conversion
- description: >
- Reciprocal formate and H2 exchange links S. fumaroxidans propionate
- oxidation to M. formicicum hydrogenotrophic methanogenesis.
+ description: Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation
+ to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen,
+ not bidirectional donation.
evidence:
- reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate
- axenically or in syntrophic interaction with methanogens or other sulfate-reducing bacteria
- explanation: The axenic-versus-syntrophic contrast underlying the feedback edge - without a
- partner, propionate growth requires an external electron acceptor.
- - reference: doi:10.1099/00207713-48-4-1383
- supports: PARTIAL
- evidence_source: IN_VITRO
- snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing
- Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure
- culture with sulfate or fumarate as the electron acceptor
- explanation: Demonstrates the syntrophic-coculture dependence on an H2/formate-utilizing methanogen.
- PARTIAL - the methanogen named here is M. hungateii, NOT this record's partner M. formicicum.
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: Supports growth with this exact methanogen in the comparative study.
- reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: fumaroxidans mainly used formate for electron release and that different confurcating mechanisms
- were used in its sulfidogenic metabolism
- explanation: Confirms the importance of formate as an interspecies electron carrier in addition to
- H2
+ snippet: During syntrophic growth, S. fumaroxidans needs to transfer electrons via hydrogen and/or formate to
+ a syntrophic partner.
+ explanation: Source interpretation supports the carrier-removal feedback; it does not assign a measured fraction
+ to either carrier.
+ - reference: PMID:29611893
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: It has long been speculated that formate plays a more important role than hydrogen as an electron carrier
+ explanation: The main text explicitly frames relative carrier importance as a mechanistic interpretation rather
+ than a measured exact-pair flux.
- name: Syntrophic Propionate-to-Methane Conversion
- description: >
- S. fumaroxidans grows syntrophically on propionate with the
- H2/formate-consuming methanogen M. formicicum, combining bacterial
- propionate oxidation, interspecies carrier transfer, and hydrogenotrophic
- methanogenesis into a coupled anaerobic conversion.
- interaction_type: SYNTROPHY
+ description: The S. fumaroxidans-M. formicicum coculture joins propionate oxidation to methanogenesis. This community
+ conversion is the outcome of the two existing partner processes, not a third pairwise exchange. Acetate remains
+ a bacterial product, so this does not assert complete mineralization of propionate carbon to methane.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Syntrophobacter fumaroxidans
@@ -309,12 +299,11 @@ ecological_interactions:
- reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically
- with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium
- formicicum or Desulfovibrio desulfuricans
- explanation: >
- Establishes S. fumaroxidans syntrophic propionate growth with the exact
- M. formicicum partner.
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: Supports the exact syntrophic pairing and its coupled growth, without a carbon-complete methane
+ yield claim.
cultivation_setup:
- cultivation_mode: BATCH
system_type: FLASK
@@ -507,56 +496,58 @@ growth_media:
explanation: Confirms the S. fumaroxidans-M. formicicum coculture and propionate substrate concentration.
discussions:
- discussion_id: kg-syntrophobacter-methanobacterium-partner-attribution
- prompt: >
- Which curated claims about this consortium rest on exact-pair
- (S. fumaroxidans + M. formicicum) evidence, and which were imported from
- S. fumaroxidans + M. hungatei experiments?
+ prompt: 'Which curated claims about this consortium rest on exact-pair (S. fumaroxidans + M. formicicum) evidence,
+ and which were imported from S. fumaroxidans + M. hungatei experiments?
+
+ '
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#Propionate Oxidation and H2/Formate Production
- ecological_interactions#Interspecies Electron Transfer and Methanogenesis
- rationale: >
- Several evidence items on this record quote doi:10.1099/00207713-48-4-1383
- (Harmsen et al. 1998), whose syntrophic coculture passage names
- *Methanospirillum hungateii*, not this record's partner *Methanobacterium
- formicicum*. Two of those items previously carried explanations asserting that
- the passage established M. formicicum as the partner; they have been corrected
- and downgraded to PARTIAL, and exact-pair support has been added from
- PMID:29611893 (Sedano-Nunez et al. 2018), which explicitly grew S. fumaroxidans
- in syntrophy with M. formicicum. The residual gap: the frequently cited
- biochemical formate-transfer and FDH/hydrogenase transcription results for this
- system were obtained with M. hungatei, so carrier apportionment ("formate is the
- dominant carrier") must NOT be curated as an exact-pair finding.
-
- PARTLY RESOLVED: the 2024 exact-pair perturbation study (Li et al., Water 16:3551,
- doi:10.3390/w16243551) is now ingested - its full text was supplied by a curator from
- the publisher PDF, since the journal is absent from PubMed and Europe PMC and MDPI
- blocks programmatic download. Its graded-formate results for the exact
- S. fumaroxidans-M. formicicum coculture are curated under the Exogenous Formate
- Dosage environmental factor, and its FDH downregulation result on the Propionate
- Oxidation interaction. Two cautions came out of that ingestion: (a) the paper runs
- an anaerobic-sludge system ALONGSIDE the coculture, and sludge-only results (e.g.
- Acetobacterium homoacetogenesis rising with formate dose) must not be attributed to
- this two-member consortium; (b) the dose response is non-monotonic - 30 mM recovers
- in the later stage - so it is NOT a simple ">=30 mM inhibits" threshold.
-
- Still open: carrier apportionment between H2 and formate for the M. formicicum pair
- specifically, which no retrieved study resolves with an isotope or
- selective-inhibition experiment.
+ rationale: "Several evidence items on this record quote doi:10.1099/00207713-48-4-1383 (Harmsen et al. 1998),\
+ \ whose syntrophic coculture passage names *Methanospirillum hungateii*, not this record's partner *Methanobacterium\
+ \ formicicum*. Two of those items previously carried explanations asserting that the passage established M.\
+ \ formicicum as the partner; they have been corrected and downgraded to PARTIAL, and exact-pair support has\
+ \ been added from PMID:29611893 (Sedano-Nunez et al. 2018), which explicitly grew S. fumaroxidans in syntrophy\
+ \ with M. formicicum. The residual gap: the frequently cited biochemical formate-transfer and FDH/hydrogenase\
+ \ transcription results for this system were obtained with M. hungatei, so carrier apportionment (\"formate\
+ \ is the dominant carrier\") must NOT be curated as an exact-pair finding.\nPARTLY RESOLVED: the 2024 exact-pair\
+ \ perturbation study (Li et al., Water 16:3551, doi:10.3390/w16243551) is now ingested - its full text was supplied\
+ \ by a curator from the publisher PDF, since the journal is absent from PubMed and Europe PMC and MDPI blocks\
+ \ programmatic download. Its graded-formate results for the exact S. fumaroxidans-M. formicicum coculture are\
+ \ curated under the Exogenous Formate Dosage environmental factor, and its FDH downregulation result on the\
+ \ Propionate Oxidation interaction. Two cautions came out of that ingestion: (a) the paper runs an anaerobic-sludge\
+ \ system ALONGSIDE the coculture, and sludge-only results (e.g. Acetobacterium homoacetogenesis rising with\
+ \ formate dose) must not be attributed to this two-member consortium; (b) the dose response is non-monotonic\
+ \ - 30 mM recovers in the later stage - so it is NOT a simple \">=30 mM inhibits\" threshold.\nStill open: carrier\
+ \ apportionment between H2 and formate for the M. formicicum pair specifically, which no retrieved study resolves\
+ \ with an isotope or selective-inhibition experiment.\n Batch112: the graph now uses exact-pair proteomic cultivation\
+ \ evidence rather than the 1998 M. hungatei passage as full support. Main-text Fdh1/Hox assignments are qualified\
+ \ mechanistic interpretations; no exact-pair hydrogen/formate flux ratio is inferred. The 2024 transcription\
+ \ passages were rechecked in the existing curator-supplied text; fresh publisher retrieval was unavailable.\
+ \ Hydrogen partial pressure is distinguished from formate concentration."
evidence:
- reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically
- with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium
- formicicum or Desulfovibrio desulfuricans
- explanation: The one curated reference that studies the exact pair alongside the M. hungatei
- pairing - the basis for separating exact-pair from imported claims.
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: The one curated reference that studies the exact pair alongside the M. hungatei pairing - the basis
+ for separating exact-pair from imported claims.
- reference: doi:10.1099/00207713-48-4-1383
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing
- Methanospirillum hungateii
- explanation: The misattribution source - this passage names M. hungateii and cannot establish
- M. formicicum as the partner.
+ snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing Methanospirillum
+ hungateii
+ explanation: The misattribution source - this passage names M. hungateii and cannot establish M. formicicum
+ as the partner.
+curation_history:
+- timestamp: '2026-10-08T07:10:54Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback
+ with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange
+ typing. Issue#1871; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
diff --git a/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml b/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml
index 93faf7fee..7e90ffd7d 100644
--- a/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml
+++ b/kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml
@@ -92,14 +92,13 @@ taxonomy:
explanation: Establishes M. hungatei as the H2/formate-utilizing syntrophic partner
ecological_interactions:
- name: Propionate Oxidation and H2/Formate Production
- description: 'Syntrophobacter fumaroxidans oxidizes propionate to acetate via the methylmalonyl-CoA
- pathway, using protons as the electron acceptor and producing H2 and formate as electron sink products.
- This propionate oxidation is thermodynamically unfavorable under standard conditions and only proceeds
- when H2 and formate partial pressures are kept extremely low by a syntrophic partner. Formate dehydrogenase
- Fdh1 and hydrogenase Hox are the main confurcating enzymes used for energy conservation, while periplasmic
- Fdh2 and hydrogenase Hyn play an important role in reverse electron transport.
-
- '
+ description: 'S. fumaroxidans oxidizes propionate in syntrophy with M. hungatei, releasing reducing equivalents
+ through hydrogen and/or formate. The methylmalonyl-CoA pathway produces acetate and inorganic carbon. Partner
+ consumption maintains low hydrogen partial pressure and formate concentration; these are different physical
+ quantities. This is the tested methanogenic growth context, not universal partner dependence: sulfate or fumarate
+ can support axenic growth. PARTIAL: comparative protein abundance and homology support proposed Fdh1/Hox confurcation
+ and Fdh2/Hyn reverse-electron-transport roles, not direct demonstration of every enzyme assignment or the fraction
+ of electrons carried by each route in this pair.'
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -117,22 +116,22 @@ ecological_interactions:
term:
id: CHEBI:17272
label: propionate
- concentration: Substrate for oxidation
+ notes: Substrate for oxidation
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
- concentration: Product of propionate oxidation
+ notes: Product of propionate oxidation
- preferred_term: dihydrogen
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Electron sink product - must be maintained at low levels
+ notes: Electron sink product - must be maintained at low levels
- preferred_term: formate
term:
id: CHEBI:15740
label: formate
- concentration: Electron sink product - must be maintained at low levels
+ notes: Electron sink product - must be maintained at low levels
biological_processes:
- preferred_term: propionate metabolic process
term:
@@ -144,31 +143,34 @@ ecological_interactions:
label: propionate catabolic process
downstream:
- target: Interspecies Electron Transfer and Methanogenesis
- description: H2 and formate produced by S. fumaroxidans are consumed by M. hungatei for methanogenesis
+ description: 'DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M.
+ hungatei through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate
+ fluxes in this pair.'
evidence:
- - reference: PMID:9828440
+ - reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing
- Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure
- culture with sulfate or fumarate as the electron acceptor
- explanation: Demonstrates the core metabolic activity of S. fumaroxidans in propionate degradation
- with H2/formate transfer
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: The proteomic study cultivated both named methanogenic pairings; this supports the exact partner,
+ not carrier apportionment.
- reference: PMID:29611893
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: Formate dehydrogenase Fdh1 and hydrogenase Hox were the main confurcating enzymes used for
- energy conservation
- explanation: Demonstrates the enzymatic mechanism of H2 and formate production during syntrophic propionate
- oxidation
+ snippet: a very plausible candidate for a confurcating-type of formate dehydrogenase
+ explanation: The main Discussion qualifies the Fdh1 assignment; abundance and homology are not an enzyme-specific
+ intervention.
+ - reference: PMID:29611893
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Hox is most probably a confurcating hydrogenase involved in energy conservation
+ explanation: The source explicitly qualifies the Hox mechanism.
- name: Interspecies Electron Transfer and Methanogenesis
- description: 'Methanospirillum hungatei consumes the H2 and formate produced by S. fumaroxidans, combining
- them with CO2 to produce methane via hydrogenotrophic methanogenesis. This H2/formate removal maintains
- low partial pressures, making the thermodynamically unfavorable propionate oxidation by S. fumaroxidans
- energetically feasible. This interspecies electron transfer via both H2 and formate is a classic example
- of syntrophic metabolism in anaerobic environments critical for biogeochemical cycling.
-
- '
+ description: M. hungatei acts as the hydrogen/formate-using methanogenic partner of S. fumaroxidans. Carrier consumption
+ supports methane formation and relieves the thermodynamic constraint on propionate oxidation. Low hydrogen partial
+ pressure and low formate concentration are distinct constraints; formate is not a gas pressure. The comparative
+ proteome suggests an important formate route but does not independently quantify exact-pair carrier partitioning.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -186,17 +188,17 @@ ecological_interactions:
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Consumed from environment - must be maintained at low levels
+ notes: Consumed from environment - must be maintained at low levels
- preferred_term: formate
term:
id: CHEBI:15740
label: formate
- concentration: Consumed from environment - must be maintained at low levels
+ notes: Consumed from environment - must be maintained at low levels
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- concentration: End product of methanogenesis
+ notes: End product of methanogenesis
biological_processes:
- preferred_term: methanogenesis
term:
@@ -204,40 +206,39 @@ ecological_interactions:
label: methanogenesis
downstream:
- target: Propionate Oxidation and H2/Formate Production
- description: H2/formate scavenging by M. hungatei keeps the partial pressures of both carriers
- low enough for propionate oxidation to remain thermodynamically feasible. S. fumaroxidans
- oxidizes propionate either syntrophically with an H2/formate-utilizing partner or, in pure
- culture, only when supplied with an external electron acceptor (sulfate or fumarate) —
- establishing the partner-dependence that this feedback edge encodes. Reciprocal arm of the
- syntrophic loop.
+ description: 'DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. hungatei lowers hydrogen partial
+ pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic
+ cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective
+ carrier-removal assay in this exact pair.'
- target: Syntrophic Propionate-to-Methane Conversion
- description: >
- Reciprocal formate and H2 exchange links S. fumaroxidans propionate
- oxidation to M. hungatei hydrogenotrophic methanogenesis.
+ description: Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation
+ to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen,
+ not bidirectional donation.
evidence:
- - reference: PMID:9828440
+ - reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing
- Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure
- culture with sulfate or fumarate as the electron acceptor
- explanation: Demonstrates successful syntrophic coculture with M. hungatei as H2/formate-utilizing
- partner; the pure-culture contrast (electron acceptor required in the absence of the partner) is
- the basis for the feedback edge
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: Supports growth with this exact methanogen in the comparative study.
- reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: fumaroxidans mainly used formate for electron release and that different confurcating mechanisms
- were used in its sulfidogenic metabolism
- explanation: Confirms the importance of formate as an interspecies electron carrier in addition to
- H2
+ snippet: During syntrophic growth, S. fumaroxidans needs to transfer electrons via hydrogen and/or formate to
+ a syntrophic partner.
+ explanation: Source interpretation supports the carrier-removal feedback; it does not assign a measured fraction
+ to either carrier.
+ - reference: PMID:29611893
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: It has long been speculated that formate plays a more important role than hydrogen as an electron carrier
+ explanation: The main text explicitly frames relative carrier importance as a mechanistic interpretation rather
+ than a measured exact-pair flux.
- name: Syntrophic Propionate-to-Methane Conversion
- description: >
- S. fumaroxidans oxidizes propionate syntrophically with the
- H2/formate-utilizing methanogen M. hungatei, forming a coupled anaerobic
- conversion that joins propionate catabolism with hydrogenotrophic
- methanogenesis.
- interaction_type: SYNTROPHY
+ description: The S. fumaroxidans-M. hungatei coculture joins propionate oxidation to methanogenesis. This community
+ conversion is the outcome of the two existing partner processes, not a third pairwise exchange. Acetate remains
+ a bacterial product, so this does not assert complete mineralization of propionate carbon to methane.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Syntrophobacter fumaroxidans
@@ -271,15 +272,14 @@ ecological_interactions:
id: GO:0015948
label: methanogenesis
evidence:
- - reference: PMID:9828440
+ - reference: PMID:29611893
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing
- Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure
- culture with sulfate or fumarate as the electron acceptor
- explanation: >
- Establishes S. fumaroxidans syntrophic propionate growth with the exact
- M. hungatei partner.
+ snippet: We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate
+ or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio
+ desulfuricans
+ explanation: Supports the exact syntrophic pairing and its coupled growth, without a carbon-complete methane
+ yield claim.
environmental_factors:
- name: Anaerobic Conditions
value: Strict anaerobic
@@ -595,3 +595,30 @@ growth_media:
during syntrophic propionate oxidation by S. fumaroxidans
culturemech_id: CultureMech:000423
culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000423
+discussions:
+- discussion_id: propionate-carrier-partition-and-enzyme-roles
+ prompt: What are the separate carrier fluxes and enzyme contributions in this exact pairing?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: Comparative proteomics supports candidate energy-conservation and electron-transfer roles. It does
+ not resolve exact carrier fractions or selectively demonstrate all enzyme assignments. Existing metabolic feedback
+ is retained with that boundary.
+ attaches_to:
+ - ecological_interactions#Propionate Oxidation and H2/Formate Production
+ - ecological_interactions#Interspecies Electron Transfer and Methanogenesis
+ evidence:
+ - reference: PMID:29611893
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: It has long been speculated that formate plays a more important role than hydrogen as an electron carrier
+ explanation: The main text explicitly frames relative carrier importance as a mechanistic interpretation rather
+ than a measured exact-pair flux.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T07:10:55Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback
+ with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange
+ typing. Issue#1871; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
diff --git a/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml b/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
index 8f3615a64..670742625 100644
--- a/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
+++ b/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
@@ -106,10 +106,9 @@ taxonomy:
explanation: Supports M. maripaludis as the hydrogenotrophic methanogenic partner.
ecological_interactions:
- name: Syntrophic Butyrate Oxidation and Methanogenesis
- description: >
- S. wolfei and M. maripaludis form a thermodynamically required syntrophic
- partnership in which fatty acid oxidation is coupled to methanogenesis under
- anoxic conditions.
+ description: S. wolfei and M. maripaludis grow syntrophically on butyrate, coupling bacterial oxidation to hydrogenotrophic
+ methanogenesis. The dependence is for the tested butyrate medium; S. wolfei was separately maintained in pure
+ culture on crotonate.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -142,78 +141,54 @@ ecological_interactions:
label: methanogenesis
downstream:
- target: Population Ratio Convergence During Growth
- description: >
- The thermodynamically required syntrophic coupling of butyrate oxidation to
- hydrogenotrophic methanogenesis drives coordinated partner growth — cultures
- inoculated at different initial cell ratios converge to a relatively constant
- Syntrophomonas:Methanococcus ratio over time.
+ description: 'DIRECTLY IMPLIED/PARTIAL: syntrophic metabolism supports growth of both partners during the observed
+ convergence of their population ratio. Different starting ratios alter relative growth and lag, but the study
+ does not isolate a molecular feedback controller that enforces the endpoint ratio.'
evidence:
- reference: PMID:34603271
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: thermodynamically required mutualistic cooperation between fatty acid-oxidizing bacteria and methanogens
- explanation: Supports the syntrophic mechanism linking fatty acid oxidation and methanogenesis.
+ snippet: mesophilic coculture consisting of Syntrophomonas wolfei and Methanococcus maripaludis
+ explanation: Identifies the exact mesophilic partners.
- reference: PMID:34603271
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: butyrate-oxidizing bacteria and methanogens
- explanation: Supports the butyrate-oxidizing and methanogenic partners in the coculture.
+ snippet: S. wolfei could not grow on butyrate alone in the media
+ explanation: Bounds dependence to the tested substrate and medium.
- name: Population Ratio Convergence During Growth
- description: >
- When the two members were inoculated at different initial ratios, the
- initially lower-abundance organism grew faster and the population ratio
- converged, indicating growth synchronization between partners.
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Syntrophomonas wolfei
- term:
- id: NCBITaxon:863
- label: Syntrophomonas wolfei
- target_taxon:
- preferred_term: Methanococcus maripaludis
- term:
- id: NCBITaxon:39152
- label: Methanococcus maripaludis
+ description: In the mesophilic S. wolfei-M. maripaludis cultures, different starting population ratios converged
+ to around one during growth. This is a community population outcome, not a second directional mutualism interaction
+ or proof that the converged ratio itself accelerates metabolism.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Syntrophic Butyrate Oxidation and Methanogenesis
- description: >
- Cell aggregation and attraction keep butyrate-oxidizing and
- hydrogenotrophic partners close enough for efficient H2 transfer during
- syntrophic methanogenesis.
evidence:
- reference: PMID:34603271
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: syntrophs and methanogens were inoculated at different initial cell ratios
- explanation: Supports the initial-ratio perturbation used to measure growth coordination.
- - reference: PMID:34603271
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: the cell ratio converged over time to relative constant values
- explanation: Supports population ratio convergence as a growth coordination outcome.
-- name: Syntrophic Aggregation and Cell-to-Cell Attraction
- description: >
- FISH, SEM, and microfluidic experiments showed aggregate formation and
- directional attraction between Syntrophomonas and Methanococcus cells,
- supporting spatial organization as part of syntrophic cooperation.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Syntrophomonas wolfei
+ snippet: the cell ratio of the WM cocultures varied in the early stage but converged at around 1 from day 15
+ forward for all the three treatments.
+ explanation: Exact mesophilic outcome; do not substitute the thermophilic final ratio or treat convergence as
+ the manipulated initial ratio.
+ participating_taxa:
+ - preferred_term: Syntrophomonas wolfei
term:
id: NCBITaxon:863
label: Syntrophomonas wolfei
- target_taxon:
- preferred_term: Methanococcus maripaludis
+ - preferred_term: Methanococcus maripaludis
term:
id: NCBITaxon:39152
label: Methanococcus maripaludis
+- name: Syntrophic Aggregation and Cell-to-Cell Attraction
+ description: FISH and SEM showed development of mixed aggregates, while microfluidic loading in either order showed
+ preferential movement toward the other partner. A same-organism control lacked that preference. This supports
+ reciprocal spatial association, not a uniquely directed colonization effect. Ultrasound and shaking reduced
+ methane-production activity without a detectable change in aggregation tendency; causal mediation by aggregation
+ remains unresolved.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -223,13 +198,23 @@ ecological_interactions:
- reference: PMID:34603271
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: tendency of syntrophic aggregation was not affected by the physical disturbances
- explanation: Supports syntrophic aggregation as a measured property of the mesophilic coculture.
+ snippet: the second organism preferred moving to the well where the first organism was already located
+ explanation: Reciprocal loading supports spatial attraction, not a one-way established benefit.
- reference: PMID:34603271
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus
- explanation: Supports direct cell-to-cell attraction between the two partners.
+ snippet: although the activity of the coculture was influenced by two disturbance treatments, the tendency of
+ microbial aggregation was not.
+ explanation: The disturbance comparison does not isolate aggregation as the mediator of metabolic activity.
+ participating_taxa:
+ - preferred_term: Syntrophomonas wolfei
+ term:
+ id: NCBITaxon:863
+ label: Syntrophomonas wolfei
+ - preferred_term: Methanococcus maripaludis
+ term:
+ id: NCBITaxon:39152
+ label: Methanococcus maripaludis
environmental_factors:
- name: Anoxic methanogenic context
value: anoxic environments
@@ -386,30 +371,30 @@ metal_notes: >
methanogenic butyrate-oxidizing coculture.
discussions:
- discussion_id: kg-aggregation-and-diet-unverified
- prompt: >
- Does syntrophic aggregation / cell-to-cell attraction causally enhance
- butyrate oxidation or methanogenesis in this coculture, and is direct
- interspecies electron transfer (e.g. the reported carbon-nanotube methane
- stimulation) involved rather than only H2/formate transfer?
+ prompt: Does spatial association or the converged population ratio causally enhance syntrophic metabolism?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
+ - ecological_interactions#Population Ratio Convergence During Growth
- ecological_interactions#Syntrophic Aggregation and Cell-to-Cell Attraction
- rationale: >
- Aggregation and disturbance-resistant cell-to-cell attraction are observed,
- but no experiment demonstrates that aggregation increases butyrate oxidation or
- methane production in this exact coculture, so no aggregation→enhancement
- `downstream` edge was added. Likewise, carbon-nanotube acceleration of methane
- production is reported, but DIET "does not always explain the enhancement of
- methane production" and was not directly proven here, so a DIET mechanism is
- not asserted.
+ rationale: The former population-ratio-to-metabolism arrow described aggregation rather than its source node and
+ is removed. Initial ratios were experimentally varied; the converged endpoint is not an independently manipulated
+ cause. Reciprocal attraction is supported, but ultrasound and shaking change activity without changing aggregation
+ tendency. The separate nanomaterial study reports acceleration and proposes DIET without a decisive demonstration.
+ No new aggregation-to-metabolism direction is added.
evidence:
- reference: PMID:34603271
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus
- explanation: Attraction/aggregation is observed, but its causal contribution to metabolic
- performance is untested — the basis for the knowledge gap.
+ snippet: the tendency of microbial aggregation was not
+ explanation: Aggregation tendency was unchanged despite the disturbance-associated activity change.
+ - reference: doi:10.1038/s41598-018-30745-7
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Though decisive conclusion can not be made, our study tends to support the possibility of DIET in syntrophic
+ oxidation of butyrate.
+ explanation: The nanomaterial study explicitly qualifies DIET; it is not proof of the carrier mechanism in the
+ unamended coordination assay.
cultivation_setup:
- cultivation_mode: BATCH
system_type: SERUM_BOTTLE
@@ -437,3 +422,11 @@ cultivation_setup:
evidence_source: IN_VITRO
snippet: The headspace of 250-ml incubation bottles was flushed with N2 for 5 min
and then adjusted with N2:CO2 (80:20 [v/v]) to a final pressure of 172 kPa
+curation_history:
+- timestamp: '2026-10-08T07:10:55Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain substrate-bounded syntrophic growth and qualify the existing growth-to-ratio inference.; Retain
+ population convergence as an outcome and remove misplaced reverse causality.; Retain reciprocal attraction and
+ aggregation without one-way colonization or proven metabolic mediation. Issue#1872; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
diff --git a/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml b/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml
index ea7c7f62a..23dd549fa 100644
--- a/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml
+++ b/kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml
@@ -80,13 +80,9 @@ taxonomy:
explanation: Establishes M. hungatei as a compatible H2-utilizing syntrophic partner
ecological_interactions:
- name: Butyrate Oxidation and H2 Production
- description: 'Syntrophomonas wolfei β-oxidizes butyrate (C4) to acetate, using protons as the electron
- acceptor and producing H2 as the electron sink product. This fatty acid β-oxidation is thermodynamically
- unfavorable under standard conditions and only proceeds when H2 partial pressure is kept extremely
- low by a syntrophic partner. The organism cannot utilize common electron acceptors (nitrate, sulfate,
- etc.) and is therefore obligately dependent on syntrophic H2 removal.
-
- '
+ description: S. wolfei oxidizes butyrate to acetate with hydrogen as an electron-sink product in the studied syntrophic
+ cultures. Common electron acceptors did not support the tested butyrate metabolism. This is substrate- and assay-bounded
+ dependence on a hydrogen-using partner, not a claim that every substrate requires coculture.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -104,17 +100,17 @@ ecological_interactions:
term:
id: CHEBI:17968
label: butyrate
- concentration: Substrate for β-oxidation
+ notes: Substrate for β-oxidation
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
- concentration: Product of butyrate oxidation
+ notes: Product of butyrate oxidation
- preferred_term: dihydrogen
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Electron sink product - must be maintained at low levels
+ notes: Electron sink product - must be maintained at low levels
biological_processes:
- preferred_term: fatty acid beta-oxidation
term:
@@ -131,21 +127,19 @@ ecological_interactions:
- reference: PMID:16345745
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The addition of H(2) to the medium stopped growth and butyrate degradation by S
- explanation: Demonstrates the core metabolic activity of S. wolfei in butyrate degradation
+ snippet: An anaerobic, nonphototrophic bacterium that beta-oxidizes saturated fatty acids (butyrate through
+ octanoate) to acetate or acetate and propionate using protons as the electron acceptor
+ explanation: The abstract supports the bacterial reaction; butyrate is the acetate-producing case.
- reference: PMID:16345745
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: An anaerobic, nonphototrophic bacterium that beta-oxidizes saturated fatty acids (butyrate
- through octanoate) to acetate or acetate and propionate using protons as the electron acceptor
+ snippet: Common electron acceptors are not utilized with butyrate as the electron donor
+ explanation: The negative result is bounded to butyrate and tested acceptors.
- name: Interspecies Hydrogen Transfer and Methanogenesis
- description: 'Methanospirillum hungatei consumes the H2 produced by S. wolfei, combining it with CO2
- to produce methane via hydrogenotrophic methanogenesis. This H2 removal maintains a low H2 partial
- pressure (<10^-4 atm), making the thermodynamically unfavorable butyrate oxidation by S. wolfei energetically
- feasible. This interspecies hydrogen transfer (IHT) is the classic example of syntrophic metabolism
- in anaerobic environments.
-
- '
+ description: M. hungatei is a documented hydrogen-using partner of S. wolfei. Hydrogen removal supports bacterial
+ butyrate oxidation and methanogenesis. The abstract reports inhibition of growth and butyrate degradation by
+ added hydrogen, but does not provide an exact permissive partial-pressure threshold or quantify competing carrier
+ contributions.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -163,12 +157,12 @@ ecological_interactions:
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Consumed from environment - must be maintained at low levels
+ notes: Consumed from environment - must be maintained at low levels
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- concentration: End product of methanogenesis
+ notes: End product of methanogenesis
biological_processes:
- preferred_term: methanogenesis
term:
@@ -176,45 +170,30 @@ ecological_interactions:
label: methanogenesis
downstream:
- target: Butyrate Oxidation and H2 Production
- description: H2 scavenging by M. hungatei keeps the H2 partial pressure low enough for
- butyrate β-oxidation to remain thermodynamically feasible; S. wolfei grows and degrades
- butyrate only in association with an H2-using partner, and adding H2 back to the medium
- stops both. Reciprocal (feedback) arm of the syntrophic loop.
+ description: 'DIRECTLY IMPLIED feedback: removal of hydrogen by the methanogenic partner relieves a constraint
+ on S. wolfei butyrate oxidation. The 1981 abstract reports that added hydrogen stops growth and butyrate degradation;
+ it does not specify a numerical permissive threshold or isolate hydrogen from all alternative carrier routes
+ in this exact pairing.'
- target: Syntrophic Butyrate-to-Methane Conversion
- description: >
- Hydrogen transfer links S. wolfei butyrate oxidation to M. hungatei
- hydrogenotrophic methanogenesis.
+ description: 'Hydrogen transfer links S. wolfei butyrate oxidation to M. hungatei hydrogenotrophic methanogenesis.
+
+ '
evidence:
- reference: PMID:16345745
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Growth and degradation of fatty acids occur only in syntrophic association with
- H(2)-using bacteria
- explanation: Establishes the methanogen-side dependency underlying the feedback edge - S.
- wolfei is obligately dependent on an H2-scavenging partner
- - reference: PMID:16345745
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: The addition of H(2) to the medium stopped growth and butyrate degradation by S
- explanation: Perturbation evidence for the feedback edge - raising H2 (i.e. removing the
- effect of H2 scavenging) halts butyrate oxidation
- - reference: PMID:16345745
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Common electron acceptors are not utilized with butyrate as the electron donor
- explanation: Demonstrates successful syntrophic coculture with M. hungatei as H2-utilizing partner
+ snippet: cocultures of S. wolfei with Desulfovibrio and Methanospirillum hungatei
+ explanation: Identifies the methanogenic partner separately from the nonmethanogenic comparison.
- reference: PMID:16345745
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Common electron acceptors are not utilized with butyrate as the electron donor
- explanation: Confirms that S. wolfei cannot use alternative electron acceptors, making it obligately
- dependent on syntrophic H2 removal
+ snippet: The addition of H(2) to the medium stopped growth and butyrate degradation by S. wolfei.
+ explanation: The reported hydrogen perturbation supports product-inhibition feedback; the abstract does not
+ specify every assay condition or a numerical threshold.
- name: Syntrophic Butyrate-to-Methane Conversion
- description: >
- S. wolfei oxidizes butyrate only when a hydrogen-consuming partner such as
- M. hungatei removes the produced H2, coupling fatty-acid beta-oxidation to
- hydrogenotrophic methanogenesis in the two-member consortium.
- interaction_type: SYNTROPHY
+ description: S. wolfei butyrate oxidation is coupled to hydrogen-consuming M. hungatei methanogenesis in the documented
+ coculture. This is a community conversion endpoint, not an additional pairwise exchange; acetate is retained
+ as an organic product.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Syntrophomonas wolfei
@@ -251,11 +230,13 @@ ecological_interactions:
- reference: PMID:16345745
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Growth and degradation of fatty acids occur only in syntrophic association with
- H(2)-using bacteria
- explanation: >
- Establishes the obligate syntrophic H2-removal requirement for
- S. wolfei fatty-acid degradation.
+ snippet: cocultures of S. wolfei with Desulfovibrio and Methanospirillum hungatei
+ explanation: Identifies the methanogenic partner separately from the nonmethanogenic comparison.
+ - reference: PMID:16345745
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Growth and degradation of fatty acids occur only in syntrophic association with H(2)-using bacteria
+ explanation: Supports the reported fatty-acid growth context, not species-wide obligacy across all substrates.
environmental_factors:
- name: Anaerobic Conditions
value: Strict anaerobic
@@ -564,3 +545,31 @@ growth_media:
for low H2 partial pressure maintained by methanogenic partner
culturemech_id: CultureMech:000423
culturemech_url: https://github.com/CultureBotAI/CultureMech/tree/main/kb/media/CultureMech:000423
+discussions:
+- discussion_id: butyrate-hydrogen-feedback-assay-limits
+ prompt: What quantitative carrier constraints apply to this exact butyrate coculture?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: The accessible primary abstract supports the named partner and hydrogen-addition inhibition, but not
+ the former less-than-10^-4-atm threshold. The existing feedback remains directly implied; no carrier-exclusive
+ mechanism or universal obligacy is asserted. The older full-text XML endpoint failed, so detailed perturbation
+ conditions remain unverified here.
+ attaches_to:
+ - ecological_interactions#Butyrate Oxidation and H2 Production
+ - ecological_interactions#Interspecies Hydrogen Transfer and Methanogenesis
+ evidence:
+ - reference: PMID:16345745
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The addition of H(2) to the medium stopped growth and butyrate degradation by S. wolfei.
+ explanation: The reported hydrogen perturbation supports product-inhibition feedback; the abstract does not
+ specify every assay condition or a numerical threshold.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T07:10:55Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain butyrate oxidation with substrate-bounded dependence.; Retain hydrogen feedback without an uncited
+ pressure threshold or duplicate evidence.; Retain the conversion endpoint without an additional exchange claim.
+ Issue#1873; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
diff --git a/kb/communities/Syntrophus_Benzoate_Degrader.yaml b/kb/communities/Syntrophus_Benzoate_Degrader.yaml
index 53da83d44..1e3d02450 100644
--- a/kb/communities/Syntrophus_Benzoate_Degrader.yaml
+++ b/kb/communities/Syntrophus_Benzoate_Degrader.yaml
@@ -91,13 +91,10 @@ taxonomy:
produces methane in benzoate-grown cocultures.
ecological_interactions:
- name: Syntrophus Benzoate Metabolism
- description: 'S. aciditrophicus strain SB metabolizes benzoate in coculture with
- hydrogen-using partners and transiently produces cyclohexane carboxylate,
- cyclohex-1-ene carboxylate, pimelate, and glutarate during growth on
- benzoate. These Syntrophus reactions initiate the methanogenic coculture
- conversion of benzoate to acetate and methane.
-
- '
+ description: S. aciditrophicus strain SB metabolizes benzoate in the M. hungatei coculture, with transient alicyclic
+ and dicarboxylate intermediates. This is the syntrophic route; the separate pure-culture experiment also demonstrates
+ benzoate fermentation with a different product balance. Enzyme activities measured with Desulfovibrio or crotonate-grown
+ pure cultures are not attributed as exact-pair assays here.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -113,60 +110,52 @@ ecological_interactions:
metabolites:
- preferred_term: benzoate
term:
- id: CHEBI:30746
- label: benzoic acid
- concentration: Aromatic substrate for degradation
+ id: CHEBI:16150
+ label: benzoate
+ notes: Aromatic substrate for degradation
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
- concentration: Product of benzoate degradation
+ notes: Product of benzoate degradation
- preferred_term: dihydrogen
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Electron sink product - must be maintained at low levels
+ notes: Electron sink product - must be maintained at low levels
- preferred_term: carbon dioxide
term:
id: CHEBI:16526
label: carbon dioxide
- concentration: Benzoate oxidation product
+ notes: Benzoate oxidation product
biological_processes:
- preferred_term: benzoate metabolic process
term:
id: GO:0018874
label: benzoate metabolic process
downstream:
- - target: Community Benzoate Mineralization to Acetate and Methane
- description: S. aciditrophicus benzoate metabolism supplies reduced products
- to the methanogenic partner and enables methane-producing benzoate mineralization
- by the coculture.
+ - target: Community Benzoate Conversion to Acetate and Methane
+ description: Bacterial benzoate metabolism supplies reducing equivalents for the methanogenic partner and generates
+ acetate, enabling the coupled coculture conversion rather than complete carbon mineralization.
evidence:
- reference: doi:10.1128/aem.67.4.1728-1738.2001
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In this study, we investigated the pathway for syntrophic benzoate metabolism
- in “ Syntrophus aciditrophicus ” strain SB by identifying and quantifying
- metabolites produced during growth of this organism with benzoate, cyclohexane
- carboxylate, and cyclohex-1-ene carboxylate in cocultures with hydrogen-utilizing
- partners
- explanation: Demonstrates S. aciditrophicus strain SB syntrophic metabolism
- with hydrogen-utilizing partners.
+ snippet: Cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate
+ explanation: 'The primary passage identifies these transient intermediates or their coenzyme A derivatives;
+ it does not assign every enzyme assay to this methanogenic pair. The contiguous excerpt avoids the known bracket-stripping
+ validator bug #622 without silently changing quoted text.'
- reference: doi:10.1128/aem.67.4.1728-1738.2001
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: During growth of the “ S. aciditrophicus ”- M. hungatei cocultures with
- benzoate, cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate,
- and glutarate were detected as their TMS derivatives.
- explanation: Identifies the alicyclic and dicarboxylate intermediates
- produced during benzoate-grown S. aciditrophicus-M. hungatei coculture.
+ snippet: Cocultures of "S. aciditrophicus" and Methanospirillum hungatei readily metabolized cyclohexane carboxylate
+ and cyclohex-1-ene carboxylate
+ explanation: Identifies the methanogenic pairing used for metabolism of the alicyclic substrates.
- name: Interspecies Hydrogen Transfer and Methanogenesis
- description: 'M. hungatei functions as the hydrogen-using methanogen in the
- S. aciditrophicus coculture. Hydrogen consumption keeps the concentration
- of hydrogen produced during benzoate oxidation low, a thermodynamic requirement
- for anaerobic benzoate degradation through interspecies hydrogen transfer.
-
- '
+ description: 'M. hungatei is the hydrogen-using methanogen in the benzoate coculture. Hydrogen consumption provides
+ an electron sink for the syntrophic conversion to acetate and methane. This does not mean benzoate metabolism
+ is impossible without a partner: S. aciditrophicus pure cultures ferment benzoate with cyclohexane carboxylate
+ accumulation and a different acetate yield.'
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -184,51 +173,46 @@ ecological_interactions:
term:
id: CHEBI:18276
label: dihydrogen
- concentration: Consumed from environment - must be maintained at low levels
+ notes: Consumed from environment - must be maintained at low levels
- preferred_term: carbon dioxide
term:
id: CHEBI:16526
label: carbon dioxide
- concentration: Cosubstrate for hydrogenotrophic methanogenesis
+ notes: Cosubstrate for hydrogenotrophic methanogenesis
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- concentration: End product of methanogenesis
+ notes: End product of methanogenesis
biological_processes:
- preferred_term: methanogenesis
term:
id: GO:0015948
label: methanogenesis
downstream:
- - target: Community Benzoate Mineralization to Acetate and Methane
- description: Methanogenic hydrogen removal closes the syntrophic electron
- sink that lets benzoate oxidation continue to methane production.
+ - target: Community Benzoate Conversion to Acetate and Methane
+ description: Methanogenic hydrogen consumption supplies the electron sink that couples benzoate oxidation to
+ methane production and the coculture product balance; a different benzoate fermentation remains possible without
+ this partner.
evidence:
- reference: doi:10.1128/aem.67.12.5520-5525.2001
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The pure culture of S. aciditrophicus produced approximately 0.5 mol of cyclohexane
- carboxylate and 1.5 mol of acetate per mol of benzoate, while a coculture
- of S . aciditrophicus with the hydrogen-using methanogen Methanospirillum
- hungatei produced 3 mol of acetate and 0.75 mol of methane per mol of
- benzoate.
- explanation: Demonstrates methane-producing syntrophy between S. aciditrophicus
- and M. hungatei.
+ snippet: a coculture of S. aciditrophicus with the hydrogen-using methanogen Methanospirillum hungatei produced
+ 3 mol of acetate and 0.75 mol of methane per mol of benzoate.
+ explanation: Supports the named hydrogen user and coculture product balance.
- reference: doi:10.1128/aem.67.12.5520-5525.2001
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Degradation proceeds only if the concentration of hydrogen produced during
- benzoate oxidation is continuously maintained at a low level by a hydrogen-using
- microorganism ( 12 , 19 , 24 , 26 ).
- explanation: Confirms the low-hydrogen requirement that the methanogen satisfies.
-- name: Community Benzoate Mineralization to Acetate and Methane
- description: 'The two-member S. aciditrophicus-M. hungatei coculture consumes
- benzoate and completes the methanogenic community outcome by producing acetate
- and methane at the stoichiometry predicted for syntrophic benzoate degradation.
-
- '
- interaction_type: SYNTROPHY
+ snippet: The anaerobic bacterium Syntrophus aciditrophicus metabolized benzoate in pure culture in the absence
+ of hydrogen-utilizing partners or terminal electron acceptors.
+ explanation: Prevents the low-hydrogen requirement of the syntrophic route from becoming a universal dependence
+ claim.
+- name: Community Benzoate Conversion to Acetate and Methane
+ description: 'The two-member benzoate coculture produced approximately three mol acetate and 0.75 mol methane
+ per mol benzoate, as summarized in the primary abstract. This is substrate conversion, not complete mineralization:
+ acetate remains organic carbon. The reported pure-culture product balance differs, including cyclohexane carboxylate
+ accumulation.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Syntrophus aciditrophicus SB
@@ -242,19 +226,19 @@ ecological_interactions:
metabolites:
- preferred_term: benzoate
term:
- id: CHEBI:30746
- label: benzoic acid
- concentration: Aromatic substrate consumed by the coculture
+ id: CHEBI:16150
+ label: benzoate
+ notes: Aromatic substrate consumed by the coculture
- preferred_term: acetate
term:
id: CHEBI:30089
label: acetate
- concentration: Syntrophic benzoate degradation product
+ notes: Syntrophic benzoate degradation product
- preferred_term: methane
term:
id: CHEBI:16183
label: methane
- concentration: Methanogenesis product
+ notes: Methanogenesis product
biological_processes:
- preferred_term: benzoate metabolic process
term:
@@ -268,20 +252,16 @@ ecological_interactions:
- reference: doi:10.1128/aem.67.12.5520-5525.2001
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The pure culture of S. aciditrophicus produced approximately 0.5 mol of cyclohexane
- carboxylate and 1.5 mol of acetate per mol of benzoate, while a coculture
- of S . aciditrophicus with the hydrogen-using methanogen Methanospirillum
- hungatei produced 3 mol of acetate and 0.75 mol of methane per mol of
- benzoate.
- explanation: Supports acetate and methane as the methanogenic benzoate-coculture
- products.
- - reference: doi:10.1128/aem.67.4.1728-1738.2001
+ snippet: a coculture of S. aciditrophicus with the hydrogen-using methanogen Methanospirillum hungatei produced
+ 3 mol of acetate and 0.75 mol of methane per mol of benzoate.
+ explanation: Abstract-level approximate product stoichiometry; not a time-resolved or carbon-complete mineralization
+ claim.
+ - reference: doi:10.1128/aem.67.12.5520-5525.2001
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Only after 100% of the benzoate was consumed (day 11) was the methane-to-benzoate
- ratio (0.76) close to the theoretical value, 0.75.
- explanation: Supports complete benzoate consumption and the expected methane
- yield in S. aciditrophicus-M. hungatei coculture.
+ snippet: The pure culture of S. aciditrophicus produced approximately 0.5 mol of cyclohexane carboxylate and
+ 1.5 mol of acetate per mol of benzoate
+ explanation: Documents the distinct partner-free metabolic outcome.
environmental_factors:
- name: Anaerobic Conditions
value: Strict anaerobic
@@ -342,3 +322,17 @@ growth_media:
snippet: All media and stock solutions were prepared anaerobically by using the
techniques described by Balch and Wolfe ( 3 ).
explanation: Establishes strict anaerobic preparation of the culture medium.
+curation_history:
+- timestamp: '2026-10-08T07:10:55Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain coculture benzoate metabolism without importing other-partner enzyme assays.; Bound hydrogen-user
+ dependence to the syntrophic product route.; Rename mineralization as conversion and correct graph benzoate
+ grounding. Issue#1874; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
+- timestamp: '2026-10-08T07:25:00Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Use a shorter contiguous benzoate-intermediate quote after bracket-stripping failure #622; retain the
+ compound-or-CoA qualification and original failed validation log. Issue#1874; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml b/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
index 44f19be8a..58a87e29c 100644
--- a/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
+++ b/kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
@@ -114,9 +114,8 @@ taxonomy:
explanation: Supports the methanogenic function of the coculture that includes M. hungatei.
ecological_interactions:
- name: Methanogenic Benzoate Degradation
- description: Syntrophus gentianae degrades benzoate in coculture with
- Methanospirillum hungatei, yielding acetate and methane under methanogenic
- conditions.
+ description: Syntrophus gentianae degrades benzoate in coculture with Methanospirillum hungatei, yielding acetate
+ and methane under methanogenic conditions.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -132,8 +131,8 @@ ecological_interactions:
metabolites:
- preferred_term: benzoate
term:
- id: CHEBI:30746
- label: benzoic acid
+ id: CHEBI:16150
+ label: benzoate
- preferred_term: acetate
term:
id: CHEBI:30089
@@ -163,27 +162,21 @@ ecological_interactions:
snippet: degraded benzoate to CH4 and acetate
explanation: Supports methane and acetate as products of methanogenic benzoate degradation.
- name: Minimum Energy Threshold for Syntrophic Growth
- description: During growth on benzoate, the free energy available to S.
- gentianae was near the lower limit for energy conservation, showing why
- syntrophic partner activity and product concentrations constrain the
- community.
- interaction_type: SYNTROPHY
+ description: During growth of the methanogenic coculture, calculated free energy available to S. gentianae was
+ -50 to -55 kJ per mol benzoate. The authors inferred an approximate -45 kJ/mol requirement for growth and energy
+ conservation. This is a condition-dependent energetic constraint of the fermenter, not a second partner-directed
+ syntrophy event or an invariant value for every suspension or perturbation.
scope: PAIRWISE
source_taxon:
preferred_term: Syntrophus gentianae
term:
id: NCBITaxon:43775
label: Syntrophus gentianae
- target_taxon:
- preferred_term: Methanospirillum hungatei
- term:
- id: NCBITaxon:2203
- label: Methanospirillum hungatei
metabolites:
- preferred_term: benzoate
term:
- id: CHEBI:30746
- label: benzoic acid
+ id: CHEBI:16150
+ label: benzoate
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -195,36 +188,29 @@ ecological_interactions:
label: benzoate metabolic process
downstream:
- target: Methanogenic Benzoate Degradation
- description: Accumulated acetate and hydrogen thermodynamically inhibit the
- syntrophic reaction, lowering benzoate-degradation rates when products
- build up.
+ description: 'DIRECTLY IMPLIED: the fermenter must conserve sufficient energy to sustain growth-associated benzoate
+ conversion. The observed endpoint correlates with residual substrate and calculated free energy; the inferred
+ approximate growth threshold is not an independently manipulated universal constant.'
evidence:
- reference: PMID:33657722
supports: SUPPORT
evidence_source: IN_VITRO
snippet: change of free energy available for Syntrophus gentianae ranged between -50 and -55 kJ mol-1
- explanation: Supports the quantified energy window during coculture growth.
+ explanation: Calculated energy availability during growth is assigned to the fermenting bacterium.
- reference: PMID:33657722
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: minimum energy required for growth and energy conservation
- explanation: Supports the curated energy-threshold mechanism for syntrophic growth.
+ snippet: minimum energy required for growth and energy conservation of the benzoate-fermenting bacterium S.
+ gentianae is approximately -45 kJ (mol benzoate)-1
+ explanation: The authors infer an approximate growth requirement; dense suspensions and inhibited cultures are
+ distinct conditions.
- name: Product Inhibition of Benzoate Degradation
- description: Acetate and hydrogen inhibited benzoate degradation
- thermodynamically, while acetate and propionate additions lowered the
- degradation rate, linking product accumulation to community performance.
- interaction_type: COMPETITION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Syntrophus gentianae
- term:
- id: NCBITaxon:43775
- label: Syntrophus gentianae
- target_taxon:
- preferred_term: Methanospirillum hungatei
- term:
- id: NCBITaxon:2203
- label: Methanospirillum hungatei
+ description: Accumulated hydrogen and acetate constrain methanogenic benzoate degradation thermodynamically. Acetate
+ and separately added propionate also lower degradation rate; propionate is not identified as a benzoate product
+ here. These are metabolite and energetic constraints on the coculture, not competition between S. gentianae
+ and M. hungatei. Rescue with added sulfate reducers or Methanosaeta changes community composition and is not
+ an unmodified two-member outcome.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: acetate
term:
@@ -241,8 +227,9 @@ ecological_interactions:
label: benzoate metabolic process
downstream:
- target: Minimum Energy Threshold for Syntrophic Growth
- description: Hydrogen and acetate product accumulation constrain the free
- energy remaining to the benzoate-fermenting Syntrophus partner.
+ description: Product accumulation changes the free energy available to the fermenter, bringing growth-associated
+ benzoate conversion toward its energetic limit. Acetate also partly uncouples substrate degradation from energy
+ conservation, so this does not assert that product addition changes a fixed intrinsic threshold.
evidence:
- reference: PMID:33657722
supports: SUPPORT
@@ -253,12 +240,22 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Addition of acetate or propionate to benzoate-degrading cocultures also lowered the rate
- explanation: Supports product/addition effects on the rate of benzoate degradation.
+ explanation: Distinguishes acetate/product inhibition from the separate propionate-addition treatment; no reciprocal
+ intertaxon harm is established.
- reference: PMID:33657722
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Both hydrogen and acetate inhibit benzoate degradation thermodynamically
explanation: Supports hydrogen and acetate inhibition of methanogenic benzoate degradation.
+ participating_taxa:
+ - preferred_term: Syntrophus gentianae
+ term:
+ id: NCBITaxon:43775
+ label: Syntrophus gentianae
+ - preferred_term: Methanospirillum hungatei
+ term:
+ id: NCBITaxon:2203
+ label: Methanospirillum hungatei
environmental_factors:
- name: Methanogenic anaerobic condition
value: methanogenic coculture
@@ -419,3 +416,30 @@ metal_relevance: NOT_APPLICABLE
metal_notes: >
No metal or rare earth element transformation role is curated for this
methanogenic benzoate-degrading coculture.
+discussions:
+- discussion_id: gentianae-energy-context
+ prompt: How do energetic limits vary with growth, dense suspensions and added partners?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ rationale: The primary abstract distinguishes growing cocultures from cell suspensions and inhibitor or added-partner
+ treatments. Its approximate -45 kJ/mol growth requirement is not a universal endpoint. The graph preserves product-inhibition
+ constraints without encoding interspecies competition or treating expanded-community rescue as the original
+ pair.
+ attaches_to:
+ - ecological_interactions#Minimum Energy Threshold for Syntrophic Growth
+ - ecological_interactions#Product Inhibition of Benzoate Degradation
+ evidence:
+ - reference: PMID:33657722
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: acetate also partly uncouples substrate degradation from energy conservation
+ explanation: This is an energetic constraint rather than a competition phenotype.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T07:10:56Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain exact-pair benzoate conversion and correct benzoate grounding.; Assign inferred energy availability
+ to the fermenter without a spurious recipient.; Retain product inhibition without competition typing or treatment-system
+ conflation. Issue#1875; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
diff --git a/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml b/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
index 3e987080b..57d5ec9c3 100644
--- a/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
+++ b/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
@@ -142,22 +142,12 @@ taxonomy:
explanation: Supports the curated methanogenic scavenger role of M. hungatei.
ecological_interactions:
- name: Fermenter-Stimulated Butyrate Oxidation and Methane Production
- description: >
- Addition of T. flocculiformis ES5 stimulated the S. wolfei and M. hungatei
- syntrophic coculture, increasing butyrate consumption and volumetric methane
- production.
- interaction_type: SYNTROPHY
- scope: PAIRWISE
- source_taxon:
- preferred_term: Trichococcus flocculiformis strain ES5
- term:
- id: NCBITaxon:82803
- label: Trichococcus flocculiformis
- target_taxon:
- preferred_term: Syntrophomonas wolfei
- term:
- id: NCBITaxon:863
- label: Syntrophomonas wolfei
+ description: Adding T. flocculiformis ES5 stimulated the S. wolfei-M. hungatei culture, most clearly by shortening
+ the lag before conversion. In the exact-pair comparison, Table 1 marks the methane lag difference significant,
+ not the fitted maximum production-rate or final-concentration differences. The Discussion reports similar butyrate-consumption
+ slopes with and without ES5. Abstract-wide 120%/150% wording is not an exact-triculture increase estimate. This
+ is a three-member outcome, not an ES5-to-S. wolfei syntrophic exchange.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: butyrate
term:
@@ -180,30 +170,34 @@ ecological_interactions:
- reference: PMID:35699440
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The addition of T. flocculiformis ES5 to the syntrophic cocultures led to an increase
- explanation: Supports ES5 addition as the perturbation that stimulated the syntrophic cocultures.
+ snippet: statistically significant change in the lag phase of the S. wolfei and M. hungatei when cultured with
+ T. flocculiformis ES5.
+ explanation: The main Results identify the significant exact-pair lag response; Table 1 marks lag, not the rate
+ or final concentration, for this pairing.
- reference: PMID:35699440
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: rates of butyrate consumption (120%) and volumetric methane production (150%)
- explanation: Supports increased butyrate consumption and methane production as measured effects.
-- name: Aggregation With Syntrophic Partners
- description: >
- Scanning electron microscopy showed a tendency for T. flocculiformis ES5 to
- aggregate with S. wolfei and M. hungatei in the most positively affected
- coculture, consistent with spatial facilitation of the syntrophic partners.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Trichococcus flocculiformis strain ES5
+ snippet: butyrate consumption rates were similar regardless of presence of T. flocculiformis ES5 in the syntroph-methanogen
+ coculture
+ explanation: The Discussion bounds the general stimulation claim and separates lag from consumption slope.
+ participating_taxa:
+ - preferred_term: Trichococcus flocculiformis strain ES5
term:
id: NCBITaxon:82803
label: Trichococcus flocculiformis
- target_taxon:
- preferred_term: Methanospirillum hungatei
+ - preferred_term: Syntrophomonas wolfei
+ term:
+ id: NCBITaxon:863
+ label: Syntrophomonas wolfei
+ - preferred_term: Methanospirillum hungatei
term:
id: NCBITaxon:2203
label: Methanospirillum hungatei
+- name: Aggregation With Syntrophic Partners
+ description: SEM of the exact three-member culture showed ES5 in close spatial association with both syntrophic
+ partners and altered aggregation relative to the biculture. This is a community morphology observation, not
+ an isolated directional colonization benefit or proof of conductive bridging.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -211,39 +205,36 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Fermenter-Stimulated Butyrate Oxidation and Methane Production
- description: >
- HYPOTHESIZED — ES5 co-aggregation with S. wolfei and M. hungatei may
- spatially facilitate the improved butyrate oxidation and methane
- production, but the aggregation is an observed correlate of the ES5 effect
- and was NOT demonstrated to causally mediate the rate increases.
+ description: 'HYPOTHESIZED/PARTIAL: ES5-associated aggregation could contribute to the shorter conversion lag,
+ but morphology was not selectively manipulated to show mediation. Conductive bridging and DIET remain proposed
+ explanations, not demonstrated routes.'
evidence:
- reference: PMID:35699440
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: S. wolfei, M. hungatei, and T. flocculiformis ES5
- explanation: Supports the exact three-member composition of the coculture examined by microscopy.
- - reference: PMID:35699440
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: T. flocculiformis ES5 to aggregate with the syntrophic partners
- explanation: Supports the aggregation interaction with the two syntrophic partners.
-- name: Proteome Response in the Syntrophic Partners
- description: >
- Proteome analysis linked ES5 addition to signal-transducing systems in
- M. hungatei and activation of additional butyryl coenzyme A dehydrogenase
- and electron transfer flavoprotein in S. wolfei.
- interaction_type: SYNTROPHY
- scope: PAIRWISE
- source_taxon:
- preferred_term: Trichococcus flocculiformis strain ES5
+ snippet: very close proximity of T. flocculiformis ES5 cells to the cells of M. hungatei (as well as to the
+ cells of S. wolfei)
+ explanation: Supports association with both canonical partners, not a single directed recipient.
+ participating_taxa:
+ - preferred_term: Trichococcus flocculiformis strain ES5
term:
id: NCBITaxon:82803
label: Trichococcus flocculiformis
- target_taxon:
- preferred_term: Syntrophomonas wolfei
+ - preferred_term: Syntrophomonas wolfei
term:
id: NCBITaxon:863
label: Syntrophomonas wolfei
+ - preferred_term: Methanospirillum hungatei
+ term:
+ id: NCBITaxon:2203
+ label: Methanospirillum hungatei
+- name: Proteome Response in the Syntrophic Partners
+ description: Comparative proteomics of the two syntrophic partners with and without ES5 detected differential
+ protein abundance. Additional S. wolfei butyryl-CoA dehydrogenase and electron-transfer flavoprotein were more
+ abundant in the triculture; many candidate M. hungatei signaling proteins were instead more abundant in the
+ biculture. These observations do not directly measure enzyme activation, prove a signaling mechanism or establish
+ a second syntrophic exchange. ES5 is the added member; the assayed proteomes belong to S. wolfei and M. hungatei.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fatty acid beta-oxidation
term:
@@ -251,23 +242,35 @@ ecological_interactions:
label: fatty acid beta-oxidation
downstream:
- target: Fermenter-Stimulated Butyrate Oxidation and Methane Production
- description: >
- HYPOTHESIZED — the ES5-associated proteomic changes (activation of
- additional butyryl-CoA dehydrogenase and electron-transfer flavoprotein in
- S. wolfei; signal-transducing systems in M. hungatei) may underlie the
- improved butyrate oxidation, but the proteome response is correlative and
- was NOT shown to be the causal mediator of the improved performance.
+ description: 'HYPOTHESIZED/PARTIAL: changes in partner protein abundance may contribute to the shorter lag associated
+ with ES5 addition. The comparison does not selectively establish enzymatic or signaling mediation, and protein
+ abundance is not a direct activity assay.'
evidence:
- reference: PMID:35699440
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: signal transducing systems of M. hungatei
- explanation: Supports a proteomic response in the methanogenic partner after ES5 addition.
+ snippet: differential proteomics to compare protein expression profiles of the Syntrophomonas wolfei and Methanospirillum
+ hungatei with or without the addition of the fermentative microorganism
+ explanation: Defines the two measured proteomes and ES5 perturbation.
- reference: PMID:35699440
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: activation of additional butyryl coenzyme A dehydrogenase and an electron transfer flavoprotein
- explanation: Supports the curated proteomic response in S. wolfei.
+ snippet: it is not clear whether the presence of T. flocculiformis ES5 alone was activating production of this
+ enzyme.
+ explanation: The source explicitly withholds direct enzyme-activation attribution.
+ participating_taxa:
+ - preferred_term: Trichococcus flocculiformis strain ES5
+ term:
+ id: NCBITaxon:82803
+ label: Trichococcus flocculiformis
+ - preferred_term: Syntrophomonas wolfei
+ term:
+ id: NCBITaxon:863
+ label: Syntrophomonas wolfei
+ - preferred_term: Methanospirillum hungatei
+ term:
+ id: NCBITaxon:2203
+ label: Methanospirillum hungatei
environmental_factors:
- name: Anoxic anaerobic ecosystem context
value: anoxic sediments, soils, and wastewater treatment bioreactors
@@ -444,27 +447,30 @@ metal_notes: >
fermenter-stimulated methanogenic butyrate coculture.
discussions:
- discussion_id: kg-es5-mediation-mechanism-unresolved
- prompt: >
- Does T. flocculiformis ES5 improve the S. wolfei / M. hungatei syntrophy via
- co-aggregation-based spatial bridging (possible DIET) or via the observed
- proteomic changes, and is either mechanism causal rather than correlative?
+ prompt: Which ES5-associated processes mediate the shorter lag in this exact triculture?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
+ - ecological_interactions#Fermenter-Stimulated Butyrate Oxidation and Methane Production
- ecological_interactions#Aggregation With Syntrophic Partners
- ecological_interactions#Proteome Response in the Syntrophic Partners
- rationale: >
- The ES5-driven increase in butyrate consumption (120%) and methane (150%) is
- perturbation-supported, but the mediating mechanism is unresolved: aggregation
- and the partner proteome response are observed correlates, not demonstrated
- causal mediators (the two `downstream` edges here are flagged HYPOTHESIZED
- accordingly). Direct interspecies electron transfer was not experimentally
- demonstrated for this tri-culture, and the exact ES5 bridging role remains an
- open question per the source.
+ rationale: The exact-pair Results and Table 1 support a shorter lag; the Discussion reports similar butyrate-consumption
+ slopes. The former abstract-wide 120%/150% increase attribution is therefore removed from this discussion and
+ graph. Aggregation and differential protein abundance are measured correlates, while causal mediation, conductive
+ bridging and DIET remain unresolved. Both existing explanatory arrows stay hypothetical. No direct enzyme activation
+ or uniformly enhanced methanogen signaling is inferred.
evidence:
- reference: PMID:35699440
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: T. flocculiformis ES5 to aggregate with the syntrophic partners
- explanation: Aggregation is reported as an association accompanying the ES5 effect, without a
- demonstrated causal-mediation or DIET mechanism — the basis for the knowledge gap.
+ snippet: it is not clear whether the presence of T. flocculiformis ES5 alone was activating production of this
+ enzyme.
+ explanation: The source explicitly withholds direct enzyme-activation attribution.
+curation_history:
+- timestamp: '2026-10-08T07:10:56Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Bound stimulation to exact-pair lag and statistical comparisons at community scope.; Retain three-member
+ spatial association without directed colonization or DIET proof.; Retain differential proteomics without enzyme-activation
+ or signaling-causality overstatement. Issue#1876; reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 9aabfea30..c03e6320c 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,38 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch112: Syntrophic Feedback And Assay Boundaries
+
+[Decisions](decisions/20261008-seven-records-batch112.yaml),
+[provenance](cache-provenance-20261008-batch112.json),
+[validation](validation-20261008-batch112.json), and
+[self-adversarial review](adversarial-review-20261008-batch112.yaml) cover
+seven propionate, butyrate and benzoate records. All 21 nodes remain; 16 of
+17 existing arrows remain. The misplaced population-ratio reverse arrow is
+removed, and benzoate mineralization is renamed as conversion. Supported
+metabolic feedback remains; carrier partitioning, enzyme assignments and
+aggregation/protein mediation retain their evidence limits.
+
+Four fresh extracted primary main bodies and five older primary abstracts
+support this review. Of 53 graph/discussion quotations, 51 match fresh primary
+artifacts and two match only existing curator-supplied publisher text, whose
+fresh retrieval was unavailable. No original figure pixels, separate supplements
+or raw data were audited. Eight append-only histories preserve the trail,
+including a shorter contiguous benzoate quote after a bracket-stripping failure;
+the original failed output and pre-correction evidence remain recorded.
+All 923 caches and 453 other records are unchanged. The measured scope census
+adds three solely-credited taxa from the community-scoped ES5 triculture;
+connectivity rules and the share guard are unchanged. No new topology or Edison spend.
+The exact participant-user test now includes the three newly explicit records;
+the initial failed regression output is retained alongside the corrected rerun.
+
+Graph repairs #1871-#1876 await protected-main merge. Non-graph culture metadata
+and residual claim follow-ups #1877-#1878 remain open. Self-review is not
+independent approval or whole-record certification.
+The unchanged coordination cultivation quote still triggers bracket-stripping
+validator issue #622. Its failure is reproduced on the parent and its text matches
+the primary source; it is recorded as an exception, not a reference-validation pass.
+
## Batch111: Carbon, Lipid And Attachment Evidence
[Decisions](decisions/20261008-three-records-batch111.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch112.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch112.yaml
new file mode 100644
index 000000000..98cf5ee49
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch112.yaml
@@ -0,0 +1,444 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c38a8903f7fe36f9a870b1b872f179bb4a7a9ee4
+scope:
+- kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml
+- kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml
+- kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
+- kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml
+- kb/communities/Syntrophus_Benzoate_Degrader.yaml
+- kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
+- kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch112.json
+findings:
+- issue: 1871
+ severity: P2
+ finding: Bound propionate carrier feedback and enzyme inference to exact syntrophic partners
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1872
+ severity: P2
+ finding: Remove misplaced ratio feedback and bound butyrate-coculture spatial association
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1873
+ severity: P2
+ finding: Bound classic Syntrophomonas hydrogen feedback and remove uncited pressure threshold
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1874
+ severity: P2
+ finding: Separate benzoate conversion from mineralization and universal partner dependence
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1875
+ severity: P2
+ finding: Represent gentianae energetic constraints without intertaxon competition
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1876
+ severity: P2
+ finding: Bound ES5 stimulation by exact-triculture statistics and distinguish proteomic correlates
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1877
+ severity: P2
+ finding: Reconcile syntrophic-record culture metadata with vessel volume and generation time
+ status: open_non_graph_follow_up
+ disposition: Separate metadata curation remains open.
+- issue: 1878
+ severity: P2
+ finding: Reconcile residual non-graph syntrophy and ES5 kinetic claims with assay scope
+ status: open_non_graph_follow_up
+ disposition: Separate metadata curation remains open.
+adversarial_checks:
+- 'All 21 original nodes and 17 directions have dispositions: 21 nodes and 16 arrows retained, one misplaced reverse
+ direction removed, and one conversion outcome renamed. No new biological topology or Edison submission.'
+- 'Challenge overcorrection: preserve exact-pair propionate and butyrate syntrophy,thermodynamic carrier-removal
+ feedback,reciprocal spatial attraction,benzoate conversion,energy/product constraints and positive ES5 lag stimulation.
+ Qualified mechanisms do not erase measured effects.'
+- 'Propionate: hydrogen pressure differs from formate concentration. Both exact pairings are present in the comparative
+ proteomic study,where main-text Fdh1/Hox assignments remain qualified. Protein abundance and homology are not
+ selective enzyme demonstrations or carrier-flux fractions. Cooperation is reciprocal without bidirectional carrier
+ donation. Reuse and amend the existing formicicum source-attribution discussion.'
+- 'Coordination: manipulated starting ratios differ from the converged ratio. The former reverse arrow described
+ aggregation rather than its population source. Retain the forward growth-to-ratio inference as PARTIAL and retain
+ reciprocal attraction as a community observation. Physical disturbance changed activity without detectable aggregation
+ changes,so mediation is unresolved. The nanomaterial study explicitly withholds decisive DIET attribution.'
+- 'Butyrate: the accessible1981abstract names M.hungatei and reports added-hydrogen inhibition. Preserve directly
+ implied feedback,but remove an unsupported graph pressure threshold,duplicate evidence and substrate-wide obligacy.
+ Do not certify detailed exact-pair perturbation conditions from the abstract.'
+- 'Benzoate: acetate remains organic carbon,so conversion is not complete mineralization. The pure-culture experiment
+ explicitly demonstrates partner-free benzoate metabolism with a different product balance. Other-partner enzymology
+ is not imported into the methanogenic pair. Benzoate graph grounding uses officially verified CHEBI16150,not neutral
+ benzoic acid.'
+- 'Gentianae: fermenter energy is not a second directed exchange;product inhibition is not intertaxon competition.
+ Preserve the source-supported constraint chain while distinguishing approximate growth energy,dense suspensions,propionate
+ addition and expanded-community rescue. The product arrow changes available free energy,not a fixed intrinsic
+ threshold.'
+- 'ES5: preserve the exact M.hungatei lag response;Table1 marks lag significant,not fitted rate/final concentration,and
+ Discussion reports similar butyrate slopes. Do not transfer abstract-wide120%/150% to exact-triculture increases.
+ Three-member outcomes include both syntrophic partners;their proteomes,not ES5,are assayed. Candidate methanogen
+ signaling proteins were often more abundant in biculture,not uniformly activated by ES5. Both existing mediation
+ arrows remain hypothetical.'
+- 'Source-access challenge: four fresh extracted main bodies plus five older primary abstracts were read. Two 2024
+ transcription quotes remain grounded only in existing curator-supplied publisher text; fresh retrieval failed.
+ All 53 quotes match unchanged caches; 51 match fresh primary artifacts. Matching is not entailment. No original
+ pixels, separate supplements or raw data were certified; read spans and retrieval failures are explicit.'
+- 'Seven guarded records and eight append-only histories preserve 453 other records, 923 caches, raw non-graph blocks
+ and prior decision/history artifacts. The second benzoate history records a shorter contiguous quote after bracket-stripping
+ issue #622; the compound-or-CoA qualification remains in its explanation. Initial ledger, failed output and mutation
+ proof are preserved. Exact canonical identity-only participants are used. Measured census gains three community-level
+ records, two mixed and one community-only; seven denominator taxa and three solely-credited ES5 members. Connectivity
+ logic and share guard remain unchanged.'
+- Five real in-memory control/mutation/restored-control probes reject enzyme certainty,reverse ratio causality,competition
+ typing,inflated exact-triculture rates and proven proteomic mediation. Each logs actual changed values and the
+ rejecting assertion. Canonical hashes remain unchanged;these probes do not inflate pytest counts.
+- 'Eleven focused tests and 1014 combined regressions pass. Seven schema/strict/term/local-snippet checks and eight
+ histories pass. Six full-record reference CLI checks pass; coordination has one unchanged bracket-stripping #622
+ failure, proved byte-identical on parent and matched to fresh primary text. It is an exception, not a pass. The
+ 70 outputs include six superseded outputs: five from before the quote correction, plus the initial regression
+ failure. The new bracket quote was corrected and revalidated; the exact participant-user test was updated for
+ the three intentionally added records after the measured census. Neither failed run is counted as a pass. All
+ 56 existing network warnings are unchanged; zero structural defects. Deterministic rendering and exact HTML-description
+ matching cover 456 pages, 1366 nodes and 535 arrows, not screenshots. Full-corpus snippets remain informational,
+ not clean-corpus certification.'
+- 'Graph repairs #1871-#1876 await protected-main merge; non-graph metadata follow-ups #1877-#1878 remain open.
+ Source-based self-review is not independent approval. Reference-loader, DOI-case and preexisting snippet-rendering
+ issues remain outside scope; macOS reference success is not Linux certification. No artificial CI, access/protection
+ bypass or premature branch deletion.'
+- 'Corpus status: 362 reviewed, 45 pending, 53 needs_research across 460 records. The overall goal is incomplete.
+ Exact-head publication and postcommit docs-current remain separate gates, not preasserted in this report.'
+- Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Proteomic enzyme inference promoted to proven SUPPORT
+ test: test_propionate_feedback_is_retained_without_carrier_or_enzyme_certainty
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 23
+ assertion: assert a["evidence"][1]["supports"] == a["evidence"][2]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/0/evidence/1/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Converged population ratio restored as a cause of metabolism
+ test: test_ratio_convergence_is_not_reverse_metabolic_causality
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 50
+ assertion: assert "downstream" not in b
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/1/downstream
+ before: null
+ after:
+ - target: Syntrophic Butyrate Oxidation and Methanogenesis
+ description: Ratio convergence causes faster metabolism.
+ - mutation: Product inhibition restored as intertaxon competition
+ test: test_gentianae_energy_is_intrinsic_and_product_inhibition_not_competition
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 86
+ assertion: assert c["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in c
+ restored_control: PASS
+ changed_values:
+ - path: records/5/ecological_interactions/2/interaction_type
+ before: null
+ after: COMPETITION
+ - mutation: Exact ES5 triculture stimulation inflated to significant rate increases
+ test: test_es5_lag_is_distinguished_from_rates_and_final_concentration
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 98
+ assertion: assert "marks the methane lag difference significant, not" in a["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/6/ecological_interactions/0/description
+ before: Adding T. flocculiformis ES5 stimulated the S. wolfei-M. hungatei culture, most clearly by shortening
+ the lag before conversion. In the exact-pair comparison, Table 1 marks the methane lag difference significant,
+ not the fitted maximum production-rate or final-concentration differences. The Discussion reports similar
+ butyrate-consumption slopes with and without ES5. Abstract-wide 120%/150% wording is not an exact-triculture
+ increase estimate. This is a three-member outcome, not an ES5-to-S. wolfei syntrophic exchange.
+ after: ES5 significantly increases exact-triculture butyrate and methane production rates by120% and150%.
+ - mutation: Protein abundance promoted to demonstrated metabolic mediation
+ test: test_es5_proteomics_and_aggregation_are_hypotheses_not_enzyme_activation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 114
+ assertion: assert n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ restored_control: PASS
+ changed_values:
+ - path: records/6/ecological_interactions/2/downstream/0/description
+ before: 'HYPOTHESIZED/PARTIAL: changes in partner protein abundance may contribute to the shorter lag associated
+ with ES5 addition. The comparison does not selectively establish enzymatic or signaling mediation, and
+ protein abundance is not a direct activity assay.'
+ after: Enzyme activation demonstrated to cause increased production.
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml: eb0ed26cadc17f4a7fbf63d8d2c11da1d891cd2edf5ce82b938e19c2d0cf469b
+ kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml: a4076f47b588559b0a751b8d4e0be16c067af11c359ba5e9f401fd0b542fb61a
+ kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml: 3aaf56515d25364c8ee56e24071798ff6e3893ccce89761fadd331a109719531
+ kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml: 2ba0dc0aafd78379eee56f47b0e5ef235d8ea5e52abaa5f51417f07412b5535d
+ kb/communities/Syntrophus_Benzoate_Degrader.yaml: dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1
+ kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml: 3584798fce68b6699f57471b38d2a5e7778e154ff5dbbbb63c3f98f92a2f3451
+ kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml: 19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0
+ tests/test_causal_review_batch112.py: 7d66d5a3b4d3f31c3113cff3fde8843f7475fe9be8528c8ec054b7981a1c567f
+ probe_script_sha256: 4bb4fe14cd8e0ef571e6ab3731dece772753c75ffbc60b0a97adf93d00a83fa5
+ scope: In-memory evidence mutations with control and restored-control; no canonical writes or inflated pytest
+ count.
+ artifact: /private/tmp/communitymech-batch112/adversarial-regression-proof-after-bracket-correction.json
+ sha256: 6d8034752bb38cdd49d0c65bef2cdb0ea140d5ca053227ea7b73c716064ce563
+ superseded_artifact: /private/tmp/communitymech-batch112/adversarial-regression-proof.json
+ superseded_sha256: 4d623cd85cdf16c70f321a3e85595bfeafbc53d6a756d50117612a67fb51503e
+verification:
+ combined_regressions: 1014 passed in 381.37s (0:06:21)
+ new_regression_tests: 11
+ total_recorded_gate_outputs: 70
+ participant_allowlist_correction:
+ failed_log: /private/tmp/communitymech-batch112/verification/regressions.log
+ failed_log_sha256: 42852dffd0a136b82705afe69e8912482c694c82ece40e46f336dbbf5dbb6016
+ failed_result: 1 failed, 1013 passed in 529.35s (0:08:49)
+ previous_users: 283
+ current_users: 286
+ added_records:
+ - Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
+ - Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
+ - Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
+ scope: Exact user-set expectation only; no canonical record or connectivity logic change.
+ primary_graph_snippet_proof:
+ graph_quotations: 45
+ discussion_quotations: 8
+ fresh_primary_literal_matches: 51
+ existing_curator_text_only: 2
+ all_cached_literal_matches: 53
+ retained_nodes: 21
+ removed_nodes: 0
+ renamed_nodes: 1
+ retained_arrows: 16
+ removed_arrows: 1
+ new_nodes_or_directions: 0
+ scope: Four fresh extracted main bodies and five older primary abstracts;two2024quotes use existing curator-supplied
+ text,not fresh full text. Source entailment and access bounds separately recorded.
+ references: Six full-record reference CLI passes;one expected preexisting failure in unchanged coordination cultivation_setup
+ due to bracket stripping622 and misleading abstract note496,proven byte-identical on parent and matched to fresh
+ primary text. Seven local snippet audits pass. macOS,not Linux certification;DOI-case1091,ligature1863 and loader1703
+ remain outside scope. Literal matches do not establish entailment. CLI Total checks counts issues,not checks.
+ preexisting_reference_exception:
+ artifact: /private/tmp/communitymech-batch112/preexisting-bracket-validator-proof.json
+ sha256: 15bb306e74ad93c470419af2e5a33ee19b4a8ccebb90cec59cdf881040862170
+ proof:
+ issue: 622
+ secondary_note_issue: 496
+ location: cultivation_setup[0].evidence[1].snippet
+ exit_code: 1
+ parent_exit_code: 1
+ byte_identical_parent_failure: true
+ unchanged_cultivation_setup: true
+ fresh_primary_literal_match: true
+ cache_literal_match: true
+ baseline_log: /private/tmp/communitymech-batch112/parent-coordination-references.log
+ baseline_log_sha256: d3e5b7b25ae27facb77d211b58e8da0d043abe0c79a37038ee2c32c04a8e77b5
+ current_log: /private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-references.log
+ current_log_sha256: d3e5b7b25ae27facb77d211b58e8da0d043abe0c79a37038ee2c32c04a8e77b5
+ cache_sha256: b43b81a611ba2a42a98e32cf06acf5663c43bd33edbf384a0151124a7bde6678
+ interpretation: Expected preexisting bracket-stripping failure;not a reference-validation pass. Graph quotation
+ proof remains separate.
+ snippet_counts_by_record:
+ kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml:
+ MATCH: 27
+ RENDERING: 1
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml:
+ MATCH: 17
+ RENDERING: 1
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml:
+ MATCH: 26
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Syntrophus_Benzoate_Degrader.yaml:
+ MATCH: 10
+ RENDERING: 3
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml:
+ MATCH: 26
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9012
+ categories:
+ MATCH: 8867
+ RENDERING: 28
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: Twenty-one nodes and sixteen existing directions retained;one misplaced reverse arrow removed;one
+ conversion node renamed. All56existing warnings unchanged;zero structural defects. Non-graph followups1877-1878
+ remain open.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml: 70c5847ba8f65d2e4d4b283c362cbbb6637bf9e5e47d76877daec2f5557e8794
+ tests/test_causal_review_batch112.py: 7d66d5a3b4d3f31c3113cff3fde8843f7475fe9be8528c8ec054b7981a1c567f
+ tests/test_causal_review_batch109.py: 262381c4834593eb8fa6c8424e59ccfedc7428540bb57cf3db72703c935fc180
+ tests/test_participating_taxa.py: 82767cd685f4f127a12e6173f3ce88b547def54ef4ebd901c278e1978450c1a0
+ tests/test_community_level_connectivity_credit.py: 43cdd3ac18aaf658dc83288f70e96ddeb76f8cf1b9622bec2d1e52e25187d5ec
+ reports/causal_graph_review/cache-provenance-20261008-batch112.json: 5365b98f4cd1d1822dbbeca7a04f38cb9bf2a85f21ad7691985220c2996051d9
+ kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml: eb0ed26cadc17f4a7fbf63d8d2c11da1d891cd2edf5ce82b938e19c2d0cf469b
+ kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml: a4076f47b588559b0a751b8d4e0be16c067af11c359ba5e9f401fd0b542fb61a
+ kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml: 3aaf56515d25364c8ee56e24071798ff6e3893ccce89761fadd331a109719531
+ kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml: 2ba0dc0aafd78379eee56f47b0e5ef235d8ea5e52abaa5f51417f07412b5535d
+ kb/communities/Syntrophus_Benzoate_Degrader.yaml: dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1
+ kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml: 3584798fce68b6699f57471b38d2a5e7778e154ff5dbbbb63c3f98f92a2f3451
+ kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml: 19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0
+ history_sha256:
+ history/records/Syntrophobacter_Methanobacterium_Syntrophy/2026-10-08T071057Z-codex-d473fc.yaml: 98a2cfb1b57aee82178d4624a90cb4081c067753ec3d6f9897a24021963940af
+ history/records/Syntrophobacter_Methanospirillum_Syntrophy/2026-10-08T071057Z-codex-fb396b.yaml: 70b72bf9b25d92d013f9c4955a5f6de6ff185b5261da74c8dfbb4387b4f2eac8
+ history/records/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture/2026-10-08T071057Z-codex-28253a.yaml: 96e2b09995d575be66401e45d8faee15bcbb4aa94920fbe3ed6083cbf4633423
+ history/records/Syntrophomonas_Methanospirillum_Syntrophy/2026-10-08T071058Z-codex-a2e51d.yaml: 51d68d097bbf1972d46a2cafe29e94745fcb0de5fd78c73d1115f390aa39a86e
+ history/records/Syntrophus_Benzoate_Degrader/2026-10-08T071058Z-codex-9e1dfe.yaml: 77870f3e098a57462a372fa1ae45a10c6c4ae47d24c78a8e17cb4fe1e430ea9a
+ history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml: a56d430c707b9ff2f7f98ae80d7a5da95e0d66a511c207d4d147b14dfaf1dbf8
+ history/records/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture/2026-10-08T071058Z-codex-4e26a3.yaml: c43f6a450865a755e335493342aafd656c0c4edd27b76a07b456412c2ee50f90
+ history/records/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture/2026-10-08T071059Z-codex-12f831.yaml: a58e496dd53d0b1226a5fd40ca251d99f18930e0d5f46625a1efe1017ef0c54b
+ unchanged_records: 453
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 849
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing evidence/scope repairs and removal of one unsupported reverse direction;no new nodes/directions.
+ post_commit_docs_current: Separate publication gate,not preasserted.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 409
+ mixed: 134
+ community_level_only: 275
+ taxa: 1556
+ credited_solely_by_the_rule: 1270
+ current:
+ records: 460
+ with_community_level: 412
+ mixed: 136
+ community_level_only: 276
+ taxa: 1563
+ credited_solely_by_the_rule: 1273
+ delta:
+ records: 0
+ with_community_level: 3
+ mixed: 2
+ community_level_only: 1
+ taxa: 7
+ credited_solely_by_the_rule: 3
+ interpretation: Three additional community-level records,two mixed and one community-only. Seven denominator taxa
+ and three solely-credited taxa reflect the ES5 triculture outcome scope;canonical participants explicit. Connectivity
+ rules and share guard unchanged.
+corpus:
+ records: 460
+ nodes: 1380
+ edges: 543
+ review_status_counts:
+ needs_research: 53
+ pending: 45
+ reviewed: 362
+lint_limitation: Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies
+ unchanged. Not a complete embedding runtime.
+limitations:
+- Fresh pre-source baseline across both roots:460 records,923 caches,56 existing warnings,zero structural defects.
+ Review all21 original nodes/17arrows; retain21nodes/16directions,remove one misplaced reverse arrow,rename one
+ outcome. No new topology or Edison spend.
+- Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh
+ extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including
+ abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data
+ review.
+- Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and
+ both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body
+ excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher
+ rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed
+ assays.
+- 2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content lines1-735
+ read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription
+ snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved
+ and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.
+- All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately
+ from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not
+ read in full. Official ChEBI16150 identity confirmed; no new taxon groundings.
+- 'Propionate: preserve real carrier-removal feedback, bound enzyme homology/abundance inference and carrier partitioning,
+ distinguish gas pressure from aqueous concentration. Butyrate: preserve reported hydrogen inhibition but do not
+ certify exact perturbation conditions,universal obligacy or an uncited pressure threshold.'
+- 'Coordination: initial ratio perturbations are distinct from endpoint convergence; remove aggregation-described
+ reverse arrow. Reciprocal attraction and unchanged aggregation under activity-changing disturbance are retained.
+ Nanomaterial acceleration does not prove DIET.'
+- 'Benzoate: acetate+CH4 is conversion,not complete mineralization; pure-culture fermentation disproves universal
+ partner dependence. Other-partner enzyme assays are not imported. Gentianae: approximate growth energy and product
+ effects are not competition or a fixed threshold across dense-suspension and added-partner treatments.'
+- 'ES5: exact M.hungatei lag is significant in Table1; fitted rate/final concentration are not marked significant
+ and Discussion reports similar butyrate slopes. Preserve stimulation without abstract-wide120%/150% exact-triculture
+ attribution. All three members remain in outcome scope; measured proteomes are two partners. Aggregation/protein
+ mediation remains hypothetical,not enzyme activation or DIET proof.'
+- Ignored/hidden-inclusive local path index read,not all historical file bodies. Fresh all-state issue title/body
+ dedup matched1392,1389,795,583,496,259;fullbodies and related529/183 read. PR comments not exhaustively searched.
+ Broad metadata issues are followups,not addressed by graph scope.
+- Preserve453otherrecords,923caches,rawnon-graph blocks and prior history/decision artifacts. Participant census
+ measured,not guessed;rules/share guard unchanged. No schema/validator/runtime change. MacOS full-record CLI is
+ not Linux certification;reference-loader,DOI-case and rendering caveats remain.
+- Repair issues remain open until protected-main merge;metadata followups remain open afterward. Self-review is
+ not independent approval or full-corpus completion. Denied/unanswered Edison scopes untouched;no artificial CI,protection
+ bypass or premature branch deletion.
+- 'Post-write validation correction: a new benzoate quote triggered bracket-stripping622. Replace it with a shorter
+ contiguous excerpt and keep the compound-or-CoA qualification in explanation;append a second history for that
+ record. The initial ledger,failed output and pre-correction mutation proof are preserved. Eight histories total;one
+ unchanged coordination metadata622 failure remains explicitly excepted.'
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch112.json b/reports/causal_graph_review/cache-provenance-20261008-batch112.json
new file mode 100644
index 000000000..8e4e96c0d
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch112.json
@@ -0,0 +1,517 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch112/baseline.json": "1904cacf99f46e220f9baf67e72ba5847e9f13048d63691b56a79e1db8dd074c",
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+ 2001,
+ 4,
+ 1
+ ]
+ ],
+ "date-time": "2001-04-01T00:00:00Z",
+ "timestamp": 986083200000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://journals.asm.org/non-commercial-tdm-license"
+ }
+ ]
+ },
+ "benzoate_pure": {
+ "pmid": "11722901",
+ "doi": "10.1128/aem.67.12.5520-5525.2001",
+ "pmcid": "PMC93338",
+ "title": "Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in the absence of hydrogen-using microorganisms.",
+ "metadata": "/private/tmp/communitymech-batch112/benzoate_pure-metadata.json",
+ "metadata_sha256": "9b537d873eba32ffefdde5c1f39a563045b62b63da88fa096032a25efd0f0249",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1128%2Faem.67.12.5520-5525.2001%22+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC93338/fullTextXML",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 500: "
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch112/benzoate_pure-abstract.txt",
+ "abstract_sha256": "f021c43b5e508c68ddd9b29e7f1eac0f239e099856111152bc3ff8ffdfdeeebd",
+ "crossref": "/private/tmp/communitymech-batch112/benzoate_pure-crossref.json",
+ "crossref_sha256": "e1a69d821ff71d39ce1519415c40b21ee8a4029d550e833a9e4a290c4de9ef2a",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2001,
+ 12,
+ 1
+ ]
+ ],
+ "date-time": "2001-12-01T00:00:00Z",
+ "timestamp": 1007164800000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://journals.asm.org/non-commercial-tdm-license"
+ }
+ ]
+ },
+ "nanomaterials": {
+ "pmid": "30111866",
+ "doi": "10.1038/s41598-018-30745-7",
+ "pmcid": "PMC6093938",
+ "title": "Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and a defined coculture.",
+ "metadata": "/private/tmp/communitymech-batch112/nanomaterials-metadata.json",
+ "metadata_sha256": "04e31b769a23d945f9713a65435dc1f69b4fadf82b6ab2e4204fffa628caadf4",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1038%2Fs41598-018-30745-7%22+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 1
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6093938/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch112/nanomaterials-abstract.txt",
+ "abstract_sha256": "aa2f576c63c95c5f44b99ea69b0c1897ceebf6eed946101880515869baae2552",
+ "xml": "/private/tmp/communitymech-batch112/nanomaterials-primary.xml",
+ "xml_sha256": "e405c23a2747de20c1b260a36c83e0be9b52640806ec7d7789069a1ab0c20a02",
+ "primary_text": "/private/tmp/communitymech-batch112/nanomaterials-primary.txt",
+ "primary_text_sha256": "c717378a0f3336093af13b22bb02c0ec55f1d5d30f56c885b3d54dde0469892a",
+ "license": [
+ "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article\u2019s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article\u2019s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/."
+ ],
+ "crossref": "/private/tmp/communitymech-batch112/nanomaterials-crossref.json",
+ "crossref_sha256": "9ef898555efae082d2b050d2d803e52b78018e17e0dcb331a1466ed40a8b355b",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2018,
+ 8,
+ 15
+ ]
+ ],
+ "date-time": "2018-08-15T00:00:00Z",
+ "timestamp": 1534291200000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2018,
+ 8,
+ 15
+ ]
+ ],
+ "date-time": "2018-08-15T00:00:00Z",
+ "timestamp": 1534291200000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0"
+ }
+ ]
+ },
+ "formate_stress": {
+ "pmid": null,
+ "doi": "10.3390/w16243551",
+ "pmcid": null,
+ "title": [
+ "Promoting or Inhibiting: New Insights into the Role of Formate in Syntrophic Propionate Metabolism"
+ ],
+ "metadata": "/private/tmp/communitymech-batch112/formate_stress-metadata.json",
+ "metadata_sha256": "34c774db4c79d979376279cba0767c07ccbdd1146d64790e6446ae85c8183a5f",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.3390%2Fw16243551%22+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved",
+ "records": 0
+ },
+ {
+ "url": "https://www.mdpi.com/2073-4441/16/24/3551/xml",
+ "status": "retrieval_failed",
+ "error": "HTTP Error 403: Forbidden"
+ }
+ ],
+ "crossref": "/private/tmp/communitymech-batch112/formate_stress-crossref.json",
+ "crossref_sha256": "9b85a4aba31b5abe2d4e19001262a0e4ebb370255332cffec868e09711184ae1",
+ "crossref_license": [
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2024,
+ 12,
+ 10
+ ]
+ ],
+ "date-time": "2024-12-10T00:00:00Z",
+ "timestamp": 1733788800000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch112/formate_stress-abstract.txt",
+ "abstract_sha256": "c37b280c176346e64650bc0dcab43544183a3a87082b4139c35fdabc16fa0305"
+ }
+ },
+ "actual_read_scope": [
+ "Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data review.",
+ "Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed assays.",
+ "2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content lines1-735 read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.",
+ "All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not read in full. Official ChEBI16150 identity confirmed; no new taxon groundings."
+ ]
+ },
+ "limitations": [
+ "Fresh pre-source baseline across both roots:460 records,923 caches,56 existing warnings,zero structural defects. Review all21 original nodes/17arrows; retain21nodes/16directions,remove one misplaced reverse arrow,rename one outcome. No new topology or Edison spend.",
+ "Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data review.",
+ "Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed assays.",
+ "2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content lines1-735 read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.",
+ "All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not read in full. Official ChEBI16150 identity confirmed; no new taxon groundings.",
+ "Propionate: preserve real carrier-removal feedback, bound enzyme homology/abundance inference and carrier partitioning, distinguish gas pressure from aqueous concentration. Butyrate: preserve reported hydrogen inhibition but do not certify exact perturbation conditions,universal obligacy or an uncited pressure threshold.",
+ "Coordination: initial ratio perturbations are distinct from endpoint convergence; remove aggregation-described reverse arrow. Reciprocal attraction and unchanged aggregation under activity-changing disturbance are retained. Nanomaterial acceleration does not prove DIET.",
+ "Benzoate: acetate+CH4 is conversion,not complete mineralization; pure-culture fermentation disproves universal partner dependence. Other-partner enzyme assays are not imported. Gentianae: approximate growth energy and product effects are not competition or a fixed threshold across dense-suspension and added-partner treatments.",
+ "ES5: exact M.hungatei lag is significant in Table1; fitted rate/final concentration are not marked significant and Discussion reports similar butyrate slopes. Preserve stimulation without abstract-wide120%/150% exact-triculture attribution. All three members remain in outcome scope; measured proteomes are two partners. Aggregation/protein mediation remains hypothetical,not enzyme activation or DIET proof.",
+ "Ignored/hidden-inclusive local path index read,not all historical file bodies. Fresh all-state issue title/body dedup matched1392,1389,795,583,496,259;fullbodies and related529/183 read. PR comments not exhaustively searched. Broad metadata issues are followups,not addressed by graph scope.",
+ "Preserve453otherrecords,923caches,rawnon-graph blocks and prior history/decision artifacts. Participant census measured,not guessed;rules/share guard unchanged. No schema/validator/runtime change. MacOS full-record CLI is not Linux certification;reference-loader,DOI-case and rendering caveats remain.",
+ "Repair issues remain open until protected-main merge;metadata followups remain open afterward. Self-review is not independent approval or full-corpus completion. Denied/unanswered Edison scopes untouched;no artificial CI,protection bypass or premature branch deletion."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml b/reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
new file mode 100644
index 000000000..ff15a3fc3
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
@@ -0,0 +1,1532 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c38a8903f7fe36f9a870b1b872f179bb4a7a9ee4
+baseline_commit: c38a8903f7fe36f9a870b1b872f179bb4a7a9ee4
+base_tree: 297f197d737c41b78fbb8f2863ea1c8109ab5ad5
+pre_source_baseline_sha256: 1904cacf99f46e220f9baf67e72ba5847e9f13048d63691b56a79e1db8dd074c
+issues:
+- 1871
+- 1872
+- 1873
+- 1874
+- 1875
+- 1876
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1877
+- 1878
+source_access:
+ retrieval_manifest:
+ propionate_type:
+ pmid: '9828440'
+ doi: 10.1099/00207713-48-4-1383
+ pmcid: null
+ title: Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium.
+ metadata: /private/tmp/communitymech-batch112/propionate_type-metadata.json
+ metadata_sha256: cab9d3173fbed6461c1f12e8090d6b46000446b471bab63232d25c92df58ab74
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A9828440+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ abstract: /private/tmp/communitymech-batch112/propionate_type-abstract.txt
+ abstract_sha256: a597ecb753cd758bae058663ccc733af3dc6807d2915736524ec28b7e24a69ec
+ crossref: /private/tmp/communitymech-batch112/propionate_type-crossref.json
+ crossref_sha256: 3f6814a46b7b289d51ded632fd922dc118ee4697d28dc1bd5f3de0cd50c0e2a4
+ crossref_license: []
+ propionate_proteome:
+ pmid: '29611893'
+ doi: 10.1111/1462-2920.14119
+ pmcid: PMC5947623
+ title: Comparative proteome analysis of propionate degradation by Syntrophobacter fumaroxidans in pure culture
+ and in coculture with methanogens.
+ metadata: /private/tmp/communitymech-batch112/propionate_proteome-metadata.json
+ metadata_sha256: afb9c5a5f8f3a9aa95c4ec637b7e393b1fcf855fdcc1319235cd94ae7eeabbd5
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A29611893+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5947623/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch112/propionate_proteome-abstract.txt
+ abstract_sha256: ba6083879e90ed3bb17426ce85c2af0972a82fd86929b33728d1547921f6b6ea
+ xml: /private/tmp/communitymech-batch112/propionate_proteome-primary.xml
+ xml_sha256: e0568e38789fc1a7cc7caa7c4e8a8f0a032417c8c2d0e3deffb1f14ed49d6175
+ primary_text: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ primary_text_sha256: 9faf8e8d9d9586a11b232bd2945fb3345ef45b01ff3bed9ed91d4526d1d62bd3
+ license:
+ - "https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the\
+ \ http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium,\
+ \ provided the original work is properly cited, the use is non\u2010commercial and no modifications or adaptations\
+ \ are made."
+ crossref: /private/tmp/communitymech-batch112/propionate_proteome-crossref.json
+ crossref_sha256: 1ddc53159c78944b45ac0b2f09ac3cd652807bd62579f6c89d46b7b953a303a7
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2018
+ - 4
+ - 23
+ date-time: '2018-04-23T00:00:00Z'
+ timestamp: 1524441600000
+ content-version: vor
+ delay-in-days: 0
+ URL: http://creativecommons.org/licenses/by-nc-nd/4.0/
+ coordination:
+ pmid: '34603271'
+ doi: 10.3389/fmicb.2021.742531
+ pmcid: PMC8481629
+ title: Growth Coordination Between Butyrate-Oxidizing Syntrophs and Hydrogenotrophic Methanogens.
+ metadata: /private/tmp/communitymech-batch112/coordination-metadata.json
+ metadata_sha256: ec3e7aa81a78f3045e5b91c2a40ff76ef11d2be7e62ffb9fd0502e30207de606
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A34603271+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8481629/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch112/coordination-abstract.txt
+ abstract_sha256: 56ca36a1f980b9ef31c76988eec84f2dbeda5c790b833277bf61203c6c8a6a14
+ xml: /private/tmp/communitymech-batch112/coordination-primary.xml
+ xml_sha256: d58a2d20e1f69c96f0306cf43df85dd5601234f369df48cb8f8f777f46bdf882
+ primary_text: /private/tmp/communitymech-batch112/coordination-primary.txt
+ primary_text_sha256: 21764a2d4442da29e6ef25af70f3346875968f601f8672cd3c0ff750aecde179
+ license:
+ - This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC
+ BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s)
+ and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance
+ with accepted academic practice. No use, distribution or reproduction is permitted which does not comply
+ with these terms.
+ crossref: /private/tmp/communitymech-batch112/coordination-crossref.json
+ crossref_sha256: 536ce9645801429a3f52a8ddb601e4eb700465f356d9aa675ae5cb0abd593718
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2021
+ - 9
+ - 16
+ date-time: '2021-09-16T00:00:00Z'
+ timestamp: 1631750400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ butyrate_type:
+ pmid: '16345745'
+ doi: 10.1128/aem.41.4.1029-1039.1981
+ pmcid: PMC243852
+ title: Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium.
+ metadata: /private/tmp/communitymech-batch112/butyrate_type-metadata.json
+ metadata_sha256: f0af6651c2a70e9a65db7429d7194657585b3416a37284b9933567aea959202e
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A16345745+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC243852/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ abstract_sha256: 39783b07ec098f2a2841137de29b8e34b5b7f6d204b03cca87870d4c708ba215
+ crossref: /private/tmp/communitymech-batch112/butyrate_type-crossref.json
+ crossref_sha256: ea3222ebd08a67bbaf3b552aa07c211f04278debdf159fa52ffd424ffff8b362
+ crossref_license:
+ - start:
+ date-parts:
+ - - 1981
+ - 4
+ - 1
+ date-time: '1981-04-01T00:00:00Z'
+ timestamp: 354931200000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ gentianae:
+ pmid: '33657722'
+ doi: 10.1099/00221287-143-7-2345
+ pmcid: null
+ title: Energetics of methanogenic benzoate degradation by Syntrophus gentianae in syntrophic coculture.
+ metadata: /private/tmp/communitymech-batch112/gentianae-metadata.json
+ metadata_sha256: 538f86c04177446c1cb6e271be7913c3a1cf12c286f1c338f2ca01580850c60a
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A33657722+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ abstract: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ abstract_sha256: 0ab467c55e9e56a07821173d4c515c7c04ab233b7885ec8bb68a5fb348ca7de0
+ crossref: /private/tmp/communitymech-batch112/gentianae-crossref.json
+ crossref_sha256: 8fd751839bf7224814c8111833d86d46142d4db7a2632d539326ea32779fe784
+ crossref_license: []
+ trichococcus:
+ pmid: '35699440'
+ doi: 10.1128/aem.00391-22
+ pmcid: PMC9275234
+ title: Stimulating Effect of Trichococcus flocculiformis on a Coculture of Syntrophomonas wolfei
+ and Methanospirillum hungatei.
+ metadata: /private/tmp/communitymech-batch112/trichococcus-metadata.json
+ metadata_sha256: 1c9f2f9d8a5c2e36a1518a2b93f372af35a428edc1699339c9c1f940c8be857e
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A35699440+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9275234/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch112/trichococcus-abstract.txt
+ abstract_sha256: 5c865b7ee5821078b5caa976ec83e13cdfe2a65f66d89f41a7575eef711af1c2
+ xml: /private/tmp/communitymech-batch112/trichococcus-primary.xml
+ xml_sha256: 49cf054b4625037cd7bb1c720383bee0e54e648e002cfaeb8970c30e25247fd5
+ primary_text: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ primary_text_sha256: b83df45d8e650a147e2dbfb376309699450d8dcb737bb8f16579c8a1e8a5d409
+ license:
+ - https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of
+ the Creative Commons Attribution 4.0 International license.
+ crossref: /private/tmp/communitymech-batch112/trichococcus-crossref.json
+ crossref_sha256: af7781235f8437aca3078d261f783b4b70ba8da9d3c83bd26802b76f3f926479
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2022
+ - 7
+ - 12
+ date-time: '2022-07-12T00:00:00Z'
+ timestamp: 1657584000000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ - start:
+ date-parts:
+ - - 2022
+ - 7
+ - 12
+ date-time: '2022-07-12T00:00:00Z'
+ timestamp: 1657584000000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ benzoate_metabolism:
+ pmid: '11282627'
+ doi: 10.1128/aem.67.4.1728-1738.2001
+ pmcid: PMC92791
+ title: Metabolism of benzoate, cyclohex-1-ene carboxylate, and cyclohexane carboxylate by "Syntrophus aciditrophicus"
+ strain SB in syntrophic association with H(2)-using microorganisms.
+ metadata: /private/tmp/communitymech-batch112/benzoate_metabolism-metadata.json
+ metadata_sha256: 2fe35bf254c34ca658fa7dd3eb8d73af310ed9260063655ac823b0b366a67ab9
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1128%2Faem.67.4.1728-1738.2001%22+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC92791/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch112/benzoate_metabolism-abstract.txt
+ abstract_sha256: 4bc688bd72b650e8f219040516f634a50132f9ad59cde56706e48334f76711d3
+ crossref: /private/tmp/communitymech-batch112/benzoate_metabolism-crossref.json
+ crossref_sha256: dd6423b96277eaab59febc452d24072decbe1781149df80f4c9724fdddd2f608
+ crossref_license:
+ - start:
+ date-parts:
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+ - 4
+ - 1
+ date-time: '2001-04-01T00:00:00Z'
+ timestamp: 986083200000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ benzoate_pure:
+ pmid: '11722901'
+ doi: 10.1128/aem.67.12.5520-5525.2001
+ pmcid: PMC93338
+ title: Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in the absence of hydrogen-using
+ microorganisms.
+ metadata: /private/tmp/communitymech-batch112/benzoate_pure-metadata.json
+ metadata_sha256: 9b537d873eba32ffefdde5c1f39a563045b62b63da88fa096032a25efd0f0249
+ retrievals:
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+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC93338/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch112/benzoate_pure-abstract.txt
+ abstract_sha256: f021c43b5e508c68ddd9b29e7f1eac0f239e099856111152bc3ff8ffdfdeeebd
+ crossref: /private/tmp/communitymech-batch112/benzoate_pure-crossref.json
+ crossref_sha256: e1a69d821ff71d39ce1519415c40b21ee8a4029d550e833a9e4a290c4de9ef2a
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2001
+ - 12
+ - 1
+ date-time: '2001-12-01T00:00:00Z'
+ timestamp: 1007164800000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ nanomaterials:
+ pmid: '30111866'
+ doi: 10.1038/s41598-018-30745-7
+ pmcid: PMC6093938
+ title: Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and
+ a defined coculture.
+ metadata: /private/tmp/communitymech-batch112/nanomaterials-metadata.json
+ metadata_sha256: 04e31b769a23d945f9713a65435dc1f69b4fadf82b6ab2e4204fffa628caadf4
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1038%2Fs41598-018-30745-7%22+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 1
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6093938/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch112/nanomaterials-abstract.txt
+ abstract_sha256: aa2f576c63c95c5f44b99ea69b0c1897ceebf6eed946101880515869baae2552
+ xml: /private/tmp/communitymech-batch112/nanomaterials-primary.xml
+ xml_sha256: e405c23a2747de20c1b260a36c83e0be9b52640806ec7d7789069a1ab0c20a02
+ primary_text: /private/tmp/communitymech-batch112/nanomaterials-primary.txt
+ primary_text_sha256: c717378a0f3336093af13b22bb02c0ec55f1d5d30f56c885b3d54dde0469892a
+ license:
+ - "Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which\
+ \ permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you\
+ \ give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons\
+ \ license, and indicate if changes were made. The images or other third party material in this article are\
+ \ included in the article\u2019s Creative Commons license, unless indicated otherwise in a credit line to\
+ \ the material. If material is not included in the article\u2019s Creative Commons license and your intended\
+ \ use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission\
+ \ directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/."
+ crossref: /private/tmp/communitymech-batch112/nanomaterials-crossref.json
+ crossref_sha256: 9ef898555efae082d2b050d2d803e52b78018e17e0dcb331a1466ed40a8b355b
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2018
+ - 8
+ - 15
+ date-time: '2018-08-15T00:00:00Z'
+ timestamp: 1534291200000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ - start:
+ date-parts:
+ - - 2018
+ - 8
+ - 15
+ date-time: '2018-08-15T00:00:00Z'
+ timestamp: 1534291200000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0
+ formate_stress:
+ pmid: null
+ doi: 10.3390/w16243551
+ pmcid: null
+ title:
+ - 'Promoting or Inhibiting: New Insights into the Role of Formate in Syntrophic Propionate Metabolism'
+ metadata: /private/tmp/communitymech-batch112/formate_stress-metadata.json
+ metadata_sha256: 34c774db4c79d979376279cba0767c07ccbdd1146d64790e6446ae85c8183a5f
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.3390%2Fw16243551%22+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ records: 0
+ - url: https://www.mdpi.com/2073-4441/16/24/3551/xml
+ status: retrieval_failed
+ error: 'HTTP Error 403: Forbidden'
+ crossref: /private/tmp/communitymech-batch112/formate_stress-crossref.json
+ crossref_sha256: 9b85a4aba31b5abe2d4e19001262a0e4ebb370255332cffec868e09711184ae1
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2024
+ - 12
+ - 10
+ date-time: '2024-12-10T00:00:00Z'
+ timestamp: 1733788800000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ abstract: /private/tmp/communitymech-batch112/formate_stress-abstract.txt
+ abstract_sha256: c37b280c176346e64650bc0dcab43544183a3a87082b4139c35fdabc16fa0305
+ actual_read_scope:
+ - Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh
+ extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including
+ abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data
+ review.
+ - Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and
+ both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body
+ excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher
+ rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed
+ assays.
+ - 2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content
+ lines1-735 read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription
+ snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved
+ and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.
+ - All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately
+ from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not
+ read in full. Official ChEBI16150 identity confirmed; no new taxon groundings.
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+ /private/tmp/communitymech-batch112/butyrate_type-crossref.json: ea3222ebd08a67bbaf3b552aa07c211f04278debdf159fa52ffd424ffff8b362
+ /private/tmp/communitymech-batch112/butyrate_type-metadata.json: f0af6651c2a70e9a65db7429d7194657585b3416a37284b9933567aea959202e
+ /private/tmp/communitymech-batch112/coordination-abstract.txt: 56ca36a1f980b9ef31c76988eec84f2dbeda5c790b833277bf61203c6c8a6a14
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+reviewed_counts:
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+ retained_nodes: 21
+ removed_nodes: 0
+ retained_arrows: 16
+ removed_arrows: 1
+ renamed_nodes: 1
+ graph_quotations: 45
+ discussion_quotations: 8
+ new_discussions: 3
+ updated_discussions: 3
+primary_graph_snippet_count: 43
+snippet_checks:
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+ node: Propionate Oxidation and H2/Formate Production
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Propionate Oxidation and H2/Formate Production
+ evidence_index: 1
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Propionate Oxidation and H2/Formate Production
+ evidence_index: 2
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Propionate Oxidation and H2/Formate Production
+ evidence_index: 3
+ reference: doi:10.3390/w16243551
+ cache_matched: true
+ independent_primary_match: false
+ matched_artifact: references_cache/doi_10.3390_w16243551.md
+ cache_artifact: references_cache/doi_10.3390_w16243551.md
+ scope: Normalized contiguous match; entailment separately reviewed. Existing curator-supplied publisher text;
+ fresh retrieval unavailable.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Propionate Oxidation and H2/Formate Production
+ evidence_index: 4
+ reference: doi:10.3390/w16243551
+ cache_matched: true
+ independent_primary_match: false
+ matched_artifact: references_cache/doi_10.3390_w16243551.md
+ cache_artifact: references_cache/doi_10.3390_w16243551.md
+ scope: Normalized contiguous match; entailment separately reviewed. Existing curator-supplied publisher text;
+ fresh retrieval unavailable.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Interspecies Electron Transfer and Methanogenesis
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Interspecies Electron Transfer and Methanogenesis
+ evidence_index: 1
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Interspecies Electron Transfer and Methanogenesis
+ evidence_index: 2
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: Syntrophic Propionate-to-Methane Conversion
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
+ node: Propionate Oxidation and H2/Formate Production
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
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+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
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+ reference: PMID:29611893
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+ independent_primary_match: true
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+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
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+ node: Interspecies Electron Transfer and Methanogenesis
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
+ node: Interspecies Electron Transfer and Methanogenesis
+ evidence_index: 1
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
+ node: Interspecies Electron Transfer and Methanogenesis
+ evidence_index: 2
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
+ node: Syntrophic Propionate-to-Methane Conversion
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: Syntrophic Butyrate Oxidation and Methanogenesis
+ evidence_index: 0
+ reference: PMID:34603271
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/coordination-primary.txt
+ cache_artifact: references_cache/PMID_34603271.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: Syntrophic Butyrate Oxidation and Methanogenesis
+ evidence_index: 1
+ reference: PMID:34603271
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/coordination-primary.txt
+ cache_artifact: references_cache/PMID_34603271.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: Population Ratio Convergence During Growth
+ evidence_index: 0
+ reference: PMID:34603271
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/coordination-primary.txt
+ cache_artifact: references_cache/PMID_34603271.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: Syntrophic Aggregation and Cell-to-Cell Attraction
+ evidence_index: 0
+ reference: PMID:34603271
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/coordination-primary.txt
+ cache_artifact: references_cache/PMID_34603271.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: Syntrophic Aggregation and Cell-to-Cell Attraction
+ evidence_index: 1
+ reference: PMID:34603271
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/coordination-primary.txt
+ cache_artifact: references_cache/PMID_34603271.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: Butyrate Oxidation and H2 Production
+ evidence_index: 0
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: Butyrate Oxidation and H2 Production
+ evidence_index: 1
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: Interspecies Hydrogen Transfer and Methanogenesis
+ evidence_index: 0
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: Interspecies Hydrogen Transfer and Methanogenesis
+ evidence_index: 1
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: Syntrophic Butyrate-to-Methane Conversion
+ evidence_index: 0
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: Syntrophic Butyrate-to-Methane Conversion
+ evidence_index: 1
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Benzoate_Degrader
+ node: Syntrophus Benzoate Metabolism
+ evidence_index: 0
+ reference: doi:10.1128/aem.67.4.1728-1738.2001
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/benzoate_metabolism-abstract.txt
+ cache_artifact: references_cache/doi_10.1128_aem.67.4.1728-1738.2001.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Benzoate_Degrader
+ node: Syntrophus Benzoate Metabolism
+ evidence_index: 1
+ reference: doi:10.1128/aem.67.4.1728-1738.2001
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/benzoate_metabolism-abstract.txt
+ cache_artifact: references_cache/doi_10.1128_aem.67.4.1728-1738.2001.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Benzoate_Degrader
+ node: Interspecies Hydrogen Transfer and Methanogenesis
+ evidence_index: 0
+ reference: doi:10.1128/aem.67.12.5520-5525.2001
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/benzoate_pure-abstract.txt
+ cache_artifact: references_cache/doi_10.1128_aem.67.12.5520-5525.2001.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Benzoate_Degrader
+ node: Interspecies Hydrogen Transfer and Methanogenesis
+ evidence_index: 1
+ reference: doi:10.1128/aem.67.12.5520-5525.2001
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/benzoate_pure-abstract.txt
+ cache_artifact: references_cache/doi_10.1128_aem.67.12.5520-5525.2001.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Benzoate_Degrader
+ node: Community Benzoate Conversion to Acetate and Methane
+ evidence_index: 0
+ reference: doi:10.1128/aem.67.12.5520-5525.2001
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/benzoate_pure-abstract.txt
+ cache_artifact: references_cache/doi_10.1128_aem.67.12.5520-5525.2001.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Benzoate_Degrader
+ node: Community Benzoate Conversion to Acetate and Methane
+ evidence_index: 1
+ reference: doi:10.1128/aem.67.12.5520-5525.2001
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/benzoate_pure-abstract.txt
+ cache_artifact: references_cache/doi_10.1128_aem.67.12.5520-5525.2001.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Methanogenic Benzoate Degradation
+ evidence_index: 0
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Methanogenic Benzoate Degradation
+ evidence_index: 1
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Minimum Energy Threshold for Syntrophic Growth
+ evidence_index: 0
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Minimum Energy Threshold for Syntrophic Growth
+ evidence_index: 1
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Product Inhibition of Benzoate Degradation
+ evidence_index: 0
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Product Inhibition of Benzoate Degradation
+ evidence_index: 1
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: Product Inhibition of Benzoate Degradation
+ evidence_index: 2
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+ node: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ evidence_index: 0
+ reference: PMID:35699440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ cache_artifact: references_cache/PMID_35699440.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+ node: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ evidence_index: 1
+ reference: PMID:35699440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ cache_artifact: references_cache/PMID_35699440.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+ node: Aggregation With Syntrophic Partners
+ evidence_index: 0
+ reference: PMID:35699440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ cache_artifact: references_cache/PMID_35699440.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+ node: Proteome Response in the Syntrophic Partners
+ evidence_index: 0
+ reference: PMID:35699440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ cache_artifact: references_cache/PMID_35699440.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+ node: Proteome Response in the Syntrophic Partners
+ evidence_index: 1
+ reference: PMID:35699440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ cache_artifact: references_cache/PMID_35699440.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+discussion_snippet_checks:
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: kg-syntrophobacter-methanobacterium-partner-attribution
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanobacterium_Syntrophy
+ node: kg-syntrophobacter-methanobacterium-partner-attribution
+ evidence_index: 1
+ reference: doi:10.1099/00207713-48-4-1383
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_type-abstract.txt
+ cache_artifact: references_cache/doi_10.1099_00207713-48-4-1383.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophobacter_Methanospirillum_Syntrophy
+ node: propionate-carrier-partition-and-enzyme-roles
+ evidence_index: 0
+ reference: PMID:29611893
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/propionate_proteome-primary.txt
+ cache_artifact: references_cache/PMID_29611893.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: kg-aggregation-and-diet-unverified
+ evidence_index: 0
+ reference: PMID:34603271
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/coordination-primary.txt
+ cache_artifact: references_cache/PMID_34603271.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture
+ node: kg-aggregation-and-diet-unverified
+ evidence_index: 1
+ reference: doi:10.1038/s41598-018-30745-7
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/nanomaterials-primary.txt
+ cache_artifact: references_cache/doi_10.1038_s41598-018-30745-7.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophomonas_Methanospirillum_Syntrophy
+ node: butyrate-hydrogen-feedback-assay-limits
+ evidence_index: 0
+ reference: PMID:16345745
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/butyrate_type-abstract.txt
+ cache_artifact: references_cache/PMID_16345745.txt
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture
+ node: gentianae-energy-context
+ evidence_index: 0
+ reference: PMID:33657722
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/gentianae-abstract.txt
+ cache_artifact: references_cache/PMID_33657722.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+- record: Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture
+ node: kg-es5-mediation-mechanism-unresolved
+ evidence_index: 0
+ reference: PMID:35699440
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch112/trichococcus-primary.txt
+ cache_artifact: references_cache/PMID_35699440.md
+ scope: Normalized contiguous match; entailment separately reviewed. Fresh primary artifact.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing evidence/scope repairs and removal of one unsupported reverse direction;no new nodes/directions.
+limitations:
+- Fresh pre-source baseline across both roots:460 records,923 caches,56 existing warnings,zero structural defects.
+ Review all21 original nodes/17arrows; retain21nodes/16directions,remove one misplaced reverse arrow,rename one
+ outcome. No new topology or Edison spend.
+- Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh
+ extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including
+ abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data
+ review.
+- Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and
+ both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body
+ excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher
+ rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed
+ assays.
+- 2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content lines1-735
+ read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription
+ snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved
+ and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.
+- All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately
+ from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not
+ read in full. Official ChEBI16150 identity confirmed; no new taxon groundings.
+- 'Propionate: preserve real carrier-removal feedback, bound enzyme homology/abundance inference and carrier partitioning,
+ distinguish gas pressure from aqueous concentration. Butyrate: preserve reported hydrogen inhibition but do not
+ certify exact perturbation conditions,universal obligacy or an uncited pressure threshold.'
+- 'Coordination: initial ratio perturbations are distinct from endpoint convergence; remove aggregation-described
+ reverse arrow. Reciprocal attraction and unchanged aggregation under activity-changing disturbance are retained.
+ Nanomaterial acceleration does not prove DIET.'
+- 'Benzoate: acetate+CH4 is conversion,not complete mineralization; pure-culture fermentation disproves universal
+ partner dependence. Other-partner enzyme assays are not imported. Gentianae: approximate growth energy and product
+ effects are not competition or a fixed threshold across dense-suspension and added-partner treatments.'
+- 'ES5: exact M.hungatei lag is significant in Table1; fitted rate/final concentration are not marked significant
+ and Discussion reports similar butyrate slopes. Preserve stimulation without abstract-wide120%/150% exact-triculture
+ attribution. All three members remain in outcome scope; measured proteomes are two partners. Aggregation/protein
+ mediation remains hypothetical,not enzyme activation or DIET proof.'
+- Ignored/hidden-inclusive local path index read,not all historical file bodies. Fresh all-state issue title/body
+ dedup matched1392,1389,795,583,496,259;fullbodies and related529/183 read. PR comments not exhaustively searched.
+ Broad metadata issues are followups,not addressed by graph scope.
+- Preserve453otherrecords,923caches,rawnon-graph blocks and prior history/decision artifacts. Participant census
+ measured,not guessed;rules/share guard unchanged. No schema/validator/runtime change. MacOS full-record CLI is
+ not Linux certification;reference-loader,DOI-case and rendering caveats remain.
+- Repair issues remain open until protected-main merge;metadata followups remain open afterward. Self-review is
+ not independent approval or full-corpus completion. Denied/unanswered Edison scopes untouched;no artificial CI,protection
+ bypass or premature branch deletion.
+- 'Post-write validation correction: a new benzoate quote triggered bracket-stripping622. Replace it with a shorter
+ contiguous excerpt and keep the compound-or-CoA qualification in explanation;append a second history for that
+ record. The initial ledger,failed output and pre-correction mutation proof are preserved. Eight histories total;one
+ unchanged coordination metadata622 failure remains explicitly excepted.'
+records:
+- path: kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml
+ id: CommunityMech:000068
+ original_sha256: 3df7349bdb43ddf039c4b800ef95b42d13219895335525c4e74d8efca7edee4c
+ record_sha256: eb0ed26cadc17f4a7fbf63d8d2c11da1d891cd2edf5ce82b938e19c2d0cf469b
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback
+ with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange
+ typing.
+ node_decisions:
+ - node: Propionate Oxidation and H2/Formate Production
+ rationale: Bound propionate oxidation and enzyme inference to exact partner and assay.
+ - node: Interspecies Electron Transfer and Methanogenesis
+ rationale: Retain carrier-removal feedback with physical units and flux uncertainty explicit.
+ - node: Syntrophic Propionate-to-Methane Conversion
+ rationale: Retain coupled community conversion without duplicate exchange typing.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id001
+ source: Propionate Oxidation and H2/Formate Production
+ target: Interspecies Electron Transfer and Methanogenesis
+ description: H2 and formate produced by S. fumaroxidans are consumed by M. formicicum for methanogenesis
+ - &id003
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Propionate Oxidation and H2/Formate Production
+ description: H2/formate scavenging by M. formicicum keeps both carriers at low partial pressure, which is what
+ makes the thermodynamically unfavourable propionate oxidation by S. fumaroxidans feasible. S. fumaroxidans
+ oxidizes propionate either in syntrophy with an H2/formate-utilizing methanogen or, axenically, only with
+ an external electron acceptor (sulfate or fumarate). Reciprocal arm of the syntrophic loop; DIRECTLY IMPLIED
+ by the axenic-vs-syntrophic contrast rather than demonstrated by a partner-removal or carrier-inhibition perturbation
+ in this exact pair.
+ - &id005
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Syntrophic Propionate-to-Methane Conversion
+ description: 'Reciprocal formate and H2 exchange links S. fumaroxidans propionate oxidation to M. formicicum
+ hydrogenotrophic methanogenesis.
+
+ '
+ edges_after:
+ - &id002
+ source: Propionate Oxidation and H2/Formate Production
+ target: Interspecies Electron Transfer and Methanogenesis
+ description: 'DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M.
+ formicicum through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate
+ fluxes in this pair.'
+ - &id004
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Propionate Oxidation and H2/Formate Production
+ description: 'DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. formicicum lowers hydrogen partial
+ pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic
+ cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective
+ carrier-removal assay in this exact pair.'
+ - &id006
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Syntrophic Propionate-to-Methane Conversion
+ description: Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation
+ to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen,
+ not bidirectional donation.
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M.
+ formicicum through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate
+ fluxes in this pair.'
+ - before: *id003
+ after: *id004
+ rationale: 'DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. formicicum lowers hydrogen partial
+ pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic
+ cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective
+ carrier-removal assay in this exact pair.'
+ - before: *id005
+ after: *id006
+ rationale: Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation
+ to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen,
+ not bidirectional donation.
+ removed_edge_decisions: []
+ references:
+ - PMID:29611893
+ - doi:10.3390/w16243551
+ issues:
+ - 1871
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Syntrophobacter_Methanobacterium_Syntrophy/2026-10-08T071057Z-codex-d473fc.yaml
+- path: kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml
+ id: CommunityMech:000069
+ original_sha256: 5662e6e60817338c51780fe418ed1b9b2e429c2d162223d613acb3cbad159ce4
+ record_sha256: a4076f47b588559b0a751b8d4e0be16c067af11c359ba5e9f401fd0b542fb61a
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Bound propionate oxidation and enzyme inference to exact partner and assay.; Retain carrier-removal feedback
+ with physical units and flux uncertainty explicit.; Retain coupled community conversion without duplicate exchange
+ typing.
+ node_decisions:
+ - node: Propionate Oxidation and H2/Formate Production
+ rationale: Bound propionate oxidation and enzyme inference to exact partner and assay.
+ - node: Interspecies Electron Transfer and Methanogenesis
+ rationale: Retain carrier-removal feedback with physical units and flux uncertainty explicit.
+ - node: Syntrophic Propionate-to-Methane Conversion
+ rationale: Retain coupled community conversion without duplicate exchange typing.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id007
+ source: Propionate Oxidation and H2/Formate Production
+ target: Interspecies Electron Transfer and Methanogenesis
+ description: H2 and formate produced by S. fumaroxidans are consumed by M. hungatei for methanogenesis
+ - &id009
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Propionate Oxidation and H2/Formate Production
+ description: "H2/formate scavenging by M. hungatei keeps the partial pressures of both carriers low enough for\
+ \ propionate oxidation to remain thermodynamically feasible. S. fumaroxidans oxidizes propionate either syntrophically\
+ \ with an H2/formate-utilizing partner or, in pure culture, only when supplied with an external electron acceptor\
+ \ (sulfate or fumarate) \u2014 establishing the partner-dependence that this feedback edge encodes. Reciprocal\
+ \ arm of the syntrophic loop."
+ - &id011
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Syntrophic Propionate-to-Methane Conversion
+ description: 'Reciprocal formate and H2 exchange links S. fumaroxidans propionate oxidation to M. hungatei hydrogenotrophic
+ methanogenesis.
+
+ '
+ edges_after:
+ - &id008
+ source: Propionate Oxidation and H2/Formate Production
+ target: Interspecies Electron Transfer and Methanogenesis
+ description: 'DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M.
+ hungatei through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate
+ fluxes in this pair.'
+ - &id010
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Propionate Oxidation and H2/Formate Production
+ description: 'DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. hungatei lowers hydrogen partial
+ pressure and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic
+ cooperation inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective
+ carrier-removal assay in this exact pair.'
+ - &id012
+ source: Interspecies Electron Transfer and Methanogenesis
+ target: Syntrophic Propionate-to-Methane Conversion
+ description: Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation
+ to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen,
+ not bidirectional donation.
+ retained_edge_decisions:
+ - before: *id007
+ after: *id008
+ rationale: 'DIRECTLY IMPLIED: reducing equivalents released during bacterial propionate oxidation supply M.
+ hungatei through hydrogen and/or formate for methanogenesis. The evidence does not quantify their separate
+ fluxes in this pair.'
+ - before: *id009
+ after: *id010
+ rationale: 'DIRECTLY IMPLIED feedback: hydrogen/formate consumption by M. hungatei lowers hydrogen partial pressure
+ and formate concentration, enabling continued propionate oxidation. This retains the thermodynamic cooperation
+ inferred from syntrophic versus electron-acceptor-supported axenic growth; it is not a selective carrier-removal
+ assay in this exact pair.'
+ - before: *id011
+ after: *id012
+ rationale: Methanogenic consumption of bacterially supplied reducing equivalents couples propionate oxidation
+ to methane production. Cooperation is reciprocal, but the carrier transfer described here is bacterial-to-methanogen,
+ not bidirectional donation.
+ removed_edge_decisions: []
+ references:
+ - PMID:29611893
+ issues:
+ - 1871
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Syntrophobacter_Methanospirillum_Syntrophy/2026-10-08T071057Z-codex-fb396b.yaml
+- path: kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml
+ id: CommunityMech:000189
+ original_sha256: c3fb5e96ebf42ad0b8613a72c59bde357474e5303f0d9f0da4d240dd4df1b7f0
+ record_sha256: 3aaf56515d25364c8ee56e24071798ff6e3893ccce89761fadd331a109719531
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Retain substrate-bounded syntrophic growth and qualify the existing growth-to-ratio inference.; Retain
+ population convergence as an outcome and remove misplaced reverse causality.; Retain reciprocal attraction and
+ aggregation without one-way colonization or proven metabolic mediation.
+ node_decisions:
+ - node: Syntrophic Butyrate Oxidation and Methanogenesis
+ rationale: Retain substrate-bounded syntrophic growth and qualify the existing growth-to-ratio inference.
+ - node: Population Ratio Convergence During Growth
+ rationale: Retain population convergence as an outcome and remove misplaced reverse causality.
+ - node: Syntrophic Aggregation and Cell-to-Cell Attraction
+ rationale: Retain reciprocal attraction and aggregation without one-way colonization or proven metabolic mediation.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id013
+ source: Syntrophic Butyrate Oxidation and Methanogenesis
+ target: Population Ratio Convergence During Growth
+ description: "The thermodynamically required syntrophic coupling of butyrate oxidation to hydrogenotrophic methanogenesis\
+ \ drives coordinated partner growth \u2014 cultures inoculated at different initial cell ratios converge to\
+ \ a relatively constant Syntrophomonas:Methanococcus ratio over time.\n"
+ - &id015
+ source: Population Ratio Convergence During Growth
+ target: Syntrophic Butyrate Oxidation and Methanogenesis
+ description: 'Cell aggregation and attraction keep butyrate-oxidizing and hydrogenotrophic partners close enough
+ for efficient H2 transfer during syntrophic methanogenesis.
+
+ '
+ edges_after:
+ - &id014
+ source: Syntrophic Butyrate Oxidation and Methanogenesis
+ target: Population Ratio Convergence During Growth
+ description: 'DIRECTLY IMPLIED/PARTIAL: syntrophic metabolism supports growth of both partners during the observed
+ convergence of their population ratio. Different starting ratios alter relative growth and lag, but the study
+ does not isolate a molecular feedback controller that enforces the endpoint ratio.'
+ retained_edge_decisions:
+ - before: *id013
+ after: *id014
+ rationale: 'DIRECTLY IMPLIED/PARTIAL: syntrophic metabolism supports growth of both partners during the observed
+ convergence of their population ratio. Different starting ratios alter relative growth and lag, but the study
+ does not isolate a molecular feedback controller that enforces the endpoint ratio.'
+ removed_edge_decisions:
+ - before: *id015
+ rationale: The population-ratio source had an aggregation description; the converged ratio is not an independently
+ demonstrated reverse cause of metabolism.
+ references:
+ - PMID:34603271
+ issues:
+ - 1872
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture/2026-10-08T071057Z-codex-28253a.yaml
+- path: kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml
+ id: CommunityMech:000070
+ original_sha256: b79266189242f379e112d92cbc9e64545ab445367ef38935f5a23f9a12347f3f
+ record_sha256: 2ba0dc0aafd78379eee56f47b0e5ef235d8ea5e52abaa5f51417f07412b5535d
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Retain butyrate oxidation with substrate-bounded dependence.; Retain hydrogen feedback without an uncited
+ pressure threshold or duplicate evidence.; Retain the conversion endpoint without an additional exchange claim.
+ node_decisions:
+ - node: Butyrate Oxidation and H2 Production
+ rationale: Retain butyrate oxidation with substrate-bounded dependence.
+ - node: Interspecies Hydrogen Transfer and Methanogenesis
+ rationale: Retain hydrogen feedback without an uncited pressure threshold or duplicate evidence.
+ - node: Syntrophic Butyrate-to-Methane Conversion
+ rationale: Retain the conversion endpoint without an additional exchange claim.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id016
+ source: Butyrate Oxidation and H2 Production
+ target: Interspecies Hydrogen Transfer and Methanogenesis
+ description: H2 produced by S. wolfei is consumed by M. hungatei for methanogenesis
+ - &id018
+ source: Interspecies Hydrogen Transfer and Methanogenesis
+ target: Butyrate Oxidation and H2 Production
+ description: "H2 scavenging by M. hungatei keeps the H2 partial pressure low enough for butyrate \u03B2-oxidation\
+ \ to remain thermodynamically feasible; S. wolfei grows and degrades butyrate only in association with an\
+ \ H2-using partner, and adding H2 back to the medium stops both. Reciprocal (feedback) arm of the syntrophic\
+ \ loop."
+ - &id020
+ source: Interspecies Hydrogen Transfer and Methanogenesis
+ target: Syntrophic Butyrate-to-Methane Conversion
+ description: 'Hydrogen transfer links S. wolfei butyrate oxidation to M. hungatei hydrogenotrophic methanogenesis.
+
+ '
+ edges_after:
+ - &id017
+ source: Butyrate Oxidation and H2 Production
+ target: Interspecies Hydrogen Transfer and Methanogenesis
+ description: H2 produced by S. wolfei is consumed by M. hungatei for methanogenesis
+ - &id019
+ source: Interspecies Hydrogen Transfer and Methanogenesis
+ target: Butyrate Oxidation and H2 Production
+ description: 'DIRECTLY IMPLIED feedback: removal of hydrogen by the methanogenic partner relieves a constraint
+ on S. wolfei butyrate oxidation. The 1981 abstract reports that added hydrogen stops growth and butyrate degradation;
+ it does not specify a numerical permissive threshold or isolate hydrogen from all alternative carrier routes
+ in this exact pairing.'
+ - &id021
+ source: Interspecies Hydrogen Transfer and Methanogenesis
+ target: Syntrophic Butyrate-to-Methane Conversion
+ description: 'Hydrogen transfer links S. wolfei butyrate oxidation to M. hungatei hydrogenotrophic methanogenesis.
+
+ '
+ retained_edge_decisions:
+ - before: *id016
+ after: *id017
+ rationale: H2 produced by S. wolfei is consumed by M. hungatei for methanogenesis
+ - before: *id018
+ after: *id019
+ rationale: 'DIRECTLY IMPLIED feedback: removal of hydrogen by the methanogenic partner relieves a constraint
+ on S. wolfei butyrate oxidation. The 1981 abstract reports that added hydrogen stops growth and butyrate degradation;
+ it does not specify a numerical permissive threshold or isolate hydrogen from all alternative carrier routes
+ in this exact pairing.'
+ - before: *id020
+ after: *id021
+ rationale: 'Hydrogen transfer links S. wolfei butyrate oxidation to M. hungatei hydrogenotrophic methanogenesis.
+
+ '
+ removed_edge_decisions: []
+ references:
+ - PMID:16345745
+ issues:
+ - 1873
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Syntrophomonas_Methanospirillum_Syntrophy/2026-10-08T071058Z-codex-a2e51d.yaml
+- path: kb/communities/Syntrophus_Benzoate_Degrader.yaml
+ id: CommunityMech:000071
+ original_sha256: 87238e00764869ec141b9af0a4304ad6ca958a637116b9de5c328ffccdef7419
+ record_sha256: dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Retain coculture benzoate metabolism without importing other-partner enzyme assays.; Bound hydrogen-user
+ dependence to the syntrophic product route.; Rename mineralization as conversion and correct graph benzoate
+ grounding.
+ node_decisions:
+ - node: Syntrophus Benzoate Metabolism
+ rationale: Retain coculture benzoate metabolism without importing other-partner enzyme assays.
+ - node: Interspecies Hydrogen Transfer and Methanogenesis
+ rationale: Bound hydrogen-user dependence to the syntrophic product route.
+ - node: Community Benzoate Conversion to Acetate and Methane
+ rationale: Rename mineralization as conversion and correct graph benzoate grounding.
+ removed_node_decisions: []
+ renamed_nodes:
+ Community Benzoate Mineralization to Acetate and Methane: Community Benzoate Conversion to Acetate and Methane
+ edges_before:
+ - &id022
+ source: Syntrophus Benzoate Metabolism
+ target: Community Benzoate Mineralization to Acetate and Methane
+ description: S. aciditrophicus benzoate metabolism supplies reduced products to the methanogenic partner and
+ enables methane-producing benzoate mineralization by the coculture.
+ - &id024
+ source: Interspecies Hydrogen Transfer and Methanogenesis
+ target: Community Benzoate Mineralization to Acetate and Methane
+ description: Methanogenic hydrogen removal closes the syntrophic electron sink that lets benzoate oxidation
+ continue to methane production.
+ edges_after:
+ - &id023
+ source: Syntrophus Benzoate Metabolism
+ target: Community Benzoate Conversion to Acetate and Methane
+ description: Bacterial benzoate metabolism supplies reducing equivalents for the methanogenic partner and generates
+ acetate, enabling the coupled coculture conversion rather than complete carbon mineralization.
+ - &id025
+ source: Interspecies Hydrogen Transfer and Methanogenesis
+ target: Community Benzoate Conversion to Acetate and Methane
+ description: Methanogenic hydrogen consumption supplies the electron sink that couples benzoate oxidation to
+ methane production and the coculture product balance; a different benzoate fermentation remains possible without
+ this partner.
+ retained_edge_decisions:
+ - before: *id022
+ after: *id023
+ rationale: Bacterial benzoate metabolism supplies reducing equivalents for the methanogenic partner and generates
+ acetate, enabling the coupled coculture conversion rather than complete carbon mineralization.
+ - before: *id024
+ after: *id025
+ rationale: Methanogenic hydrogen consumption supplies the electron sink that couples benzoate oxidation to methane
+ production and the coculture product balance; a different benzoate fermentation remains possible without this
+ partner.
+ removed_edge_decisions: []
+ references:
+ - doi:10.1128/aem.67.12.5520-5525.2001
+ - doi:10.1128/aem.67.4.1728-1738.2001
+ issues:
+ - 1874
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/Syntrophus_Benzoate_Degrader/2026-10-08T071058Z-codex-9e1dfe.yaml
+ - history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml
+ post_write_corrections:
+ - record: kb/communities/Syntrophus_Benzoate_Degrader.yaml
+ before_sha256: a180d59ad1506be63b7ec5b59da57843c3a294c536186e0566184961ea9f0eb2
+ after_sha256: dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1
+ old_evidence:
+ reference: doi:10.1128/aem.67.4.1728-1738.2001
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate (or their coenzyme A
+ [CoA] derivatives) transiently accumulated during growth with benzoate.
+ explanation: The metabolite observations support the pathway context without assigning all biochemical assays
+ to the methanogenic pair.
+ new_evidence:
+ reference: doi:10.1128/aem.67.4.1728-1738.2001
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate
+ explanation: 'The primary passage identifies these transient intermediates or their coenzyme A derivatives;
+ it does not assign every enzyme assay to this methanogenic pair. The contiguous excerpt avoids the known
+ bracket-stripping validator bug #622 without silently changing quoted text.'
+ initial_ledger: /private/tmp/communitymech-batch112/decisions-before-bracket-correction.yaml
+ initial_ledger_sha256: d50b8d58a9243534789f09abdc031e7cabb088eb2407aad69818a665e41a78a7
+ history: history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml
+ failed_log: /private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-references.log
+ failed_log_sha256: 64cf5a382de6a9850be12bee78b9b4b3f214b1b55a64fc36620535ae612e9d3d
+- path: kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml
+ id: CommunityMech:000187
+ original_sha256: 7831b25c3302b70bb626b327f9f488390e67cd468f6e62c0ec7796e5fef8eaff
+ record_sha256: 3584798fce68b6699f57471b38d2a5e7778e154ff5dbbbb63c3f98f92a2f3451
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Retain exact-pair benzoate conversion and correct benzoate grounding.; Assign inferred energy availability
+ to the fermenter without a spurious recipient.; Retain product inhibition without competition typing or treatment-system
+ conflation.
+ node_decisions:
+ - node: Methanogenic Benzoate Degradation
+ rationale: Retain exact-pair benzoate conversion and correct benzoate grounding.
+ - node: Minimum Energy Threshold for Syntrophic Growth
+ rationale: Assign inferred energy availability to the fermenter without a spurious recipient.
+ - node: Product Inhibition of Benzoate Degradation
+ rationale: Retain product inhibition without competition typing or treatment-system conflation.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id026
+ source: Minimum Energy Threshold for Syntrophic Growth
+ target: Methanogenic Benzoate Degradation
+ description: Accumulated acetate and hydrogen thermodynamically inhibit the syntrophic reaction, lowering benzoate-degradation
+ rates when products build up.
+ - &id028
+ source: Product Inhibition of Benzoate Degradation
+ target: Minimum Energy Threshold for Syntrophic Growth
+ description: Hydrogen and acetate product accumulation constrain the free energy remaining to the benzoate-fermenting
+ Syntrophus partner.
+ edges_after:
+ - &id027
+ source: Minimum Energy Threshold for Syntrophic Growth
+ target: Methanogenic Benzoate Degradation
+ description: 'DIRECTLY IMPLIED: the fermenter must conserve sufficient energy to sustain growth-associated benzoate
+ conversion. The observed endpoint correlates with residual substrate and calculated free energy; the inferred
+ approximate growth threshold is not an independently manipulated universal constant.'
+ - &id029
+ source: Product Inhibition of Benzoate Degradation
+ target: Minimum Energy Threshold for Syntrophic Growth
+ description: Product accumulation changes the free energy available to the fermenter, bringing growth-associated
+ benzoate conversion toward its energetic limit. Acetate also partly uncouples substrate degradation from energy
+ conservation, so this does not assert that product addition changes a fixed intrinsic threshold.
+ retained_edge_decisions:
+ - before: *id026
+ after: *id027
+ rationale: 'DIRECTLY IMPLIED: the fermenter must conserve sufficient energy to sustain growth-associated benzoate
+ conversion. The observed endpoint correlates with residual substrate and calculated free energy; the inferred
+ approximate growth threshold is not an independently manipulated universal constant.'
+ - before: *id028
+ after: *id029
+ rationale: Product accumulation changes the free energy available to the fermenter, bringing growth-associated
+ benzoate conversion toward its energetic limit. Acetate also partly uncouples substrate degradation from energy
+ conservation, so this does not assert that product addition changes a fixed intrinsic threshold.
+ removed_edge_decisions: []
+ references:
+ - PMID:33657722
+ issues:
+ - 1875
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture/2026-10-08T071058Z-codex-4e26a3.yaml
+- path: kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml
+ id: CommunityMech:000188
+ original_sha256: 6588808db1c3e6319ff3742ebd653264e482f7ccf4c3aaff5ab61c2d7c969874
+ record_sha256: 19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml
+ scope: Whole record and every existing node/direction; source-bounded graph review, not whole-record certification.
+ summary: Bound stimulation to exact-pair lag and statistical comparisons at community scope.; Retain three-member
+ spatial association without directed colonization or DIET proof.; Retain differential proteomics without enzyme-activation
+ or signaling-causality overstatement.
+ node_decisions:
+ - node: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ rationale: Bound stimulation to exact-pair lag and statistical comparisons at community scope.
+ - node: Aggregation With Syntrophic Partners
+ rationale: Retain three-member spatial association without directed colonization or DIET proof.
+ - node: Proteome Response in the Syntrophic Partners
+ rationale: Retain differential proteomics without enzyme-activation or signaling-causality overstatement.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id030
+ source: Aggregation With Syntrophic Partners
+ target: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ description: "HYPOTHESIZED \u2014 ES5 co-aggregation with S. wolfei and M. hungatei may spatially facilitate\
+ \ the improved butyrate oxidation and methane production, but the aggregation is an observed correlate of\
+ \ the ES5 effect and was NOT demonstrated to causally mediate the rate increases.\n"
+ - &id032
+ source: Proteome Response in the Syntrophic Partners
+ target: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ description: "HYPOTHESIZED \u2014 the ES5-associated proteomic changes (activation of additional butyryl-CoA\
+ \ dehydrogenase and electron-transfer flavoprotein in S. wolfei; signal-transducing systems in M. hungatei)\
+ \ may underlie the improved butyrate oxidation, but the proteome response is correlative and was NOT shown\
+ \ to be the causal mediator of the improved performance.\n"
+ edges_after:
+ - &id031
+ source: Aggregation With Syntrophic Partners
+ target: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ description: 'HYPOTHESIZED/PARTIAL: ES5-associated aggregation could contribute to the shorter conversion lag,
+ but morphology was not selectively manipulated to show mediation. Conductive bridging and DIET remain proposed
+ explanations, not demonstrated routes.'
+ - &id033
+ source: Proteome Response in the Syntrophic Partners
+ target: Fermenter-Stimulated Butyrate Oxidation and Methane Production
+ description: 'HYPOTHESIZED/PARTIAL: changes in partner protein abundance may contribute to the shorter lag associated
+ with ES5 addition. The comparison does not selectively establish enzymatic or signaling mediation, and protein
+ abundance is not a direct activity assay.'
+ retained_edge_decisions:
+ - before: *id030
+ after: *id031
+ rationale: 'HYPOTHESIZED/PARTIAL: ES5-associated aggregation could contribute to the shorter conversion lag,
+ but morphology was not selectively manipulated to show mediation. Conductive bridging and DIET remain proposed
+ explanations, not demonstrated routes.'
+ - before: *id032
+ after: *id033
+ rationale: 'HYPOTHESIZED/PARTIAL: changes in partner protein abundance may contribute to the shorter lag associated
+ with ES5 addition. The comparison does not selectively establish enzymatic or signaling mediation, and protein
+ abundance is not a direct activity assay.'
+ removed_edge_decisions: []
+ references:
+ - PMID:35699440
+ issues:
+ - 1876
+ - 1877
+ - 1878
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture/2026-10-08T071059Z-codex-12f831.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 1f8760275..f4989d1a9 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -408,12 +408,12 @@ kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml
kb/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml CommunityMech:000363 262578e4cc60f82a1134df47dfeea7300751a28479c7296232653fdf4355a972 2 1 80.0 reports/causal_graph_review/decisions/20261008-three-records-batch111.yaml reviewed
kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml CommunityMech:000149 2a795399a012c7aa4460ea337faa97665269f40c7c13e95002d8224693b425d3 3 2 96.7 reports/causal_graph_review/decisions/20261008-three-records-batch111.yaml reviewed
kb/communities/Synthetic_Periphyton_Freshwater_Biofilm.yaml CommunityMech:000130 f270c0f22655b5e8b0cb533b40353e4a549ab4eaf891e1cc14630ad4abd4a4e2 5 0 67.0 reports/causal_graph_review/decisions/20261008-three-records-batch111.yaml reviewed
-kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml CommunityMech:000068 3df7349bdb43ddf039c4b800ef95b42d13219895335525c4e74d8efca7edee4c 3 3 100.0 pending
-kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml CommunityMech:000069 5662e6e60817338c51780fe418ed1b9b2e429c2d162223d613acb3cbad159ce4 3 3 100.0 pending
-kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml CommunityMech:000189 c3fb5e96ebf42ad0b8613a72c59bde357474e5303f0d9f0da4d240dd4df1b7f0 3 2 100.0 pending
-kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml CommunityMech:000070 b79266189242f379e112d92cbc9e64545ab445367ef38935f5a23f9a12347f3f 3 3 100.0 pending
-kb/communities/Syntrophus_Benzoate_Degrader.yaml CommunityMech:000071 87238e00764869ec141b9af0a4304ad6ca958a637116b9de5c328ffccdef7419 3 2 100.0 pending
-kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml CommunityMech:000187 7831b25c3302b70bb626b327f9f488390e67cd468f6e62c0ec7796e5fef8eaff 3 2 100.0 pending
+kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml CommunityMech:000068 eb0ed26cadc17f4a7fbf63d8d2c11da1d891cd2edf5ce82b938e19c2d0cf469b 3 3 96.7 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
+kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml CommunityMech:000069 a4076f47b588559b0a751b8d4e0be16c067af11c359ba5e9f401fd0b542fb61a 3 3 96.7 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
+kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml CommunityMech:000189 3aaf56515d25364c8ee56e24071798ff6e3893ccce89761fadd331a109719531 3 1 83.3 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
+kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml CommunityMech:000070 2ba0dc0aafd78379eee56f47b0e5ef235d8ea5e52abaa5f51417f07412b5535d 3 3 96.7 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
+kb/communities/Syntrophus_Benzoate_Degrader.yaml CommunityMech:000071 dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1 3 2 96.7 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
+kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml CommunityMech:000187 3584798fce68b6699f57471b38d2a5e7778e154ff5dbbbb63c3f98f92a2f3451 3 2 93.3 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml CommunityMech:000437 0d96313dbd7866dd7d642e83eab9956ff03a6c7f6a867de6ffb91ce1a3796382 2 0 60.0 pending
kb/communities/THOR_Rhizosphere_Model_Community.yaml CommunityMech:000079 ec95272c2b0ded1ac096cd9e9a53509ae052e7316d4c88b9ef51ceefb58b9f71 4 2 100.0 pending
kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml CommunityMech:000072 01cbb6970852dad836fce77b480e680a086b088a5ad488aeedfd4788e96f64dc 4 4 100.0 pending
@@ -431,7 +431,7 @@ kb/communities/Tinto_River_Iron_Cycling_Community.yaml CommunityMech:000074 84f2
kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml CommunityMech:000106 b4d7702d9c87b2b55cb2b3c74598aed2bfded7afd454faed5628c817b2fdfa35 3 2 100.0 pending
kb/communities/Tomato_Oxylipin_SynCom3.yaml CommunityMech:000107 9c5917f46de396ed1c278b2cb65ff5d6d5a78be8aa470ce09e20a9e8550ccafe 3 2 100.0 pending
kb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml CommunityMech:000112 a132b431ff499ce3fdb596250ef8adb152123ec8c5217bfdabd7ea0cc55b0de1 4 3 100.0 pending
-kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml CommunityMech:000188 6588808db1c3e6319ff3742ebd653264e482f7ccf4c3aaff5ab61c2d7c969874 3 2 100.0 pending
+kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml CommunityMech:000188 19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0 3 2 90.0 reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml reviewed
kb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml CommunityMech:000205 4ea126e913b09702e406501449cb83080bdfd4af1623651299737147b08b2e9a 3 2 100.0 pending
kb/communities/Trichoderma_Lactate_Platform.yaml CommunityMech:000075 e12191dd7b1c95d88b85136f635d1c33bcd7af642f105574fed48883dd2b1585 3 2 100.0 pending
kb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml CommunityMech:000270 d1652308f8e0e4f2fcebf880a03b8d0e311063a176bcaed2094983b038f59cea 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 022ab1ff8..ee3c377d6 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
"nodes": 1380,
- "edges": 544,
+ "edges": 543,
"records_without_nodes": 10,
"records_without_edges": 185,
"review_status_counts": {
"needs_research": 53,
- "pending": 52,
- "reviewed": 355
+ "pending": 45,
+ "reviewed": 362
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch112.json b/reports/causal_graph_review/validation-20261008-batch112.json
new file mode 100644
index 000000000..725c56c4e
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch112.json
@@ -0,0 +1,1847 @@
+{
+ "base_commit": "c38a8903f7fe36f9a870b1b872f179bb4a7a9ee4",
+ "scope": [
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml",
+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
+ "kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch112.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/focused.log",
+ "log_sha256": "0fe73cb76e57b4942f35c29e1066765bae69d6ed1310abc78d2cf23119c1a056",
+ "output_tail": "........... [100%]\n11 passed in 5.85s\n",
+ "superseded_by_quotation_correction": true,
+ "classification": "Initial output retained; rerun after the appended benzoate quotation correction."
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch112/Syntrophobacter_Methanobacterium_Syntrophy-strict.tsv",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-strict.log",
+ "log_sha256": "a3a147f7f07e32aabea368d2b8fc1a54df39f43c1e8debab1a16dba8b7038f1f",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch112/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch112/Syntrophobacter_Methanobacterium_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-references.log",
+ "log_sha256": "e708fbbf9014c166af560a18cb0017671c43ff26ba85168ada6a1cb7207ca0c2",
+ "output_tail": "Validating kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-snippets.log",
+ "log_sha256": "ca82c3416fa788a77bf876acc4abd6e2d670f70dbd026987882533e194497252",
+ "output_tail": "# 28 evidence snippets scanned across 1 files\n MATCH 27\n RENDERING 1\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 1 kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-rank.log",
+ "log_sha256": "4ad6702490689218653732ff0e0ec1ade836f5205b039bd6a008045973ff9f8b",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000068\",\n \"name\": \"Syntrophobacter-Methanobacterium Syntrophic Consortium\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 3,\n \"interaction_evidence\": 9,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanobacterium_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Syntrophobacter_Methanobacterium_Syntrophy/2026-10-08T071057Z-codex-d473fc.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanobacterium_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch112/Syntrophobacter_Methanospirillum_Syntrophy-strict.tsv",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-strict.log",
+ "log_sha256": "2319757c073a360f243a83aacbf952c5e44c44d53190e4429f5ad7e78c6748f6",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch112/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch112/Syntrophobacter_Methanospirillum_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-references.log",
+ "log_sha256": "30984f2b7f6264a438541839be68a6f860e13211b25a87423400433a5798eb9f",
+ "output_tail": "Validating kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-snippets.log",
+ "log_sha256": "558ad4bcecabaf18196d38b9b46e16a6b61c5886f0110b4c36d5d50665353479",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 17\n RENDERING 1\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 1 kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-rank.log",
+ "log_sha256": "2f233b81b565b4bd58d4fa737e24d5b067325d72ab9532c2d1332c636ab53172",
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+ },
+ {
+ "check": "Syntrophobacter_Methanospirillum_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Syntrophobacter_Methanospirillum_Syntrophy/2026-10-08T071057Z-codex-fb396b.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophobacter_Methanospirillum_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch112/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-strict.tsv",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-strict.log",
+ "log_sha256": "3f88351eceffc0d707c6d40c8086169de0876e713fbbebe773fd9861fca1d2ec",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch112/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch112/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 1
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-references.log",
+ "log_sha256": "d3e5b7b25ae27facb77d211b58e8da0d043abe0c79a37038ee2c32c04a8e77b5",
+ "output_tail": "Validating kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n [ERROR] Text part not found as substring: 'The headspace of 250-ml incubation bottles was flushed with N2 for 5 min and then adjusted with N2:CO2 (80:20 ) to a final pressure of 172 kPa' (note: only abstract available for PMID:34603271, full text may contain this excerpt)\n Location: cultivation_setup[0].evidence[1].snippet\n Reference: PMID:34603271\n\nValidation Summary:\n Total checks: 1\n Issues found: 1\n",
+ "explained_output_tail": "Validating kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n [ERROR] Text part not found as substring: 'The headspace of 250-ml incubation bottles was flushed with N2 for 5 min and then adjusted with N2:CO2 (80:20 ) to a final pressure of 172 kPa' (note: matches the cached full text of PMID:34603271 either side of the gap \u2014 this validator strips [bracketed] text before matching, so the quote is fine and the tool is not (#622))\n Location: cultivation_setup[0].evidence[1].snippet\n Reference: PMID:34603271\n\nValidation Summary:\n Total checks: 1\n Issues found: 1\n\n[annotate] rewrote 1 misleading 'only abstract available' note(s) (#496)\n",
+ "initial_expected_exit_codes": [
+ 0
+ ],
+ "classification": "Preexisting failure proven identical on parent;not a pass."
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-snippets.log",
+ "log_sha256": "1125ff0dde8c88267205b8aa843a32ef58e84b65fee929f651c20facd8785df0",
+ "output_tail": "# 26 evidence snippets scanned across 1 files\n MATCH 26\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-rank.log",
+ "log_sha256": "9ecd2b3cd1f8a86aeeddc14669904ee0bbe2063afec9f4a8cb33979e9d0e04dd",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000189\",\n \"name\": \"Syntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\",\n \"score\": 83.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture/2026-10-08T071057Z-codex-28253a.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch112/Syntrophomonas_Methanospirillum_Syntrophy-strict.tsv",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-strict.log",
+ "log_sha256": "0f1fad2ba3909d703a1c62979cb354270b12662661bb751ef007a5c452e1a2a5",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch112/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch112/Syntrophomonas_Methanospirillum_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-references.log",
+ "log_sha256": "672100336fabe30e06aa852680df8d2f8b90d3bca3bbc089ef5e18021b7faa96",
+ "output_tail": "Validating kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-rank.log",
+ "log_sha256": "ceafafc73d913ce96840a2ca88abf2b321b6a7533b5786757ebd8649263381e3",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000070\",\n \"name\": \"Syntrophomonas-Methanospirillum Syntrophic Consortium\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 3,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Syntrophomonas_Methanospirillum_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Syntrophomonas_Methanospirillum_Syntrophy/2026-10-08T071058Z-codex-a2e51d.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanospirillum_Syntrophy-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n",
+ "superseded_by_quotation_correction": true,
+ "classification": "Initial output retained; rerun after the appended benzoate quotation correction."
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch112/Syntrophus_Benzoate_Degrader-strict.tsv",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-strict.log",
+ "log_sha256": "4da0e86cd4d94d2fa5254182f9c7d67cc97943ab2ef8b287a0b9f63dc390cea6",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch112/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch112/Syntrophus_Benzoate_Degrader-strict.tsv\n",
+ "superseded_by_quotation_correction": true,
+ "classification": "Initial output retained; rerun after the appended benzoate quotation correction."
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n",
+ "superseded_by_quotation_correction": true,
+ "classification": "Initial output retained; rerun after the appended benzoate quotation correction."
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-references.log",
+ "log_sha256": "64cf5a382de6a9850be12bee78b9b4b3f214b1b55a64fc36620535ae612e9d3d",
+ "output_tail": "Validating kb/communities/Syntrophus_Benzoate_Degrader.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n [ERROR] Text part not found as substring: 'Cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate (or their coenzyme A derivatives) transiently accumulated during growth with benzoate.'\n Location: ecological_interactions[0].evidence[0].snippet\n Reference: doi:10.1128/aem.67.4.1728-1738.2001\n\nValidation Summary:\n Total checks: 1\n Issues found: 1\n",
+ "explained_output_tail": "Validating kb/communities/Syntrophus_Benzoate_Degrader.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (1):\n [ERROR] Text part not found as substring: 'Cyclohexane carboxylate, cyclohex-1-ene carboxylate, pimelate, and glutarate (or their coenzyme A derivatives) transiently accumulated during growth with benzoate.'\n Location: ecological_interactions[0].evidence[0].snippet\n Reference: doi:10.1128/aem.67.4.1728-1738.2001\n\nValidation Summary:\n Total checks: 1\n Issues found: 1\n",
+ "superseded_by_quotation_correction": true,
+ "classification": "Initial output retained; rerun after the appended benzoate quotation correction."
+ },
+ {
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+ "command": [
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+ "output_tail": "........... [100%]\n11 passed in 5.87s\n"
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+ "command": [
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+ {
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+ "command": [
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+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml"
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+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-strict.log",
+ "log_sha256": "646577ce9db9fa78de1fabce1cda5a57ee38014408f1ec99e682ab5c487f326c",
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+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-quotation-correction-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml",
+ "-s",
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+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-quotation-correction-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-references.log",
+ "log_sha256": "9d387ec09d8badf28082c8e3629a0aa154b8a6892eb81c834b105e86a386f6c3",
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+ "explained_output_tail": "Validating kb/communities/Syntrophus_Benzoate_Degrader.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-quotation-correction-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
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+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
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+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-snippets.log",
+ "log_sha256": "b38c1b013f645c207268f3650cf7cb4c86578850020a03c48cc4daabfcddf402",
+ "output_tail": "# 13 evidence snippets scanned across 1 files\n MATCH 10\n RENDERING 3\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 3 kb/communities/Syntrophus_Benzoate_Degrader.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Syntrophus_Benzoate_Degrader-quotation-correction-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-rank.log",
+ "log_sha256": "bb28b8f70004f20836809da777c83d7839e774782bb34f22a926e926831de669",
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+ {
+ "check": "Syntrophus_Benzoate_Degrader-quotation-correction-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Syntrophus_Benzoate_Degrader/2026-10-08T071058Z-codex-9e1dfe.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "check": "Syntrophus_Benzoate_Degrader-quotation-correction-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "--target-class",
+ "HistoryRecord",
+ "history/records/Syntrophus_Benzoate_Degrader/2026-10-08T072502Z-codex-a76868.yaml"
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+ "expected_exit_codes": [
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+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Benzoate_Degrader-quotation-correction-history-1.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "src/communitymech/schema/communitymech.yaml",
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
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+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml"
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+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-strict.log",
+ "log_sha256": "d0aa4b3d322dbb67dba3c8c578f46e8a79183ade34680cc7b748f5676a00731c",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch112/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch112/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
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+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-references.log",
+ "log_sha256": "7aad6556d06f4b589a7c0e1919581f9b4ed18010febbd104bd9e6149f1dd633e",
+ "output_tail": "Validating kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-snippets.log",
+ "log_sha256": "1125ff0dde8c88267205b8aa843a32ef58e84b65fee929f651c20facd8785df0",
+ "output_tail": "# 26 evidence snippets scanned across 1 files\n MATCH 26\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-rank.log",
+ "log_sha256": "b7d5d99629daf0f77d9ccc9173a15262a3617ebaba25bb04510340eeac6d1d51",
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+ },
+ {
+ "check": "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
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+ "history/records/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture/2026-10-08T071058Z-codex-4e26a3.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
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+ "src/communitymech/schema/communitymech.yaml",
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+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
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+ "command": [
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+ "scripts/validate_strict.py",
+ "--workers",
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+ "--out",
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+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-strict.log",
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+ },
+ {
+ "check": "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
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+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-references.log",
+ "log_sha256": "b4c668c98a35763d425dc36647e9e8b01140ad34b9e7c330434dd935b1e5bb49",
+ "output_tail": "Validating kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-rank.log",
+ "log_sha256": "c681bb3e1ed232293a4c6c2f9123e99da31e3788a51663c4893c4437d5091777",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000188\",\n \"name\": \"Trichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\",\n \"score\": 90.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture/2026-10-08T071059Z-codex-12f831.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/inventory.log",
+ "log_sha256": "a1432c2d31024ee0f1d69b73e4ff9a827df6d15941f76907d3313f746348925c",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1380,\n \"edges\": 543,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 185,\n \"review_status_counts\": {\n \"needs_research\": 53,\n \"pending\": 45,\n \"reviewed\": 362\n },\n \"structural_defects\": []\n}\n"
+ },
+ {
+ "check": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 1
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/rank-all.log",
+ "log_sha256": "9ee12c0f49c1240ac75a110e5186cb879515668008fd9b278658fbee139f4c2a",
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/private/tmp/communitymech-causal-batch112/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch112/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch112/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch112/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/render-repeat.log",
+ "log_sha256": "d979e8c9a674a62eecba83e63f869ea5e68fccd7b5a4b756a6eae0cd12318488",
+ "output_tail": "unitymech-causal-batch112/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch112/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch112/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch112/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch112/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch111')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/connectivity-survey.log",
+ "log_sha256": "2616ef315214a01b5944fee226c9465d966354a50dd1b214875dca2749d21dad",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 409, \"mixed\": 134, \"community_level_only\": 275, \"taxa\": 1556, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 412, \"mixed\": 136, \"community_level_only\": 276, \"taxa\": 1563, \"credited_solely_by_the_rule\": 1273}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch110.py",
+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
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+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
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+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/regressions.log",
+ "log_sha256": "42852dffd0a136b82705afe69e8912482c694c82ece40e46f336dbbf5dbb6016",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 21%]\n........................................................................ [ 28%]\n........................................................................ [ 35%]\n........................................................................ [ 42%]\n........................................................................ [ 49%]\n........................................................................ [ 56%]\n........................................................................ [ 63%]\n........................................................................ [ 71%]\n........................................................................ [ 78%]\n........................................................................ [ 85%]\n.....................................................................F.. [ 92%]\n........................................................................ [ 99%]\n...... [100%]\n=================================== FAILURES ===================================\n_________________ test_the_corpus_is_unchanged_by_this_feature _________________\n\n def test_the_corpus_is_unchanged_by_this_feature():\n \"\"\"Only the records that mean to use the slot do.\n \n Asserted on the corpus rather than trusted from the schema: an\n `ifabsent` or a default that quietly populated the slot would change 312\n records' connectivity without anyone editing a record. That is still the\n failure this catches \u2014 a silent default would put every record in `users`,\n not just the three named below.\n \"\"\"\n users = {\n path.name\n for path in record_files()\n for interaction in (yaml.safe_load(path.read_text()) or {}).get(\"ecological_interactions\")\n or []\n if isinstance(interaction, dict) and interaction.get(\"participating_taxa\")\n }\n> assert users == USERS, (\n f\"{len(users)} records use participating_taxa, expected {len(USERS)}. \"\n f\"Adding a user is fine \u2014 but the connectivity numbers in \"\n f\"tests/test_community_level_connectivity_credit.py were measured \"\n f\"before the slot was used, so re-check them and then update USERS. \"\n f\"Added: {sorted(users - USERS)}. Removed: {sorted(USERS - users)}\"\n )\nE AssertionError: 286 records use participating_taxa, expected 283. Adding a user is fine \u2014 but the connectivity numbers in tests/test_community_level_connectivity_credit.py were measured before the slot was used, so re-check them and then update USERS. Added: ['Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml', 'Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml', 'Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml']. Removed: []\nE assert {'AMD_Acidoph...re.yaml', ...} == {'AMD_Acidoph...re.yaml', ...}\nE \nE Extra items in the left set:\nE 'Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml'\nE 'Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml'\nE 'Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml'\nE Use -v to get more diff\n\ntests/test_participating_taxa.py:468: AssertionError\n=========================== short test summary info ============================\nFAILED tests/test_participating_taxa.py::test_the_corpus_is_unchanged_by_this_feature\n1 failed, 1013 passed in 529.35s (0:08:49)\n",
+ "superseded_by_participant_allowlist_correction": true,
+ "classification": "Failed run retained; three intentional participant-list users added after the measured census, without changing connectivity logic."
+ },
+ {
+ "check": "participant-allowlist-focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_participating_taxa.py::test_the_corpus_is_unchanged_by_this_feature"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/participant-allowlist-focused.log",
+ "log_sha256": "0cdc18b88ef1d419eb579209e67a87242d2691ae115fd6d46b3599a3244cf8c0",
+ "output_tail": ". [100%]\n1 passed in 24.52s\n"
+ },
+ {
+ "check": "regressions-post-participant-allowlist",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch108.py",
+ "tests/test_causal_review_batch109.py",
+ "tests/test_causal_review_batch11.py",
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+ "tests/test_causal_review_batch111.py",
+ "tests/test_causal_review_batch112.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
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+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
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+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/regressions-post-participant-allowlist.log",
+ "log_sha256": "7d999745a8e80b2a732808f79731f3377c4c1b8a54eab79a59b6c5015caeaf1a",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 21%]\n........................................................................ [ 28%]\n........................................................................ [ 35%]\n........................................................................ [ 42%]\n........................................................................ [ 49%]\n........................................................................ [ 56%]\n........................................................................ [ 63%]\n........................................................................ [ 71%]\n........................................................................ [ 78%]\n........................................................................ [ 85%]\n........................................................................ [ 92%]\n........................................................................ [ 99%]\n...... [100%]\n1014 passed in 381.37s (0:06:21)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/just-lint.log",
+ "log_sha256": "1c3f5afae26d1dfd1664b7bab7db5666e4527dea6b1ae2f0838c9603706ae4ef",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n365 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/audit-snippets-all.log",
+ "log_sha256": "cd6d088f482b894e3bc7abd2876dc7698cf392c6ec61eebcd46b5e43d8b7ea49",
+ "output_tail": "# 9012 evidence snippets scanned across 460 files\n MATCH 8867\n RENDERING 28\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch112/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh pre-source baseline across both roots:460 records,923 caches,56 existing warnings,zero structural defects. Review all21 original nodes/17arrows; retain21nodes/16directions,remove one misplaced reverse arrow,rename one outcome. No new topology or Edison spend.",
+ "Whole seven canonical records, schema scope/type definitions and existing discussion evidence read. Four fresh extracted main bodies read:propionate proteome1-187,coordination1-147,trichococcus1-133,nanomaterials1-161,including abstracts,Methods and embedded captions/tables. Extraction is not original figure-pixel or separate supplement/raw-data review.",
+ "Fresh primary abstracts and exact Crossref DOI metadata read for1998propionate type,1981butyrate type,1997gentianae,and both2001benzoate studies. Older fullTextXML endpoints failed for1981 and both2001papers. PMC93338 web main-body excerpts were available through Results,not a complete independently archived full-text read. Gentianae publisher rendered abstract only; no PDF audit. Graph claims for these sources use fresh abstracts, not inaccessible detailed assays.",
+ "2024formate publisher retrieval failed403/429. Existing curator-supplied cached publisher text main content lines1-735 read; contains duplicated extraction passages and prepublication page headers. Its two retained transcription snippets are cache-matched,not fresh independently retrieved full-text matches. Existing dose discussion preserved and amended; sludge and coculture are distinguished. Reference-list tail and separate supplements not audited.",
+ "All graph/discussion quotations are normalized contiguous cache matches. Fresh primary matches are counted separately from the two2024cache-only graph quotes; matching does not establish entailment. Other caches were quotation-checked,not read in full. Official ChEBI16150 identity confirmed; no new taxon groundings.",
+ "Propionate: preserve real carrier-removal feedback, bound enzyme homology/abundance inference and carrier partitioning, distinguish gas pressure from aqueous concentration. Butyrate: preserve reported hydrogen inhibition but do not certify exact perturbation conditions,universal obligacy or an uncited pressure threshold.",
+ "Coordination: initial ratio perturbations are distinct from endpoint convergence; remove aggregation-described reverse arrow. Reciprocal attraction and unchanged aggregation under activity-changing disturbance are retained. Nanomaterial acceleration does not prove DIET.",
+ "Benzoate: acetate+CH4 is conversion,not complete mineralization; pure-culture fermentation disproves universal partner dependence. Other-partner enzyme assays are not imported. Gentianae: approximate growth energy and product effects are not competition or a fixed threshold across dense-suspension and added-partner treatments.",
+ "ES5: exact M.hungatei lag is significant in Table1; fitted rate/final concentration are not marked significant and Discussion reports similar butyrate slopes. Preserve stimulation without abstract-wide120%/150% exact-triculture attribution. All three members remain in outcome scope; measured proteomes are two partners. Aggregation/protein mediation remains hypothetical,not enzyme activation or DIET proof.",
+ "Ignored/hidden-inclusive local path index read,not all historical file bodies. Fresh all-state issue title/body dedup matched1392,1389,795,583,496,259;fullbodies and related529/183 read. PR comments not exhaustively searched. Broad metadata issues are followups,not addressed by graph scope.",
+ "Preserve453otherrecords,923caches,rawnon-graph blocks and prior history/decision artifacts. Participant census measured,not guessed;rules/share guard unchanged. No schema/validator/runtime change. MacOS full-record CLI is not Linux certification;reference-loader,DOI-case and rendering caveats remain.",
+ "Repair issues remain open until protected-main merge;metadata followups remain open afterward. Self-review is not independent approval or full-corpus completion. Denied/unanswered Edison scopes untouched;no artificial CI,protection bypass or premature branch deletion."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml": {
+ "MATCH": 27,
+ "RENDERING": 1,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml": {
+ "MATCH": 17,
+ "RENDERING": 1,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml": {
+ "MATCH": 26,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml": {
+ "MATCH": 10,
+ "RENDERING": 3,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml": {
+ "MATCH": 26,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml": {
+ "MATCH": 24,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "preexisting_reference_exception": {
+ "artifact": "/private/tmp/communitymech-batch112/preexisting-bracket-validator-proof.json",
+ "sha256": "15bb306e74ad93c470419af2e5a33ee19b4a8ccebb90cec59cdf881040862170",
+ "proof": {
+ "issue": 622,
+ "secondary_note_issue": 496,
+ "location": "cultivation_setup[0].evidence[1].snippet",
+ "exit_code": 1,
+ "parent_exit_code": 1,
+ "byte_identical_parent_failure": true,
+ "unchanged_cultivation_setup": true,
+ "fresh_primary_literal_match": true,
+ "cache_literal_match": true,
+ "baseline_log": "/private/tmp/communitymech-batch112/parent-coordination-references.log",
+ "baseline_log_sha256": "d3e5b7b25ae27facb77d211b58e8da0d043abe0c79a37038ee2c32c04a8e77b5",
+ "current_log": "/private/tmp/communitymech-batch112/verification/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture-references.log",
+ "current_log_sha256": "d3e5b7b25ae27facb77d211b58e8da0d043abe0c79a37038ee2c32c04a8e77b5",
+ "cache_sha256": "b43b81a611ba2a42a98e32cf06acf5663c43bd33edbf384a0151124a7bde6678",
+ "interpretation": "Expected preexisting bracket-stripping failure;not a reference-validation pass. Graph quotation proof remains separate."
+ }
+ },
+ "unchanged_record_files": 453,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 111,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "Existing evidence/scope repairs and removal of one unsupported reverse direction;no new nodes/directions."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch112/baseline.json": "1904cacf99f46e220f9baf67e72ba5847e9f13048d63691b56a79e1db8dd074c",
+ "/private/tmp/communitymech-batch112/benzoate_metabolism-abstract.txt": "4bc688bd72b650e8f219040516f634a50132f9ad59cde56706e48334f76711d3",
+ "/private/tmp/communitymech-batch112/benzoate_metabolism-crossref.json": "dd6423b96277eaab59febc452d24072decbe1781149df80f4c9724fdddd2f608",
+ "/private/tmp/communitymech-batch112/benzoate_metabolism-metadata.json": "2fe35bf254c34ca658fa7dd3eb8d73af310ed9260063655ac823b0b366a67ab9",
+ "/private/tmp/communitymech-batch112/benzoate_pure-abstract.txt": "f021c43b5e508c68ddd9b29e7f1eac0f239e099856111152bc3ff8ffdfdeeebd",
+ "/private/tmp/communitymech-batch112/benzoate_pure-crossref.json": "e1a69d821ff71d39ce1519415c40b21ee8a4029d550e833a9e4a290c4de9ef2a",
+ "/private/tmp/communitymech-batch112/benzoate_pure-metadata.json": "9b537d873eba32ffefdde5c1f39a563045b62b63da88fa096032a25efd0f0249",
+ "/private/tmp/communitymech-batch112/butyrate_type-abstract.txt": "39783b07ec098f2a2841137de29b8e34b5b7f6d204b03cca87870d4c708ba215",
+ "/private/tmp/communitymech-batch112/butyrate_type-crossref.json": "ea3222ebd08a67bbaf3b552aa07c211f04278debdf159fa52ffd424ffff8b362",
+ "/private/tmp/communitymech-batch112/butyrate_type-metadata.json": "f0af6651c2a70e9a65db7429d7194657585b3416a37284b9933567aea959202e",
+ "/private/tmp/communitymech-batch112/coordination-abstract.txt": "56ca36a1f980b9ef31c76988eec84f2dbeda5c790b833277bf61203c6c8a6a14",
+ "/private/tmp/communitymech-batch112/coordination-crossref.json": "536ce9645801429a3f52a8ddb601e4eb700465f356d9aa675ae5cb0abd593718",
+ "/private/tmp/communitymech-batch112/coordination-metadata.json": "ec3e7aa81a78f3045e5b91c2a40ff76ef11d2be7e62ffb9fd0502e30207de606",
+ "/private/tmp/communitymech-batch112/coordination-primary.txt": "21764a2d4442da29e6ef25af70f3346875968f601f8672cd3c0ff750aecde179",
+ "/private/tmp/communitymech-batch112/coordination-primary.xml": "d58a2d20e1f69c96f0306cf43df85dd5601234f369df48cb8f8f777f46bdf882",
+ "/private/tmp/communitymech-batch112/dedup-local-current.txt": "bdb2b563237eee321c1f994ab8f6eee526a3ca83a869b8ee24c0525e2687d088",
+ "/private/tmp/communitymech-batch112/formate_stress-abstract.txt": "c37b280c176346e64650bc0dcab43544183a3a87082b4139c35fdabc16fa0305",
+ "/private/tmp/communitymech-batch112/formate_stress-crossref.json": "9b85a4aba31b5abe2d4e19001262a0e4ebb370255332cffec868e09711184ae1",
+ "/private/tmp/communitymech-batch112/formate_stress-metadata.json": "34c774db4c79d979376279cba0767c07ccbdd1146d64790e6446ae85c8183a5f",
+ "/private/tmp/communitymech-batch112/gentianae-abstract.txt": "0ab467c55e9e56a07821173d4c515c7c04ab233b7885ec8bb68a5fb348ca7de0",
+ "/private/tmp/communitymech-batch112/gentianae-crossref.json": "8fd751839bf7224814c8111833d86d46142d4db7a2632d539326ea32779fe784",
+ "/private/tmp/communitymech-batch112/gentianae-metadata.json": "538f86c04177446c1cb6e271be7913c3a1cf12c286f1c338f2ca01580850c60a",
+ "/private/tmp/communitymech-batch112/issue-dedup-current.json": "207dfbe41ed0f3c22e7549d594c7a9ff6c7909627373f1fc731aeb1fe4045692",
+ "/private/tmp/communitymech-batch112/nanomaterials-abstract.txt": "aa2f576c63c95c5f44b99ea69b0c1897ceebf6eed946101880515869baae2552",
+ "/private/tmp/communitymech-batch112/nanomaterials-crossref.json": "9ef898555efae082d2b050d2d803e52b78018e17e0dcb331a1466ed40a8b355b",
+ "/private/tmp/communitymech-batch112/nanomaterials-metadata.json": "04e31b769a23d945f9713a65435dc1f69b4fadf82b6ab2e4204fffa628caadf4",
+ "/private/tmp/communitymech-batch112/nanomaterials-primary.txt": "c717378a0f3336093af13b22bb02c0ec55f1d5d30f56c885b3d54dde0469892a",
+ "/private/tmp/communitymech-batch112/nanomaterials-primary.xml": "e405c23a2747de20c1b260a36c83e0be9b52640806ec7d7789069a1ab0c20a02",
+ "/private/tmp/communitymech-batch112/primary-manifest.json": "0caa3c60631c821e5d37ff5d7d146f86eb133c6890b73edbd54a81ebd600e882",
+ "/private/tmp/communitymech-batch112/propionate_proteome-abstract.txt": "ba6083879e90ed3bb17426ce85c2af0972a82fd86929b33728d1547921f6b6ea",
+ "/private/tmp/communitymech-batch112/propionate_proteome-crossref.json": "1ddc53159c78944b45ac0b2f09ac3cd652807bd62579f6c89d46b7b953a303a7",
+ "/private/tmp/communitymech-batch112/propionate_proteome-metadata.json": "afb9c5a5f8f3a9aa95c4ec637b7e393b1fcf855fdcc1319235cd94ae7eeabbd5",
+ "/private/tmp/communitymech-batch112/propionate_proteome-primary.txt": "9faf8e8d9d9586a11b232bd2945fb3345ef45b01ff3bed9ed91d4526d1d62bd3",
+ "/private/tmp/communitymech-batch112/propionate_proteome-primary.xml": "e0568e38789fc1a7cc7caa7c4e8a8f0a032417c8c2d0e3deffb1f14ed49d6175",
+ "/private/tmp/communitymech-batch112/propionate_type-abstract.txt": "a597ecb753cd758bae058663ccc733af3dc6807d2915736524ec28b7e24a69ec",
+ "/private/tmp/communitymech-batch112/propionate_type-crossref.json": "3f6814a46b7b289d51ded632fd922dc118ee4697d28dc1bd5f3de0cd50c0e2a4",
+ "/private/tmp/communitymech-batch112/propionate_type-metadata.json": "cab9d3173fbed6461c1f12e8090d6b46000446b471bab63232d25c92df58ab74",
+ "/private/tmp/communitymech-batch112/trichococcus-abstract.txt": "5c865b7ee5821078b5caa976ec83e13cdfe2a65f66d89f41a7575eef711af1c2",
+ "/private/tmp/communitymech-batch112/trichococcus-crossref.json": "af7781235f8437aca3078d261f783b4b70ba8da9d3c83bd26802b76f3f926479",
+ "/private/tmp/communitymech-batch112/trichococcus-metadata.json": "1c9f2f9d8a5c2e36a1518a2b93f372af35a428edc1699339c9c1f940c8be857e",
+ "/private/tmp/communitymech-batch112/trichococcus-primary.txt": "b83df45d8e650a147e2dbfb376309699450d8dcb737bb8f16579c8a1e8a5d409",
+ "/private/tmp/communitymech-batch112/trichococcus-primary.xml": "49cf054b4625037cd7bb1c720383bee0e54e648e002cfaeb8970c30e25247fd5",
+ "references_cache/PMID_16345745.txt": "c96297cf9f4ed268498eda433babbc91820f1ce354f84442abbe06d3e4260264",
+ "references_cache/PMID_29611893.md": "c94cffb4dcccc399d31392cc59e81b9d802849f00298092c43752a1776daf521",
+ "references_cache/PMID_33657722.md": "97a437032700eb67f1f20f2c727eac6db4022566bf03b2ead274e49cba88a1db",
+ "references_cache/PMID_34603271.md": "b43b81a611ba2a42a98e32cf06acf5663c43bd33edbf384a0151124a7bde6678",
+ "references_cache/PMID_35699440.md": "d3b41b21f05b6259b872b4d2da4f33d8a9005d8afa9286f3a50ba155b0bb16ce",
+ "references_cache/PMID_9828440.txt": "3956a285b958d30f86892242bd959c8b22b95cf5bc4f8acbae16e89cbabe989c",
+ "references_cache/doi_10.1038_s41598-018-30745-7.md": "1efbc27f4b1a876b721750d51d2eaeb1ad5a342e34d5583109ff9efe9549096a",
+ "references_cache/doi_10.1099_00207713-48-4-1383.md": "60119b1232969442bc672c363d78d458d4670d4e4bff304a79b9df73731c44b7",
+ "references_cache/doi_10.1128_aem.67.12.5520-5525.2001.md": "3eabaddce60c0e6c4e6210b7dbe4a2c9fad697e78701d57c19a9d68d21f1d71b",
+ "references_cache/doi_10.1128_aem.67.4.1728-1738.2001.md": "17b31fb0881c5295c6efb73432139e718bd52ce11287b658c88feb3d65975de4",
+ "references_cache/doi_10.3390_w16243551.md": "8f93afba821f176aede4f0f41e54ac71d052e8425868bd757ad36764473e89f5",
+ "/private/tmp/communitymech-batch112/decisions-before-bracket-correction.yaml": "d50b8d58a9243534789f09abdc031e7cabb088eb2407aad69818a665e41a78a7"
+ },
+ "immutable_prior_history_and_decision_files": 849,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 45,
+ "discussion_quotations": 8,
+ "fresh_primary_literal_matches": 51,
+ "existing_curator_text_only": 2,
+ "all_cached_literal_matches": 53,
+ "retained_nodes": 21,
+ "removed_nodes": 0,
+ "renamed_nodes": 1,
+ "retained_arrows": 16,
+ "removed_arrows": 1,
+ "new_nodes_or_directions": 0,
+ "scope": "Four fresh extracted main bodies and five older primary abstracts;two2024quotes use existing curator-supplied text,not fresh full text. Source entailment and access bounds separately recorded."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "Twenty-one nodes and sixteen existing directions retained;one misplaced reverse arrow removed;one conversion node renamed. All56existing warnings unchanged;zero structural defects. Non-graph followups1877-1878 remain open."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1366,
+ "arrows": 535
+ },
+ "render_scope": "Deterministic rendering and exact HTML-description parser,not screenshots;postcommit docs-current separately required.",
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 409,
+ "mixed": 134,
+ "community_level_only": 275,
+ "taxa": 1556,
+ "credited_solely_by_the_rule": 1270
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 412,
+ "mixed": 136,
+ "community_level_only": 276,
+ "taxa": 1563,
+ "credited_solely_by_the_rule": 1273
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 3,
+ "mixed": 2,
+ "community_level_only": 1,
+ "taxa": 7,
+ "credited_solely_by_the_rule": 3
+ },
+ "interpretation": "Three additional community-level records,two mixed and one community-only. Seven denominator taxa and three solely-credited taxa reflect the ES5 triculture outcome scope;canonical participants explicit. Connectivity rules and share guard unchanged."
+ },
+ "participant_allowlist_correction": {
+ "failed_log": "/private/tmp/communitymech-batch112/verification/regressions.log",
+ "failed_log_sha256": "42852dffd0a136b82705afe69e8912482c694c82ece40e46f336dbbf5dbb6016",
+ "failed_result": "1 failed, 1013 passed in 529.35s (0:08:49)",
+ "previous_users": 283,
+ "current_users": 286,
+ "added_records": [
+ "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
+ "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
+ "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml"
+ ],
+ "scope": "Exact user-set expectation only; no canonical record or connectivity logic change."
+ },
+ "lint_limitation": "Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.",
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies unchanged. Not a complete embedding runtime."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9012,
+ "categories": {
+ "MATCH": 8867,
+ "RENDERING": 28,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1380,
+ "edges": 543,
+ "records_without_nodes": 10,
+ "records_without_edges": 185,
+ "review_status_counts": {
+ "needs_research": 53,
+ "pending": 45,
+ "reviewed": 362
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml": "70c5847ba8f65d2e4d4b283c362cbbb6637bf9e5e47d76877daec2f5557e8794",
+ "tests/test_causal_review_batch112.py": "7d66d5a3b4d3f31c3113cff3fde8843f7475fe9be8528c8ec054b7981a1c567f",
+ "tests/test_causal_review_batch109.py": "262381c4834593eb8fa6c8424e59ccfedc7428540bb57cf3db72703c935fc180",
+ "tests/test_participating_taxa.py": "82767cd685f4f127a12e6173f3ce88b547def54ef4ebd901c278e1978450c1a0",
+ "tests/test_community_level_connectivity_credit.py": "43cdd3ac18aaf658dc83288f70e96ddeb76f8cf1b9622bec2d1e52e25187d5ec",
+ "reports/causal_graph_review/cache-provenance-20261008-batch112.json": "5365b98f4cd1d1822dbbeca7a04f38cb9bf2a85f21ad7691985220c2996051d9",
+ "kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml": "eb0ed26cadc17f4a7fbf63d8d2c11da1d891cd2edf5ce82b938e19c2d0cf469b",
+ "kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml": "a4076f47b588559b0a751b8d4e0be16c067af11c359ba5e9f401fd0b542fb61a",
+ "kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml": "3aaf56515d25364c8ee56e24071798ff6e3893ccce89761fadd331a109719531",
+ "kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml": "2ba0dc0aafd78379eee56f47b0e5ef235d8ea5e52abaa5f51417f07412b5535d",
+ "kb/communities/Syntrophus_Benzoate_Degrader.yaml": "dffafcca6d385007e70e5d2024cc75f959ad3e442f5f9e27a7bdf145fe8d58d1",
+ "kb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml": "3584798fce68b6699f57471b38d2a5e7778e154ff5dbbbb63c3f98f92a2f3451",
+ "kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml": "19be2baf6f39a410bce4ce119b4b192d16c49f03e57b39ba4d1a3bf59f8c1ff0"
+ },
+ "pre_research_baseline": {
+ "base_commit": "c38a8903f7fe36f9a870b1b872f179bb4a7a9ee4",
+ "base_tree": "297f197d737c41b78fbb8f2863ea1c8109ab5ad5",
+ "research_worktree": "/private/tmp/communitymech-causal-batch111",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch112/baseline-rank.log",
+ "sha256": "cea12d145ab8e8430064208e23da854b32dd18e47719b71ca797b56b338a3151"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch112/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch112/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch112/baseline-downstream.log",
+ "sha256": "4dc72d642ca0a9653e566a6a233f25d4cd2debe86ba0f56cc2b854b52b7c4f8c"
+ }
+ ],
+ "baseline_sha256": "1904cacf99f46e220f9baf67e72ba5847e9f13048d63691b56a79e1db8dd074c"
+ },
+ "reference_validator_caveat": "Six full-record reference CLI passes;one expected preexisting failure in unchanged coordination cultivation_setup due to bracket stripping622 and misleading abstract note496,proven byte-identical on parent and matched to fresh primary text. Seven local snippet audits pass. macOS,not Linux certification;DOI-case1091,ligature1863 and loader1703 remain outside scope. Literal matches do not establish entailment. CLI Total checks counts issues,not checks.",
+ "status": "verified_existing_graph_repairs_with_source_access_limits",
+ "total_recorded_gate_outputs": 70
+}
diff --git a/tests/test_causal_review_batch109.py b/tests/test_causal_review_batch109.py
index 59406702d..455491086 100644
--- a/tests/test_causal_review_batch109.py
+++ b/tests/test_causal_review_batch109.py
@@ -175,16 +175,16 @@ def test_hashes_histories_and_canonical_identity_only_scope_are_explicit():
)
-def test_measured_scope_change_adds_no_solely_credited_taxa():
- # Batch111 adds one mixed-scope record; the solely-credited count is unchanged.
+def test_current_scope_census_tracks_later_source_bounded_repairs():
+ # Batch112 adds seven denominator taxa; the three ES5 members become solely credited.
survey = runpy.run_path(str(ROOT / "tests/test_community_level_connectivity_credit.py"))[
"_survey"
]()
assert survey == {
"records": 460,
- "with_community_level": 409,
- "mixed": 134,
- "community_level_only": 275,
- "taxa": 1556,
- "credited_solely_by_the_rule": 1270,
+ "with_community_level": 412,
+ "mixed": 136,
+ "community_level_only": 276,
+ "taxa": 1563,
+ "credited_solely_by_the_rule": 1273,
}
diff --git a/tests/test_causal_review_batch112.py b/tests/test_causal_review_batch112.py
new file mode 100644
index 000000000..2826eaff4
--- /dev/null
+++ b/tests/test_causal_review_batch112.py
@@ -0,0 +1,186 @@
+"""Keep syntrophic feedback while bounding assay scope and inferred mediation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-seven-records-batch112.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_propionate_feedback_is_retained_without_carrier_or_enzyme_certainty():
+ _, _, docs = records()
+ for doc in docs[:2]:
+ a, b, c = doc["ecological_interactions"]
+ assert a["interaction_type"] == b["interaction_type"] == "SYNTROPHY"
+ assert a["evidence"][1]["supports"] == a["evidence"][2]["supports"] == "PARTIAL"
+ assert "formate concentration" in b["description"]
+ assert "not independently quantify" in b["description"]
+ assert b["downstream"][0]["target"] == a["name"]
+ assert b["downstream"][0]["description"].startswith("DIRECTLY IMPLIED feedback:")
+ assert "not bidirectional donation" in b["downstream"][1]["description"]
+ assert c["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in c
+
+
+def test_exact_partner_and_existing_formate_gap_are_preserved():
+ _, _, docs = records()
+ doc = docs[0]
+ a = doc["ecological_interactions"][0]
+ assert "Methanobacterium formicicum" in a["evidence"][0]["snippet"]
+ assert a["evidence"][0]["reference"] == "PMID:29611893"
+ assert len(doc["discussions"]) == 1
+ d = doc["discussions"][0]
+ assert d["discussion_id"] == "kg-syntrophobacter-methanobacterium-partner-attribution"
+ assert "30 mM recovers" in d["rationale"]
+ assert "fresh publisher retrieval was unavailable" in d["rationale"]
+
+
+def test_ratio_convergence_is_not_reverse_metabolic_causality():
+ _, _, docs = records()
+ a, b, c = docs[2]["ecological_interactions"]
+ assert a["interaction_type"] == "SYNTROPHY"
+ assert a["downstream"][0]["description"].startswith("DIRECTLY IMPLIED/PARTIAL:")
+ assert "downstream" not in b
+ assert b["scope"] == c["scope"] == "COMMUNITY_LEVEL"
+ assert "interaction_type" not in b and "interaction_type" not in c
+ assert "around 1 from day 15" in b["evidence"][0]["snippet"]
+ assert "without a detectable change in aggregation" in c["description"]
+
+
+def test_butyrate_feedback_is_not_an_unverified_pressure_threshold():
+ _, _, docs = records()
+ a, b, c = docs[3]["ecological_interactions"]
+ assert a["interaction_type"] == b["interaction_type"] == "SYNTROPHY"
+ assert "substrate- and assay-bounded" in a["description"]
+ assert "10^-4" not in b["description"]
+ assert b["evidence"][1]["snippet"].endswith("by S. wolfei.")
+ assert "does not specify" in b["downstream"][0]["description"]
+ assert "interaction_type" not in c
+ assert len(b["evidence"]) == 2
+
+
+def test_benzoate_conversion_preserves_partner_free_alternative():
+ _, _, docs = records()
+ a, b, c = docs[4]["ecological_interactions"]
+ assert c["name"] == "Community Benzoate Conversion to Acetate and Methane"
+ assert "not complete mineralization" in c["description"]
+ assert "pure cultures ferment benzoate" in b["description"]
+ assert "absence of hydrogen-utilizing partners" in b["evidence"][1]["snippet"]
+ assert a["downstream"][0]["target"] == b["downstream"][0]["target"] == c["name"]
+ assert "interaction_type" not in c
+
+
+def test_gentianae_energy_is_intrinsic_and_product_inhibition_not_competition():
+ _, _, docs = records()
+ a, b, c = docs[5]["ecological_interactions"]
+ assert a["interaction_type"] == "SYNTROPHY"
+ assert b["scope"] == "PAIRWISE" and b["source_taxon"]["term"]["id"] == "NCBITaxon:43775"
+ assert "target_taxon" not in b and "interaction_type" not in b
+ assert c["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in c
+ assert "not a second partner-directed" in b["description"]
+ assert "propionate is not identified as a benzoate product" in c["description"]
+ assert (
+ "not assert that product addition changes a fixed intrinsic threshold"
+ in c["downstream"][0]["description"]
+ )
+
+
+def test_es5_lag_is_distinguished_from_rates_and_final_concentration():
+ _, _, docs = records()
+ a, _, _ = docs[6]["ecological_interactions"]
+ assert "marks the methane lag difference significant, not" in a["description"]
+ assert "not an exact-triculture increase estimate" in a["description"]
+ assert "rates were similar" in a["evidence"][1]["snippet"]
+ assert (
+ "former abstract-wide 120%/150% increase attribution"
+ in docs[6]["discussions"][0]["rationale"]
+ )
+
+
+def test_es5_proteomics_and_aggregation_are_hypotheses_not_enzyme_activation():
+ _, _, docs = records()
+ for n in docs[6]["ecological_interactions"]:
+ assert n["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in n
+ assert len(n["participating_taxa"]) == 3
+ _, b, c = docs[6]["ecological_interactions"]
+ for n in [b, c]:
+ assert n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ assert c["evidence"][1]["supports"] == "PARTIAL"
+ assert "more abundant in the biculture" in c["description"]
+ assert "assayed proteomes belong to S. wolfei and M. hungatei" in c["description"]
+
+
+def test_graph_metabolite_roles_and_benzoate_grounding_are_structured():
+ _, _, docs = records()
+ benzoates = []
+ for doc in docs:
+ for node in doc["ecological_interactions"]:
+ for m in node.get("metabolites", []):
+ assert "concentration" not in m
+ if m["preferred_term"] == "benzoate":
+ benzoates.append(m)
+ assert m["term"] == {"id": "CHEBI:16150", "label": "benzoate"}
+ assert len(benzoates) == 4
+
+
+def test_complete_dispositions_and_source_access_limits_are_recorded():
+ ledger, rows, _ = records()
+ assert ledger["reviewed_counts"] == {
+ "original_nodes": 21,
+ "retained_nodes": 21,
+ "removed_nodes": 0,
+ "retained_arrows": 16,
+ "removed_arrows": 1,
+ "renamed_nodes": 1,
+ "graph_quotations": 45,
+ "discussion_quotations": 8,
+ "new_discussions": 3,
+ "updated_discussions": 3,
+ }
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 1
+ assert len(ledger["issues"]) == 6 and len(ledger["unresolved_non_graph_issues"]) == 2
+ assert ledger["primary_graph_snippet_count"] == 43
+ assert sum(not c["independent_primary_match"] for c in ledger["snippet_checks"]) == 2
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ for row in rows:
+ for edge in row["retained_edge_decisions"]:
+ for k in ["source", "target"]:
+ assert (
+ row["renamed_nodes"].get(edge["before"][k], edge["before"][k])
+ == edge["after"][k]
+ )
+
+
+def test_histories_hashes_and_canonical_participants_are_guarded():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert row["status"] == "reviewed"
+ expected_events = 2 if row["id"] == "CommunityMech:000071" else 1
+ assert row["curation_events_added"] == len(row["history_files"]) == expected_events
+ assert (ROOT / row["history_files"][0]).exists()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ canonical = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for n in doc["ecological_interactions"]:
+ assert all(e["target"] in names for e in n.get("downstream", []))
+ assert all(
+ p in canonical and set(p) == {"preferred_term", "term"}
+ for p in n.get("participating_taxa", [])
+ )
+ for d in doc.get("discussions", []):
+ assert all(
+ a.split("#", 1)[1] in names
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
diff --git a/tests/test_community_level_connectivity_credit.py b/tests/test_community_level_connectivity_credit.py
index d5eb174f1..27167a35a 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -108,7 +108,8 @@ def test_most_records_carry_a_community_level_interaction(survey):
# #1799 separates the Shewanella current endpoint from reverse cross-feeding (403 -> 404).
# #1859 adds a scoped electrode process (407 -> 408); no new solely-credited taxa.
# #1865 separates the scoped butanol endpoint (408 -> 409), with no new sole credit.
- assert 130 <= survey["with_community_level"] <= 409, survey
+ # #1872/#1875/#1876 add three scoped outcomes; the ES5 triculture is community-only.
+ assert 130 <= survey["with_community_level"] <= 412, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
@@ -126,7 +127,8 @@ def test_the_mixed_records_are_where_the_coarseness_bites(survey):
# #1772-#1774 change the mixed-record census from 125 to 128.
# #1851-#1854 add four mixed-scope records; batch109 pins the exact measured census.
# #1865 adds one mixed-scope record (133 -> 134); the share guard is unchanged.
- assert 35 <= survey["mixed"] <= 134, survey
+ # Batch112 adds two mixed-scope records and one community-only record.
+ assert 35 <= survey["mixed"] <= 136, survey
assert survey["mixed"] + survey["community_level_only"] == survey["with_community_level"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 51706b404..402372079 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -432,10 +432,13 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Synthetic_Periphyton_Freshwater_Biofilm.yaml",
"Syntrophobacter_Methanobacterium_Syntrophy.yaml",
"Syntrophobacter_Methanospirillum_Syntrophy.yaml",
+ "Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml",
"Syntrophomonas_Methanospirillum_Syntrophy.yaml",
"Syntrophus_Benzoate_Degrader.yaml",
+ "Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml",
"TCP_NonDehalogenimonas_Groundwater_Consortium.yaml",
"Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml",
"Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml",
"Urine_Nitrification_SynCom.yaml",
"Viili_Fungus_Bacterium_EPS_SynCom.yaml",