diff --git a/docs/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.html b/docs/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.html
index e43b2ffd7..ca9faa8a8 100644
--- a/docs/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.html
+++ b/docs/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.html
@@ -570,21 +570,56 @@ Ecological Interactions
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
KNOWLEDGE_GAP
OPEN
- Which wastewater source and initial chemistry, MLSS source, bacterial activation procedure, HRAP geometry, working volume, retention time, outdoor light and temperature regime, and inoculation ratio were used for the AM-AB Chlorella-MLSS consortium?
+ Which reported HRAP conditions can now be curated from the full text, and which outdoor operating conditions remain unspecified?
-
The PubMed abstract names the Chlorella vulgaris/MLSS partners, separate activation before AM-AB assembly, outdoor HRAP cultivation, and the nitrogen, phosphate, ammonia, and BOD endpoints, but it does not report the underlying wastewater chemistry, mixed-liquor source, MLSS activation recipe, inoculation ratio, or HRAP operating conditions.
+
The full primary Methods and Tables 1-3 are now available and identify wastewater/sludge sources, activation, pond geometry, inoculation and initial chemistry. These are no longer abstract-access gaps. Reconcile the non-graph fields with those sections; do not transfer indoor algal-stock light and temperature settings to outdoor treatment. The graph review leaves that metadata curation separate.
Attaches to: taxonomy#Activated MLSS bacterial consortium, growth_media#wastewater outdoor HRAP medium, cultivation_setup
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which consortium-level treatment effects and qualified mechanisms belong in the currently empty graph?
+
+
The primary study compares the combined culture with activated algae alone. Retain improved late total-nitrogen removal, but early nitrogen removal is slower, phosphate reaches the detection limit in both conditions, and BOD removal is not uniformly better. Biomass correlations do not establish a transfer mechanism. New nodes require a separately authorized Edison causal-graph review; none were added in this repair pass.
+
+
Attaches to: ecological_interactions
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
phycoremediation using the AM–AB consortium delayed the removal of nitrogen compared to standalone activated C. vulgaris treatment
+
The algae-only control prevents an unqualified faster-removal or universal-synergy graph.
+
+
+
diff --git a/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html b/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html
index 27f09a52c..4ed4f3c49 100644
--- a/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html
+++ b/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html
@@ -650,9 +650,9 @@ Ecological Interactions
-
Metagenomic analysis connected the four-genus synergistic alliance to a coupled metabolic module containing hydrogen production, cofactor synthesis, and reductive dechlorination functions during TCP transformation.
+
HYPOTHESIZED functional coupling: community and metagenomic analyses associate the four named genera with hydrogen production, cofactor synthesis and reductive dechlorination. This is a consortium-level reconstruction, not measured intergenus hydrogen/cofactor transfer or a demonstrated genus-specific dechlorination pathway.
@@ -709,7 +709,7 @@
Evidence
PMID:41736479
- - SUPPORT (IN_VITRO)
+ - PARTIAL (COMPUTATIONAL)
"realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination""
@@ -724,7 +724,7 @@ Evidence
- Sodium acetate and lactate stimulation increased the consortium's TCP degradation efficiency and supported complete removal in the domesticated culture.
+ Sodium acetate and lactate amendments enhanced TCP degradation in the domesticated consortium. The abstract reports an overall average degradation rate of 19.06 umol L-1 d-1 and complete removal within 3.5 days; those values are not separately assigned to each amendment or to an individual genus.
@@ -804,7 +804,7 @@ Evidence
- Knowledge gaps & discussions (1)
+ Knowledge gaps & discussions (2)
@@ -814,9 +814,44 @@
The accessible PubMed abstract names the four-genera consortium and overall hydrogen/cofactor/reductive-dechlorination module, but it does not expose species or strain IDs, original inoculum details, full medium composition, substrate concentrations, transfer cadence, or the role of each named genus within the module.
-
Attaches to: taxonomy, engineering_design, growth_media, ecological_interactions#Hydrogen Cofactor Reductive-Dechlorination Module
+
Attaches to: taxonomy, engineering_design, growth_media, ecological_interactions#Inferred Hydrogen Cofactor Reductive-Dechlorination Module
+
+
+
+
+
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which inferred functions actually mediate the observed amendment response?
+
+
Positive substrate-amendment effects remain distinct from metagenome-inferred coupling. The retrieved abstract does not resolve intergenus transfer, necessary cofactors or functional perturbations; the publisher full text was not retrieved. Keep the two existing nodes without inventing a module-to-removal arrow. Prior removal of syntrophy assertions and dangling phenotype arrows is preserved.
+
Attaches to: ecological_interactions#Inferred Hydrogen Cofactor Reductive-Dechlorination Module, ecological_interactions#Co-Metabolic Substrate Enhanced TCP Removal
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination"
+
The abstract attributes this coupled module to community and metagenomic analyses; it does not independently demonstrate transfer or assign each function to a named genus.
+
Evidence
nodes.push({
id: intId,
- label: "Hydrogen Cofactor Reductive-Dechlorination Module",
+ label: "Inferred Hydrogen Cofactor Reductive-Dechlorination Module",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html b/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html
index ac44cbf73..1f03149b0 100644
--- a/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html
+++ b/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html
@@ -569,7 +569,7 @@ Ecological Interactions
Ecological interaction network for Yarrowia lipolytica Division-of-Labor Lipid Consortium
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for niche partitioning.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for niche partitioning. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -580,16 +580,20 @@
Ecological Interactions
aria-hidden="true" data-symbol="symbolSquare2"
data-color="#1212ed"> Niche partitioning
+
+
-
The two engineered Y. lipolytica members partition lignocellulose oligosaccharide use between a cellobiose-specialized YBGL3 or YBGL1 strain and a xylooligosaccharide-specialized YBXT-XR strain, creating a mixed-substrate consortium rather than burdening one strain with every hydrolysis and assimilation function.
+
YBGL3 and YBXT-XR distribute cellobiose and xylooligosaccharide hydrolysis, respectively. Both can use glucose, and the experiments did not achieve simultaneous glucose/xylose consumption. The tested coculture uses YBGL3, not an interchangeable YBGL1 partner. Division of enzyme production is not proof of reduced competition, cross-feeding or relief of a demonstrated prohibitive metabolic burden.
@@ -618,23 +622,6 @@
Cellobiose-Xylooligosaccharide Division of Labor
-
Biological Processes:
-
-
-
- cellulose catabolic process
- (GO:0030245 )
-
-
-
- xylan catabolic process
- (GO:0045493 )
-
-
-
-
@@ -642,12 +629,12 @@
Cellobiose-Xylooligosaccharide Division of Labor
→ Population Shift to YBXT-XR
-
Cellobiose depletion precedes enrichment of YBXT-XR and preferential use of the remaining xylooligosaccharides for lipid synthesis.
+
PARTIAL: Differential substrate capacities are consistent with the population shift after cellobiose depletion. The time course supports temporal succession but does not isolate depletion from other changing culture conditions.
-
→ Enhanced Lipid Accumulation
-
Distributed oligosaccharide hydrolysis and assimilation yielded higher lipid accumulation than the multifunctional monoculture benchmark.
+
→ Higher Lipid Fraction in the 1:5 Consortium
+
PARTIAL: The tested division-of-labor design yielded the higher final lipid fraction in the nitrogen-limited 1:5 consortium. The comparison does not identify burden relief as mediator or establish superior titer or performance at every inoculum ratio.
@@ -670,6 +657,19 @@
Evidence
+
+
+
+ "the YBGL3 + YBXT-XR cocultures"
+
+
+
Evidence
Population Shift to YBXT-XR
NICHE_PARTITIONING
- After the consortium depleted cellobiose, the YBXT-XR member became predominant and consumed the remaining xylooligosaccharides mostly for lipid synthesis.
+ In the mixed-substrate cocultures, YBXT-XR became predominant after cellobiose depletion, while YBGL3 could not use the remaining xylose resource. This is observed temporal succession consistent with differential substrate use, not proof that engineered partners avoid early glucose competition or that depletion was selectively manipulated as the sole cause.
@@ -745,10 +745,9 @@ Evidence
-
The distributed, two-strain consortium accumulated a greater lipid fraction than the single multifunctional YBXT-XR-BGL3 monoculture under comparable mixed-oligosaccharide conditions.
+
The nitrogen-limited 1:5 YBGL3:YBXT-XR consortium reached a lipid fraction of 34% versus 26.3% in the multifunctional monoculture. The best consortium and monoculture reached comparable lipid titers, while the 1:2 consortium performed worse. A higher lipid fraction is not a general increase in titer, growth or productivity, nor evidence of lower metabolic burden.
@@ -804,6 +803,19 @@
Evidence
+
+
+
+ "the 1:5 consortium ultimately reached a comparable lipid titer at 168 h"
+
+
+
Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which strain-level processes account for the lipid-fraction difference without a titer advantage?
+
+
The full-text Results and Discussion identify YBGL3/YBXT-XR, shared glucose use and an inoculum-dependent outcome. Distinguish lipid fraction from titer and rate, and substrate succession from true co-consumption. Resolve apparent Methods/Results inoculum-ratio wording inconsistencies before extending quantitative metadata. The source is bioRxiv version 1, not certified peer-reviewed evidence.
+
+
Attaches to: ecological_interactions#Oligosaccharide Hydrolysis Division of Labor, ecological_interactions#Population Shift to YBXT-XR, ecological_interactions#Higher Lipid Fraction in the 1:5 Consortium
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
the 1:5 consortium ultimately reached a comparable lipid titer at 168 h
+
The primary comparison limits the performance claim.
+
+
+
+
@@ -1110,7 +1159,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1121,17 +1170,11 @@ Evidence
var processes = [];
-
- processes.push("cellulose catabolic process");
-
- processes.push("xylan catabolic process");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Cellobiose-Xylooligosaccharide Division of Labor",
+ label: "Oligosaccharide Hydrolysis Division of Labor",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1206,7 +1249,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1219,11 +1262,11 @@ Evidence
processes.push("lipid biosynthetic process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Enhanced Lipid Accumulation",
+ label: "Higher Lipid Fraction in the 1:5 Consortium",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html b/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html
index 5ade005d6..3daab105a 100644
--- a/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html
+++ b/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html
@@ -600,7 +600,7 @@ Ecological Interactions
Ecological interaction network for Yogurt Two-Species Starter Culture
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding, mutualism, colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -613,13 +613,8 @@
Ecological Interactions
-
-
@@ -630,7 +625,7 @@ Ecological Interactions
Streptococcus Formate and Carbon Dioxide Support
CROSS_FEEDING
- S. thermophilus produces formate and carbon dioxide-linked growth factors that stimulate L. delbrueckii subsp. bulgaricus, accelerating yogurt fermentation and acidification.
+ PARTIAL mechanistic model: supplementation and transcriptome responses in S. thermophilus CNRZ1066 with L. bulgaricus ATCC BAA-365 support formate-related nutritional assistance. Carbon-dioxide provision is inferred rather than a quantified transfer in that study; urease experiments distinguish CO2-responsive from unresponsive lactobacillus strains. This species-level record combines exact strain-pair studies, not one universally beneficial pair.
Source Taxon: Streptococcus thermophilus
@@ -685,7 +680,7 @@ Evidence
PMID:20889781
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"formic acid, folic acid, and fatty acids are provided by S. thermophilus"
@@ -698,7 +693,7 @@ Evidence
PMID:20889781
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"folic acid and carbon dioxide"
@@ -711,7 +706,7 @@ Evidence
PMID:24936380
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"earlier l-lactate and formate accumulation"
@@ -727,7 +722,7 @@ Evidence
Lactobacillus Proteolytic Nitrogen Support
CROSS_FEEDING
- L. delbrueckii subsp. bulgaricus releases peptides and amino acids from milk proteins, supporting S. thermophilus growth and acidification in milk.
+ L. bulgaricus proteolysis supplies peptides and amino acids that support S. thermophilus in milk. The CNRZ1066/ATCC BAA-365 experiments support this contribution but show that it does not satisfy all sulfur and branched-chain amino-acid demands. LMG 18311/ATCC 11842 expression responses are contextual evidence, not a direct nitrogen-flux measurement or proof of reciprocal final growth benefit.
Source Taxon: Lactobacillus delbrueckii subsp. bulgaricus
@@ -776,8 +771,7 @@ Lactobacillus Proteolytic Nitrogen Support
→ Streptococcus Formate and Carbon Dioxide Support
-
Proteolytic nitrogen released by L. delbrueckii supports S. thermophilus growth, enabling the formate and carbon dioxide return flow that accelerates protocooperative acidification.
-
+
HYPOTHESIZED mediation: nitrogen support can sustain S. thermophilus growth and hence potential return metabolites. The cited strain-pair experiments do not selectively establish proteolysis as the cause of formate/CO2 return flow; this is not a demonstrated universal feedback loop.
@@ -806,7 +800,7 @@ Evidence
PMID:19114510
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"implicated mainly in the metabolism of nitrogen"
@@ -820,16 +814,19 @@ Evidence
-
S. thermophilus urease activity generates ammonia nitrogen and carbon dioxide effects that help maintain rapid acidification during protocooperative yogurt fermentation.
+
Urease-deficient S. thermophilus mutants and supplementation experiments support a contribution of urease to rapid yogurt acidification across the tested strain combinations. Ammonia shortage mainly limits S. thermophilus, whereas CO2 shortage affects responsive L. bulgaricus strains. The culture-level benefit is not equivalent to direct reciprocal benefit of every strain pair; ammonia effects were stronger and coculture could mask the deficiency.
-
Source Taxon: Streptococcus thermophilus
+
Participating Taxa:
-
Target Taxon: Lactobacillus delbrueckii subsp. bulgaricus
+ Streptococcus thermophilus,
+
+ Lactobacillus delbrueckii subsp. bulgaricus
+
+
@@ -885,17 +882,20 @@
Evidence
-
S. thermophilus NADH oxidase removes dissolved oxygen in milk, allowing faster coculture fermentation with L. delbrueckii subsp. bulgaricus.
+
In the S. thermophilus 1131/L. bulgaricus 2038 pair, disrupting S. thermophilus nox reduced oxygen removal and slowed skim-milk acidification. Pre-fermentation deoxygenation mainly accelerated early S. thermophilus growth and formate/lactate accumulation, not L. bulgaricus growth; final Streptococcus counts converged. This is a fermentation phenotype, not colonization facilitation. A direct Nox-to-Pfl mechanism remains HYPOTHESIZED.
-
Source Taxon: Streptococcus thermophilus
+
Participating Taxa:
-
Target Taxon: Lactobacillus delbrueckii subsp. bulgaricus
+ Streptococcus thermophilus,
+
+ Lactobacillus delbrueckii subsp. bulgaricus
+
+
@@ -919,7 +919,7 @@
Oxygen Removal by Streptococcus Thermophilus
→ Streptococcus Formate and Carbon Dioxide Support
-
S. thermophilus oxygen removal relieves dissolved-oxygen suppression of yogurt fermentation and is associated with earlier formate accumulation during the two-species acidification process.
+
PARTIAL: Oxygen removal promotes early formate accumulation in the 1131/2038 system, and the nox mutant lacks detected formate in the tested monoculture. Protection of oxygen-sensitive Pfl is HYPOTHESIZED; the study also considers other Nox functions and does not establish the CO2 branch or universal transfer to L. bulgaricus.
@@ -955,6 +955,19 @@
Evidence
+
+
+
+ "deoxygenated fermentation primarily increased the cell number of S. thermophilus 1131 rather than that of L. bulgaricus 2038"
+
+
+
Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which return-flow mechanisms and benefits hold for each tested strain pair and growth stage?
+
+
Keep the CNRZ1066/ATCC BAA-365 nutritional model, LMG 18311/ATCC 11842 expression study, 1131/2038 Nox experiment and urease strain panel separate. In the LMG 18311 pair, faster acidification accompanied lower final lactobacillus counts. In the Nox study, early effects did not imply a higher final Streptococcus yield. Nutrient supplementation and knockout phenotypes remain positive evidence without universal mutualism or proven mediation.
+
+
Attaches to: ecological_interactions#Streptococcus Formate and Carbon Dioxide Support, ecological_interactions#Lactobacillus Proteolytic Nitrogen Support, ecological_interactions#Urease-Dependent Acidification Acceleration, ecological_interactions#Streptococcus Nox-Dependent Milk Fermentation
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
the coculture resulted in a threefold decrease of the final bacterial counts
+
Faster coculture acidification did not imply a final population benefit to both partners.
+
+
+
+
@@ -1455,7 +1507,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1477,23 +1529,26 @@ Evidence
});
- var srcKey = "Streptococcus thermophilus";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Lactobacillus delbrueckii subsp. bulgaricus";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Streptococcus thermophilus",
+
+ "Lactobacillus delbrueckii subsp. bulgaricus"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:3";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1502,11 +1557,11 @@ Evidence
processes.push("fermentation");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "Oxygen Removal by Streptococcus Thermophilus",
+ label: "Streptococcus Nox-Dependent Milk Fermentation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1515,17 +1570,20 @@ Evidence
});
- var srcKey = "Streptococcus thermophilus";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Lactobacillus delbrueckii subsp. bulgaricus";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Streptococcus thermophilus",
+
+ "Lactobacillus delbrueckii subsp. bulgaricus"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html b/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html
index 76fae9a4c..6099bcf34 100644
--- a/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html
+++ b/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html
@@ -606,7 +606,7 @@ Ecological Interactions
Zymomonas Amino Acid Rescue of E. coli Auxotrophs
CROSS_FEEDING
- Z. mobilis releases amino acid exometabolites in spent medium, and those exometabolites were used to select E. coli proA, pheA, and ilvA auxotrophs as coculture partners.
+ Wild-type Z. mobilis ZM4 spent medium and individual amino-acid supplementation rescued the selected E. coli proA, pheA and ilvA auxotrophs. This supports nutritional rescue, beyond candidate selection alone. The reciprocal experiments paired each E. coli mutant separately with the Z. mobilis ZMO0748 mutant; they do not describe a four-member consortium or establish a dedicated export mechanism.
Source Taxon: Zymomonas mobilis
@@ -645,8 +645,7 @@ Zymomonas Amino Acid Rescue of E. coli Auxotrophs
→ Reciprocal Auxotroph Coculture Growth
-
Z. mobilis amino acid exometabolites rescue E. coli amino acid auxotrophs selected for the validated reciprocal cocultures.
-
+
Partner spent-medium and amino-acid rescue support the nutritional contribution to the three separately tested reciprocal pairs. The molecular release route and all additional interactions are not resolved.
@@ -682,16 +681,29 @@ Evidence
+
+
+
+ "they all successfully grew in 50% spent medium and metabolite supplemented medium"
+
+
+
-
E. coli spent medium contained glutathione-related metabolites that were identified as potential rescue compounds for the Z. mobilis ZMO0748 cysteine synthase-like auxotroph.
+
E. coli spent medium rescued the Z. mobilis ZMO0748 cysteine-synthase-like mutant. Cysteine and glutathione supplementation independently supported rescue. Glutathione-related compounds were detected in spent medium, but free cysteine below detection was not excluded. Thus the phenotype is experimentally supported while the exact naturally transferred sulfur compound and release/uptake route remain PARTIAL.
Source Taxon: Escherichia coli
@@ -730,8 +742,7 @@
E. coli Glutathione-Related Rescue of Zymomonas Auxotroph
→ Reciprocal Auxotroph Coculture Growth
-
E. coli glutathione-related metabolites are candidate rescue compounds for the Z. mobilis ZMO0748 auxotroph used in the reciprocal cocultures.
-
+
PARTIAL molecular assignment: sulfur-metabolite rescue supports the ZMO0748 contribution to reciprocal growth, and glutathione is sufficient in supplementation. Its exclusive necessity in coculture and the exact exchanged sulfur species were not established.
Evidence
PMID:26885935
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"identified glutathione related metabolites as potentially available for rescue"
@@ -760,13 +771,26 @@ Evidence
PMID:26885935
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"rescue of the Z. mobilis cysteine synthase mutant"
+
+
+
+ "both cysteine and glutathione are capable of rescuing Z. mobilis"
+
+
+
@@ -776,7 +800,7 @@ Evidence
Reciprocal Auxotroph Coculture Growth
MUTUALISM
- The selected Z. mobilis auxotroph was tested in coculture with each of the three E. coli auxotrophs, and growth of both species was confirmed by optical density and flow cytometry.
+ Each of three separate pairs containing the Z. mobilis ZMO0748 auxotroph and an E. coli proA, pheA or ilvA auxotroph grew in unsupplemented ZMMG, where the individual auxotrophs did not. Optical density and species-resolved flow cytometry support growth of both partners under those conditions. This does not establish long-term community stability or the absence of additional beneficial or inhibitory exchanges.
Source Taxon: Zymomonas mobilis
@@ -833,6 +857,19 @@ Evidence
+
+
+
+ "analyzed by flow cytometry to confirm high cell counts for each species"
+
+
+
@@ -842,6 +879,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which sulfur species and cellular release/uptake routes mediate rescue in the live pairs?
+
+
Do not downgrade the positive spent-medium, supplementation and reciprocal-growth controls to mere correlation. Distinguish those controls from exclusive glutathione necessity and active secretion: alternative sulfur compounds and release by extracellular processing or lysis remain possible. The three pairs were tested separately; longitudinal stability was outside the reported experiment.
+
+
Attaches to: ecological_interactions#Zymomonas Amino Acid Rescue of E. coli Auxotrophs, ecological_interactions#E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph, ecological_interactions#Reciprocal Auxotroph Coculture Growth
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
identified glutathione related metabolites as potentially available for rescue
+
The abstract itself distinguishes candidate sulfur metabolites from the demonstrated growth phenotype.
+
+
+
+
@@ -1217,7 +1293,7 @@ Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1259,11 +1335,11 @@ Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "E. coli Glutathione-Related Rescue of Zymomonas Auxotroph",
+ label: "E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1297,7 +1373,7 @@ Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
diff --git a/docs/communities/hCom2_Complex_Gut_Microbiome.html b/docs/communities/hCom2_Complex_Gut_Microbiome.html
index df41ade82..3ac8940f8 100644
--- a/docs/communities/hCom2_Complex_Gut_Microbiome.html
+++ b/docs/communities/hCom2_Complex_Gut_Microbiome.html
@@ -516,7 +516,7 @@ Ecological Interactions
Ecological interaction network for hCom2 Complex Gut Microbiome
- Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for colonization facilitation.
+ Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
@@ -524,8 +524,8 @@
Ecological Interactions
@@ -533,10 +533,9 @@ Ecological Interactions
-
Species that engrafted after hCom1 fecal challenge were added to the defined gut consortium, filling open ecological niches to yield hCom2.
+
Species identified after challenging hCom1-colonized mice with fecal communities informed the assembly of hCom2. The intervention changes community membership; filling open niches is its ecological interpretation, not a directly measured complete metabolic or spatial niche map.
@@ -563,12 +562,12 @@
Fecal-Challenge Open Niche Filling
→ hCom2 Fecal-Challenge Stability
-
Filling hCom1's open niches with engrafting gut species produced hCom2's higher stability when challenged again with human fecal microbiota.
+
Membership augmentation produced a community with greater fecal-challenge resilience in the tested mice. PARTIAL mechanism: niche occupancy is a proposed explanation rather than a selectively measured mediator, and unrelated donors expose residual invasibility.
→ hCom2 Escherichia coli Colonization Resistance
-
Occupying the open gut niches left in hCom1 produced a more complete hCom2 consortium that resisted pathogenic Escherichia coli colonization.
+
HYPOTHESIZED mediation: broader niche occupancy could contribute to hCom2 resistance, but observing resistance in hCom2 does not establish that the augmentation step or any added species is necessary. The study does not resolve the protective strains or molecular pathway.
Evidence
-
The augmented hCom2 community remains more stable than hCom1 when challenged with a human fecal community in gnotobiotic mice.
+
In gnotobiotic mice, hCom2 was more resilient than hCom1 to fecal challenge. The primary study also reports weaker resilience to unrelated fecal donors. Stability is therefore donor- and experiment-dependent, not complete exclusion or universal human-microbiome equivalence.
@@ -636,7 +634,7 @@
Evidence
- SUPPORT (IN_VIVO)
"We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2."
+ "hCom2 exhibited increased stability to fecal challenge"
@@ -647,9 +645,8 @@ Evidence
-
The niche-filled hCom2 consortium provides robust colonization resistance against pathogenic Escherichia coli in gnotobiotic mice.
+
hCom2 conferred robust resistance to the tested pathogenic E. coli challenge in gnotobiotic mice. The phenotype is community-level resistance, not facilitation of the invader and not proof that each bacterial member is protective. The responsible strains and molecular mechanism remain unresolved.
@@ -685,7 +682,7 @@
Evidence
- SUPPORT (IN_VIVO)
"We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2."
+ "robust colonization resistance against pathogenic Escherichia coli"
@@ -698,6 +695,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which membership changes and ecological mechanisms cause the challenge phenotypes?
+
+
Preserve the augmented-community and pathogenic-challenge outcomes without assigning colonization-facilitation labels. Phylum-dropout results narrow candidate explanations but do not identify a necessary individual strain or distinguish direct protection from altered community architecture. Unrelated-donor invasion limits universal stability. Existing non-graph re-evidencing debt remains under issue 765; no restricted article body is reintroduced into the repository.
+
+
Attaches to: ecological_interactions#Fecal-Challenge-Guided Community Augmentation, ecological_interactions#hCom2 Fecal-Challenge Stability, ecological_interactions#hCom2 Escherichia coli Colonization Resistance
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
robust colonization resistance against pathogenic Escherichia coli
+
Direct abstract evidence for the challenge phenotype; assembly alone is not outcome evidence.
+
+
+
+
@@ -866,7 +902,7 @@
(function() {
var intId = "interaction:0";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -879,7 +915,7 @@
nodes.push({
id: intId,
- label: "Fecal-Challenge Open Niche Filling",
+ label: "Fecal-Challenge-Guided Community Augmentation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -894,7 +930,7 @@
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -922,7 +958,7 @@
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
diff --git a/history/records/AM_AB_Chlorella_MLSS_Wastewater_Consortium/2026-10-08T175132Z-codex-665b31.yaml b/history/records/AM_AB_Chlorella_MLSS_Wastewater_Consortium/2026-10-08T175132Z-codex-665b31.yaml
new file mode 100644
index 000000000..c8847ff66
--- /dev/null
+++ b/history/records/AM_AB_Chlorella_MLSS_Wastewater_Consortium/2026-10-08T175132Z-codex-665b31.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml
+ slug: AM_AB_Chlorella_MLSS_Wastewater_Consortium
+session:
+ id: 2026-10-08T175132Z-codex-665b31
+ timestamp: '2026-10-08T17:51:32Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1968
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Review empty graph against full-text controls; retain a substantive extension gap
+ without inventing nodes, and update the stale abstract-access discussion.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
diff --git a/history/records/TCP_NonDehalogenimonas_Groundwater_Consortium/2026-10-08T175132Z-codex-e21077.yaml b/history/records/TCP_NonDehalogenimonas_Groundwater_Consortium/2026-10-08T175132Z-codex-e21077.yaml
new file mode 100644
index 000000000..51dca9cb4
--- /dev/null
+++ b/history/records/TCP_NonDehalogenimonas_Groundwater_Consortium/2026-10-08T175132Z-codex-e21077.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml
+ slug: TCP_NonDehalogenimonas_Groundwater_Consortium
+session:
+ id: 2026-10-08T175132Z-codex-e21077
+ timestamp: '2026-10-08T17:51:32Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1963
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Qualify reconstructed coupling and correct computational provenance without genus-specific
+ functions.; Retain positive amendment and removal endpoints without assigning culture-wide
+ rates to each substrate.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
diff --git a/history/records/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium/2026-10-08T175133Z-codex-bf87bc.yaml b/history/records/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium/2026-10-08T175133Z-codex-bf87bc.yaml
new file mode 100644
index 000000000..ce618931c
--- /dev/null
+++ b/history/records/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium/2026-10-08T175133Z-codex-bf87bc.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml
+ slug: Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium
+session:
+ id: 2026-10-08T175133Z-codex-bf87bc
+ timestamp: '2026-10-08T17:51:33Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1964
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain engineered hydrolysis division without polymer-catabolism, exclusive-niche
+ or burden-relief overclaims.; Retain temporal succession while qualifying its mechanism.;
+ Retain the condition-specific lipid-fraction benefit and comparable-titer counterpoint.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
diff --git a/history/records/Yogurt_TwoSpecies_Starter_Culture/2026-10-08T175133Z-codex-114f8d.yaml b/history/records/Yogurt_TwoSpecies_Starter_Culture/2026-10-08T175133Z-codex-114f8d.yaml
new file mode 100644
index 000000000..f29af02d8
--- /dev/null
+++ b/history/records/Yogurt_TwoSpecies_Starter_Culture/2026-10-08T175133Z-codex-114f8d.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml
+ slug: Yogurt_TwoSpecies_Starter_Culture
+session:
+ id: 2026-10-08T175133Z-codex-114f8d
+ timestamp: '2026-10-08T17:51:33Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1965
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Qualify the strain-specific formate/CO2 model.; Retain nitrogen support without
+ nutritional sufficiency or demonstrated return-flow mediation.; Represent the urease effect
+ at culture level with distinct ammonia/CO2 recipients.; Preserve the Nox intervention
+ and early-growth evidence without colonization or universal-recipient claims.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
diff --git a/history/records/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism/2026-10-08T175133Z-codex-2cd46c.yaml b/history/records/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism/2026-10-08T175133Z-codex-2cd46c.yaml
new file mode 100644
index 000000000..ccdf483b1
--- /dev/null
+++ b/history/records/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism/2026-10-08T175133Z-codex-2cd46c.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml
+ slug: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+session:
+ id: 2026-10-08T175133Z-codex-2cd46c
+ timestamp: '2026-10-08T17:51:33Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1966
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain experimental amino-acid rescue and distinguish three alternative pairs.;
+ Retain sulfur-rescue controls while qualifying the exact transferred compound.; Retain
+ condition-specific obligate growth and species-resolved counts without long-term stability
+ claims.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
diff --git a/history/records/hCom2_Complex_Gut_Microbiome/2026-10-08T175134Z-codex-9059ef.yaml b/history/records/hCom2_Complex_Gut_Microbiome/2026-10-08T175134Z-codex-9059ef.yaml
new file mode 100644
index 000000000..7e97c4971
--- /dev/null
+++ b/history/records/hCom2_Complex_Gut_Microbiome/2026-10-08T175134Z-codex-9059ef.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/hCom2_Complex_Gut_Microbiome.yaml
+ slug: hCom2_Complex_Gut_Microbiome
+session:
+ id: 2026-10-08T175134Z-codex-9059ef
+ timestamp: '2026-10-08T17:51:34Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1967
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain augmentation while separating niche-filling interpretation from measurement.;
+ Re-evidence the stability endpoint and preserve unrelated-donor limits.; Re-evidence community
+ resistance without facilitation typing or strain-specific causality.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
diff --git a/kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml b/kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml
index 2814d88e9..9c2c27ea5 100644
--- a/kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml
+++ b/kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml
@@ -190,31 +190,56 @@ external_resources:
explanation: Supports the DOI assigned to the primary AM-AB consortium publication.
discussions:
- discussion_id: am_ab_hrAp_conditions
- prompt: Which wastewater source and initial chemistry, MLSS source, bacterial activation procedure, HRAP geometry, working
- volume, retention time, outdoor light and temperature regime, and inoculation ratio were used for the AM-AB Chlorella-MLSS
- consortium?
+ prompt: Which reported HRAP conditions can now be curated from the full text, and which outdoor operating conditions
+ remain unspecified?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- taxonomy#Activated MLSS bacterial consortium
- growth_media#wastewater outdoor HRAP medium
- cultivation_setup
- rationale: The PubMed abstract names the Chlorella vulgaris/MLSS partners, separate activation before AM-AB assembly, outdoor
- HRAP cultivation, and the nitrogen, phosphate, ammonia, and BOD endpoints, but it does not report the underlying wastewater
- chemistry, mixed-liquor source, MLSS activation recipe, inoculation ratio, or HRAP operating conditions.
+ rationale: The full primary Methods and Tables 1-3 are now available and identify wastewater/sludge sources, activation,
+ pond geometry, inoculation and initial chemistry. These are no longer abstract-access gaps. Reconcile the non-graph
+ fields with those sections; do not transfer indoor algal-stock light and temperature settings to outdoor treatment.
+ The graph review leaves that metadata curation separate.
+- discussion_id: am_ab_control_bounded_graph_extension
+ prompt: Which consortium-level treatment effects and qualified mechanisms belong in the currently empty graph?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions
+ rationale: The primary study compares the combined culture with activated algae alone. Retain improved late total-nitrogen
+ removal, but early nitrogen removal is slower, phosphate reaches the detection limit in both conditions, and
+ BOD removal is not uniformly better. Biomass correlations do not establish a transfer mechanism. New nodes require
+ a separately authorized Edison causal-graph review; none were added in this repair pass.
+ evidence:
+ - reference: PMID:42429207
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: phycoremediation using the AM–AB consortium delayed the removal of nitrogen compared to standalone
+ activated C. vulgaris treatment
+ explanation: The algae-only control prevents an unqualified faster-removal or universal-synergy graph.
+ posed_by: codex
+ posed_date: '2026-10-08'
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare-earth processing role is reported for the AM-AB Chlorella-MLSS wastewater consortium.
curation_history:
- timestamp: '2026-09-27T01:25:49Z'
curator: codex
action: CREATE_AM_AB_CHLORELLA_MLSS_WASTEWATER_CONSORTIUM
- changes: Created CommunityMech:000444 from PMID:42429207 and DOI 10.1002/wer.70489 with evidence-backed C. vulgaris and
- activated MLSS bacterial membership, AM-AB assembly, outdoor HRAP wastewater-treatment context, and nitrogen, phosphate,
- and BOD endpoints.
+ changes: Created CommunityMech:000444 from PMID:42429207 and DOI 10.1002/wer.70489 with evidence-backed C. vulgaris
+ and activated MLSS bacterial membership, AM-AB assembly, outdoor HRAP wastewater-treatment context, and nitrogen,
+ phosphate, and BOD endpoints.
llm_assisted: true
- timestamp: '2026-09-27T01:32:47Z'
curator: codex
action: FIX_AM_AB_ENVIRONMENT_TERM
- changes: Addressed issue 1130 by regrounding the AM-AB outdoor HRAP environment from laboratory environment to wastewater
- treatment plant while keeping the wastewater treatment matrix under modeled_environment.
+ changes: Addressed issue 1130 by regrounding the AM-AB outdoor HRAP environment from laboratory environment to
+ wastewater treatment plant while keeping the wastewater treatment matrix under modeled_environment.
+ llm_assisted: true
+- timestamp: '2026-10-08T17:51:29Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Review empty graph against full-text controls; retain a substantive extension gap without inventing nodes,
+ and update the stale abstract-access discussion. Issue#1968; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
llm_assisted: true
diff --git a/kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml b/kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml
index 667ef0a23..730add63e 100644
--- a/kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml
+++ b/kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml
@@ -110,9 +110,10 @@ taxonomy:
and Parabacteroides
explanation: Identifies Parabacteroides as one of the four genera comprising the synergistic TCP-transforming consortium.
ecological_interactions:
-- name: Hydrogen Cofactor Reductive-Dechlorination Module
- description: Metagenomic analysis connected the four-genus synergistic alliance to a coupled metabolic module containing
- hydrogen production, cofactor synthesis, and reductive dechlorination functions during TCP transformation.
+- name: Inferred Hydrogen Cofactor Reductive-Dechlorination Module
+ description: 'HYPOTHESIZED functional coupling: community and metagenomic analyses associate the four named genera
+ with hydrogen production, cofactor synthesis and reductive dechlorination. This is a consortium-level reconstruction,
+ not measured intergenus hydrogen/cofactor transfer or a demonstrated genus-specific dechlorination pathway.'
scope: COMMUNITY_LEVEL
participating_taxa: &id001
- preferred_term: Fusibacter
@@ -148,14 +149,22 @@ ecological_interactions:
label: halogenated hydrocarbon metabolic process
evidence:
- reference: PMID:41736479
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination"
- explanation: Supports a consortium-level module that combines hydrogen production, cofactor synthesis, and TCP reductive
- dechlorination.
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive
+ dechlorination"
+ explanation: The abstract attributes this coupled module to community and metagenomic analyses; it does not
+ independently demonstrate transfer or assign each function to a named genus.
+ computational_provenance:
+ prediction_type: OTHER
+ model_source: Community and metagenomic analyses described in the primary abstract.
+ input_accession: PMID:41736479
+ parameters: Genus-level coupled-module interpretation; exact tools, genomes, versions and flux measurements
+ were not available in the retrieved abstract. No FBA or interaction simulation is asserted.
- name: Co-Metabolic Substrate Enhanced TCP Removal
- description: Sodium acetate and lactate stimulation increased the consortium's TCP degradation efficiency and supported
- complete removal in the domesticated culture.
+ description: Sodium acetate and lactate amendments enhanced TCP degradation in the domesticated consortium. The
+ abstract reports an overall average degradation rate of 19.06 umol L-1 d-1 and complete removal within 3.5 days;
+ those values are not separately assigned to each amendment or to an individual genus.
scope: COMMUNITY_LEVEL
participating_taxa: *id001
metabolites:
@@ -289,28 +298,49 @@ related_ingredients:
associated_datasets: []
discussions:
- discussion_id: tcp_nondehalogenimonas_species_roles_and_dosing
- prompt: Resolve species or strain IDs, initial inoculum source, the directed domestication passaging regimen, quantitative
- member abundances, co-metabolic substrate concentrations, and genus-specific assignment of hydrogen-production, cofactor-synthesis,
- and reductive-dechlorination roles.
+ prompt: Resolve species or strain IDs, initial inoculum source, the directed domestication passaging regimen,
+ quantitative member abundances, co-metabolic substrate concentrations, and genus-specific assignment of hydrogen-production,
+ cofactor-synthesis, and reductive-dechlorination roles.
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- taxonomy
- engineering_design
- growth_media
- - ecological_interactions#Hydrogen Cofactor Reductive-Dechlorination Module
+ - ecological_interactions#Inferred Hydrogen Cofactor Reductive-Dechlorination Module
rationale: The accessible PubMed abstract names the four-genera consortium and overall hydrogen/cofactor/reductive-dechlorination
- module, but it does not expose species or strain IDs, original inoculum details, full medium composition, substrate concentrations,
- transfer cadence, or the role of each named genus within the module.
+ module, but it does not expose species or strain IDs, original inoculum details, full medium composition, substrate
+ concentrations, transfer cadence, or the role of each named genus within the module.
posed_by: codex
posed_date: '2026-09-26'
+- discussion_id: tcp_module_mediation_vs_amendment_response
+ prompt: Which inferred functions actually mediate the observed amendment response?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Inferred Hydrogen Cofactor Reductive-Dechlorination Module
+ - ecological_interactions#Co-Metabolic Substrate Enhanced TCP Removal
+ rationale: Positive substrate-amendment effects remain distinct from metagenome-inferred coupling. The retrieved
+ abstract does not resolve intergenus transfer, necessary cofactors or functional perturbations; the publisher
+ full text was not retrieved. Keep the two existing nodes without inventing a module-to-removal arrow. Prior
+ removal of syntrophy assertions and dangling phenotype arrows is preserved.
+ evidence:
+ - reference: PMID:41736479
+ supports: PARTIAL
+ evidence_source: COMPUTATIONAL
+ snippet: realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive
+ dechlorination"
+ explanation: The abstract attributes this coupled module to community and metagenomic analyses; it does not
+ independently demonstrate transfer or assign each function to a named genus.
+ posed_by: codex
+ posed_date: '2026-10-08'
curation_history:
- timestamp: '2026-09-26T13:58:15Z'
curator: codex
action: ADD_COMMUNITY_RECORD
- changes: Created CommunityMech:000437 from PMID:41736479 and DOI 10.1002/wer.70318 for the long-term domesticated TCP-degrading
- non-Dehalogenimonas groundwater-bioremediation consortium containing Fusibacter, Desulfovibrio, Nitratidesulfovibrio,
- and Parabacteroides genus-level members.
+ changes: Created CommunityMech:000437 from PMID:41736479 and DOI 10.1002/wer.70318 for the long-term domesticated
+ TCP-degrading non-Dehalogenimonas groundwater-bioremediation consortium containing Fusibacter, Desulfovibrio,
+ Nitratidesulfovibrio, and Parabacteroides genus-level members.
llm_assisted: true
- timestamp: '2026-09-26T14:03:55Z'
curator: codex
@@ -319,3 +349,10 @@ curation_history:
from the abstract-backed four-genus module and by dropping two dangling downstream edges that pointed at a non-existent
TCP Bioremediation Performance interaction.
llm_assisted: true
+- timestamp: '2026-10-08T17:51:30Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Qualify reconstructed coupling and correct computational provenance without genus-specific functions.;
+ Retain positive amendment and removal endpoints without assigning culture-wide rates to each substrate. Issue#1963;
+ reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ llm_assisted: true
diff --git a/kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml b/kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml
index 8cef57ff5..b73c8a283 100644
--- a/kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml
+++ b/kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml
@@ -184,14 +184,11 @@ related_ingredients:
Supports lipid as the enhanced target product of the division-of-labor
consortium relative to the multifunctional monoculture.
ecological_interactions:
-- name: Cellobiose-Xylooligosaccharide Division of Labor
- description: >-
- The two engineered Y. lipolytica members partition lignocellulose
- oligosaccharide use between a cellobiose-specialized YBGL3 or YBGL1 strain
- and a xylooligosaccharide-specialized YBXT-XR strain, creating a
- mixed-substrate consortium rather than burdening one strain with every
- hydrolysis and assimilation function.
- interaction_type: NICHE_PARTITIONING
+- name: Oligosaccharide Hydrolysis Division of Labor
+ description: YBGL3 and YBXT-XR distribute cellobiose and xylooligosaccharide hydrolysis, respectively. Both can
+ use glucose, and the experiments did not achieve simultaneous glucose/xylose consumption. The tested coculture
+ uses YBGL3, not an interchangeable YBGL1 partner. Division of enzyme production is not proof of reduced competition,
+ cross-feeding or relief of a demonstrated prohibitive metabolic burden.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: cellobiose-specialized Yarrowia lipolytica strain
@@ -211,39 +208,33 @@ ecological_interactions:
term:
id: CHEBI:18222
label: xylose
- biological_processes:
- - preferred_term: cellulose catabolic process
- term:
- id: GO:0030245
- label: cellulose catabolic process
- - preferred_term: xylan catabolic process
- term:
- id: GO:0045493
- label: xylan catabolic process
downstream:
- target: Population Shift to YBXT-XR
- description: >-
- Cellobiose depletion precedes enrichment of YBXT-XR and preferential use
- of the remaining xylooligosaccharides for lipid synthesis.
- - target: Enhanced Lipid Accumulation
- description: >-
- Distributed oligosaccharide hydrolysis and assimilation yielded higher
- lipid accumulation than the multifunctional monoculture benchmark.
+ description: 'PARTIAL: Differential substrate capacities are consistent with the population shift after cellobiose
+ depletion. The time course supports temporal succession but does not isolate depletion from other changing
+ culture conditions.'
+ - target: Higher Lipid Fraction in the 1:5 Consortium
+ description: 'PARTIAL: The tested division-of-labor design yielded the higher final lipid fraction in the nitrogen-limited
+ 1:5 consortium. The comparison does not identify burden relief as mediator or establish superior titer or
+ performance at every inoculum ratio.'
evidence:
- reference: doi:10.64898/2025.12.19.695487
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- we also developed a cellobiose-specialized strain (YBGL3 or YBGL1) and a
- xylooligosaccharide-specialized strain (YBXT-XR)
- explanation: >-
- Supports assignment of cellulose- and hemicellulose-derived
- oligosaccharides to distinct engineered Y. lipolytica specialists.
+ snippet: we also developed a cellobiose-specialized strain (YBGL3 or YBGL1) and a xylooligosaccharide-specialized
+ strain (YBXT-XR)
+ explanation: Supports assignment of cellulose- and hemicellulose-derived oligosaccharides to distinct engineered
+ Y. lipolytica specialists.
+ - reference: doi:10.64898/2025.12.19.695487
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the YBGL3 + YBXT-XR cocultures
+ explanation: The Results identify the actual coculture strain pair; BGL1 characterization is not this consortium.
- name: Population Shift to YBXT-XR
- description: >-
- After the consortium depleted cellobiose, the YBXT-XR member became
- predominant and consumed the remaining xylooligosaccharides mostly for lipid
- synthesis.
+ description: In the mixed-substrate cocultures, YBXT-XR became predominant after cellobiose depletion, while YBGL3
+ could not use the remaining xylose resource. This is observed temporal succession consistent with differential
+ substrate use, not proof that engineered partners avoid early glucose competition or that depletion was selectively
+ manipulated as the sole cause.
interaction_type: NICHE_PARTITIONING
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -273,19 +264,15 @@ ecological_interactions:
- reference: doi:10.64898/2025.12.19.695487
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- following cellobiose depletion (after 72 h), YBXT-XR became predominant
- and utilized the remaining xylooligosaccharides almost exclusively for
- lipid synthesis
- explanation: >-
- Supports the observed population shift and YBXT-XR lipid-production role
- after depletion of the cellobiose niche.
-- name: Enhanced Lipid Accumulation
- description: >-
- The distributed, two-strain consortium accumulated a greater lipid fraction
- than the single multifunctional YBXT-XR-BGL3 monoculture under comparable
- mixed-oligosaccharide conditions.
- interaction_type: NICHE_PARTITIONING
+ snippet: following cellobiose depletion (after 72 h), YBXT-XR became predominant and utilized the remaining
+ xylooligosaccharides almost exclusively for lipid synthesis
+ explanation: Supports the observed population shift and YBXT-XR lipid-production role after depletion of the
+ cellobiose niche.
+- name: Higher Lipid Fraction in the 1:5 Consortium
+ description: The nitrogen-limited 1:5 YBGL3:YBXT-XR consortium reached a lipid fraction of 34% versus 26.3% in
+ the multifunctional monoculture. The best consortium and monoculture reached comparable lipid titers, while
+ the 1:2 consortium performed worse. A higher lipid fraction is not a general increase in titer, growth or productivity,
+ nor evidence of lower metabolic burden.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: cellobiose-specialized Yarrowia lipolytica strain
@@ -310,12 +297,15 @@ ecological_interactions:
- reference: doi:10.64898/2025.12.19.695487
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >-
- the division-of-labor approach led to higher lipid accumulation (34%
- versus 26.3% in the monoculture)
- explanation: >-
- Supports the improved lipid-accumulation endpoint for the consortium
- relative to the multifunctional Y. lipolytica monoculture.
+ snippet: the division-of-labor approach led to higher lipid accumulation (34% versus 26.3% in the monoculture)
+ explanation: Supports the improved lipid-accumulation endpoint for the consortium relative to the multifunctional
+ Y. lipolytica monoculture.
+ - reference: doi:10.64898/2025.12.19.695487
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the 1:5 consortium ultimately reached a comparable lipid titer at 168 h
+ explanation: 'Bounds the higher lipid fraction: the best consortium ultimately matched, rather than exceeded,
+ monoculture titer.'
environmental_factors:
- name: Mixed lignocellulose-derived oligosaccharide substrate
value: glucose, cellobiose, and xylooligosaccharides
@@ -388,3 +378,32 @@ metal_relevance: NOT_APPLICABLE
metal_notes: >-
No metal or rare-earth processing role is reported for the engineered
Y. lipolytica lipid-production consortium.
+discussions:
+- discussion_id: yarrowia_fraction_titer_and_competing_glucose_use
+ prompt: Which strain-level processes account for the lipid-fraction difference without a titer advantage?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Oligosaccharide Hydrolysis Division of Labor
+ - ecological_interactions#Population Shift to YBXT-XR
+ - ecological_interactions#Higher Lipid Fraction in the 1:5 Consortium
+ rationale: The full-text Results and Discussion identify YBGL3/YBXT-XR, shared glucose use and an inoculum-dependent
+ outcome. Distinguish lipid fraction from titer and rate, and substrate succession from true co-consumption.
+ Resolve apparent Methods/Results inoculum-ratio wording inconsistencies before extending quantitative metadata.
+ The source is bioRxiv version 1, not certified peer-reviewed evidence.
+ evidence:
+ - reference: doi:10.64898/2025.12.19.695487
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the 1:5 consortium ultimately reached a comparable lipid titer at 168 h
+ explanation: The primary comparison limits the performance claim.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T17:51:30Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain engineered hydrolysis division without polymer-catabolism, exclusive-niche or burden-relief overclaims.;
+ Retain temporal succession while qualifying its mechanism.; Retain the condition-specific lipid-fraction benefit
+ and comparable-titer counterpoint. Issue#1964; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ llm_assisted: true
diff --git a/kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml b/kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml
index 6b0578e94..fe6b3128a 100644
--- a/kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml
+++ b/kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml
@@ -115,8 +115,11 @@ taxonomy:
explanation: Supports a strain-specific L. delbrueckii subsp. bulgaricus member in one coculture.
ecological_interactions:
- name: Streptococcus Formate and Carbon Dioxide Support
- description: S. thermophilus produces formate and carbon dioxide-linked growth factors that stimulate
- L. delbrueckii subsp. bulgaricus, accelerating yogurt fermentation and acidification.
+ description: 'PARTIAL mechanistic model: supplementation and transcriptome responses in S. thermophilus CNRZ1066
+ with L. bulgaricus ATCC BAA-365 support formate-related nutritional assistance. Carbon-dioxide provision is
+ inferred rather than a quantified transfer in that study; urease experiments distinguish CO2-responsive from
+ unresponsive lactobacillus strains. This species-level record combines exact strain-pair studies, not one universally
+ beneficial pair.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -149,23 +152,28 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
evidence:
- reference: PMID:20889781
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: formic acid, folic acid, and fatty acids are provided by S. thermophilus
- explanation: Supports formate/formic-acid transfer from S. thermophilus to L. bulgaricus.
+ explanation: The physiological/transcriptome results support a nutritional model, not a measured interspecies
+ formate flux.
- reference: PMID:20889781
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: folic acid and carbon dioxide
- explanation: Supports carbon dioxide as a growth-enhancing metabolite in the interaction.
+ explanation: This abstract phrase describes believed growth-enhancing exchange; it alone does not demonstrate
+ CO2 transfer.
- reference: PMID:24936380
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: earlier l-lactate and formate accumulation
- explanation: Supports formate accumulation during effective yogurt fermentation by the two-member culture.
+ explanation: Earlier formate accumulation was measured in the separate 1131/2038 oxygen study, not in all yogurt
+ strain pairs.
- name: Lactobacillus Proteolytic Nitrogen Support
- description: L. delbrueckii subsp. bulgaricus releases peptides and amino acids from milk proteins,
- supporting S. thermophilus growth and acidification in milk.
+ description: L. bulgaricus proteolysis supplies peptides and amino acids that support S. thermophilus in milk.
+ The CNRZ1066/ATCC BAA-365 experiments support this contribution but show that it does not satisfy all sulfur
+ and branched-chain amino-acid demands. LMG 18311/ATCC 11842 expression responses are contextual evidence, not
+ a direct nitrogen-flux measurement or proof of reciprocal final growth benefit.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -198,10 +206,9 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Streptococcus Formate and Carbon Dioxide Support
- description: >
- Proteolytic nitrogen released by L. delbrueckii supports
- S. thermophilus growth, enabling the formate and carbon dioxide return
- flow that accelerates protocooperative acidification.
+ description: 'HYPOTHESIZED mediation: nitrogen support can sustain S. thermophilus growth and hence potential
+ return metabolites. The cited strain-pair experiments do not selectively establish proteolysis as the cause
+ of formate/CO2 return flow; this is not a demonstrated universal feedback loop.'
evidence:
- reference: PMID:20889781
supports: SUPPORT
@@ -209,25 +216,18 @@ ecological_interactions:
snippet: Proteolysis by L. bulgaricus supplies both strains with amino acids
explanation: Supports nitrogen cross-feeding from proteolytic L. bulgaricus to S. thermophilus.
- reference: PMID:19114510
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: implicated mainly in the metabolism of nitrogen
- explanation: Supports nitrogen metabolism as a coculture-specific response in S. thermophilus.
+ explanation: Coculture nitrogen-metabolism responses support nutritional involvement but do not identify a measured
+ transfer flux.
- name: Urease-Dependent Acidification Acceleration
- description: S. thermophilus urease activity generates ammonia nitrogen and carbon dioxide effects that
- help maintain rapid acidification during protocooperative yogurt fermentation.
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Streptococcus thermophilus
- term:
- id: NCBITaxon:1308
- label: Streptococcus thermophilus
- target_taxon:
- preferred_term: Lactobacillus delbrueckii subsp. bulgaricus
- term:
- id: NCBITaxon:1585
- label: Lactobacillus delbrueckii subsp. bulgaricus
+ description: Urease-deficient S. thermophilus mutants and supplementation experiments support a contribution of
+ urease to rapid yogurt acidification across the tested strain combinations. Ammonia shortage mainly limits S.
+ thermophilus, whereas CO2 shortage affects responsive L. bulgaricus strains. The culture-level benefit is not
+ equivalent to direct reciprocal benefit of every strain pair; ammonia effects were stronger and coculture could
+ mask the deficiency.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fermentation
term:
@@ -243,22 +243,23 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: NH3 and CO2 that it generates
- explanation: Supports ammonia and carbon dioxide as urease-linked factors in the interaction.
-- name: Oxygen Removal by Streptococcus Thermophilus
- description: S. thermophilus NADH oxidase removes dissolved oxygen in milk, allowing faster coculture
- fermentation with L. delbrueckii subsp. bulgaricus.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Streptococcus thermophilus
+ explanation: The full abstract distinguishes ammonia nutrition of S. thermophilus from CO2 responsiveness of
+ L. bulgaricus.
+ participating_taxa:
+ - preferred_term: Streptococcus thermophilus
term:
id: NCBITaxon:1308
label: Streptococcus thermophilus
- target_taxon:
- preferred_term: Lactobacillus delbrueckii subsp. bulgaricus
+ - preferred_term: Lactobacillus delbrueckii subsp. bulgaricus
term:
id: NCBITaxon:1585
label: Lactobacillus delbrueckii subsp. bulgaricus
+- name: Streptococcus Nox-Dependent Milk Fermentation
+ description: In the S. thermophilus 1131/L. bulgaricus 2038 pair, disrupting S. thermophilus nox reduced oxygen
+ removal and slowed skim-milk acidification. Pre-fermentation deoxygenation mainly accelerated early S. thermophilus
+ growth and formate/lactate accumulation, not L. bulgaricus growth; final Streptococcus counts converged. This
+ is a fermentation phenotype, not colonization facilitation. A direct Nox-to-Pfl mechanism remains HYPOTHESIZED.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: fermentation
term:
@@ -266,9 +267,10 @@ ecological_interactions:
label: fermentation
downstream:
- target: Streptococcus Formate and Carbon Dioxide Support
- description: S. thermophilus oxygen removal relieves dissolved-oxygen
- suppression of yogurt fermentation and is associated with earlier
- formate accumulation during the two-species acidification process.
+ description: 'PARTIAL: Oxygen removal promotes early formate accumulation in the 1131/2038 system, and the nox
+ mutant lacks detected formate in the tested monoculture. Protection of oxygen-sensitive Pfl is HYPOTHESIZED;
+ the study also considers other Nox functions and does not establish the CO2 branch or universal transfer to
+ L. bulgaricus.'
evidence:
- reference: PMID:24936380
supports: SUPPORT
@@ -280,6 +282,21 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: Nox of S. thermophilus 1131 contributes greatly to yogurt fermentation
explanation: Supports S. thermophilus NADH oxidase as an oxygen-removal mechanism promoting fermentation.
+ - reference: PMID:24936380
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: deoxygenated fermentation primarily increased the cell number of S. thermophilus 1131 rather than that
+ of L. bulgaricus 2038
+ explanation: Preserves the principal early beneficiary of oxygen removal.
+ participating_taxa:
+ - preferred_term: Streptococcus thermophilus
+ term:
+ id: NCBITaxon:1308
+ label: Streptococcus thermophilus
+ - preferred_term: Lactobacillus delbrueckii subsp. bulgaricus
+ term:
+ id: NCBITaxon:1585
+ label: Lactobacillus delbrueckii subsp. bulgaricus
environmental_factors:
- name: milk substrate
value: skim milk or milk used for thermophilic yogurt fermentation
@@ -400,3 +417,35 @@ associated_datasets:
snippet: Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures
explanation: Lists a computational/genomic publication with the same two-species yogurt starter composition.
metal_relevance: NOT_APPLICABLE
+discussions:
+- discussion_id: yogurt_strain_stage_and_mediator_boundaries
+ prompt: Which return-flow mechanisms and benefits hold for each tested strain pair and growth stage?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Streptococcus Formate and Carbon Dioxide Support
+ - ecological_interactions#Lactobacillus Proteolytic Nitrogen Support
+ - ecological_interactions#Urease-Dependent Acidification Acceleration
+ - ecological_interactions#Streptococcus Nox-Dependent Milk Fermentation
+ rationale: Keep the CNRZ1066/ATCC BAA-365 nutritional model, LMG 18311/ATCC 11842 expression study, 1131/2038
+ Nox experiment and urease strain panel separate. In the LMG 18311 pair, faster acidification accompanied lower
+ final lactobacillus counts. In the Nox study, early effects did not imply a higher final Streptococcus yield.
+ Nutrient supplementation and knockout phenotypes remain positive evidence without universal mutualism or proven
+ mediation.
+ evidence:
+ - reference: PMID:19114510
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: the coculture resulted in a threefold decrease of the final bacterial counts
+ explanation: Faster coculture acidification did not imply a final population benefit to both partners.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T17:51:30Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Qualify the strain-specific formate/CO2 model.; Retain nitrogen support without nutritional sufficiency
+ or demonstrated return-flow mediation.; Represent the urease effect at culture level with distinct ammonia/CO2
+ recipients.; Preserve the Nox intervention and early-growth evidence without colonization or universal-recipient
+ claims. Issue#1965; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ llm_assisted: true
diff --git a/kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml b/kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml
index 553575bc8..2a278296c 100644
--- a/kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml
+++ b/kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml
@@ -107,8 +107,10 @@ taxonomy:
explanation: Supports the E. coli auxotroph variants used as coculture partners.
ecological_interactions:
- name: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
- description: Z. mobilis releases amino acid exometabolites in spent medium, and those exometabolites
- were used to select E. coli proA, pheA, and ilvA auxotrophs as coculture partners.
+ description: Wild-type Z. mobilis ZM4 spent medium and individual amino-acid supplementation rescued the selected
+ E. coli proA, pheA and ilvA auxotrophs. This supports nutritional rescue, beyond candidate selection alone.
+ The reciprocal experiments paired each E. coli mutant separately with the Z. mobilis ZMO0748 mutant; they do
+ not describe a four-member consortium or establish a dedicated export mechanism.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -126,8 +128,8 @@ ecological_interactions:
term:
id: CHEBI:33709
label: amino acid
- notes: The source abstract identifies amino acid exometabolites but does not enumerate the exact
- amino acid identities in the curated snippet.
+ notes: The manuscript identifies proline, phenylalanine and isoleucine as the selected rescue amino acids; the
+ existing generic amino-acid grounding is retained.
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -135,9 +137,8 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Reciprocal Auxotroph Coculture Growth
- description: >
- Z. mobilis amino acid exometabolites rescue E. coli amino acid auxotrophs
- selected for the validated reciprocal cocultures.
+ description: Partner spent-medium and amino-acid rescue support the nutritional contribution to the three separately
+ tested reciprocal pairs. The molecular release route and all additional interactions are not resolved.
evidence:
- reference: PMID:26885935
supports: SUPPORT
@@ -149,9 +150,17 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: used to select three corresponding E. coli auxotrophs
explanation: Supports selection of E. coli auxotrophs based on Z. mobilis exometabolites.
-- name: E. coli Glutathione-Related Rescue of Zymomonas Auxotroph
- description: E. coli spent medium contained glutathione-related metabolites that were identified as
- potential rescue compounds for the Z. mobilis ZMO0748 cysteine synthase-like auxotroph.
+ - reference: PMID:26885935
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: they all successfully grew in 50% spent medium and metabolite supplemented medium
+ explanation: Rescue was tested using partner spent medium and metabolite-supplemented medium, with no growth
+ in unsupplemented ZMMG.
+- name: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ description: E. coli spent medium rescued the Z. mobilis ZMO0748 cysteine-synthase-like mutant. Cysteine and glutathione
+ supplementation independently supported rescue. Glutathione-related compounds were detected in spent medium,
+ but free cysteine below detection was not excluded. Thus the phenotype is experimentally supported while the
+ exact naturally transferred sulfur compound and release/uptake route remain PARTIAL.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -169,8 +178,8 @@ ecological_interactions:
term:
id: CHEBI:16856
label: glutathione
- notes: Curated as glutathione-related metabolites because the source does not narrow the exact
- transferred molecule in the abstract.
+ notes: Glutathione supplementation supports rescue; it is not established as the sole necessary transferred
+ molecule in coculture.
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -178,23 +187,31 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Reciprocal Auxotroph Coculture Growth
- description: >
- E. coli glutathione-related metabolites are candidate rescue compounds
- for the Z. mobilis ZMO0748 auxotroph used in the reciprocal cocultures.
+ description: 'PARTIAL molecular assignment: sulfur-metabolite rescue supports the ZMO0748 contribution to reciprocal
+ growth, and glutathione is sufficient in supplementation. Its exclusive necessity in coculture and the exact
+ exchanged sulfur species were not established.'
evidence:
- reference: PMID:26885935
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: identified glutathione related metabolites as potentially available for rescue
explanation: Supports E. coli metabolite availability for rescue of the Z. mobilis auxotroph.
- reference: PMID:26885935
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: rescue of the Z. mobilis cysteine synthase mutant
explanation: Supports the target Z. mobilis auxotroph rescue mechanism.
+ - reference: PMID:26885935
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: both cysteine and glutathione are capable of rescuing Z. mobilis
+ explanation: Preserves the positive metabolite-supplementation result without claiming exclusive glutathione
+ mediation.
- name: Reciprocal Auxotroph Coculture Growth
- description: The selected Z. mobilis auxotroph was tested in coculture with each of the three E. coli
- auxotrophs, and growth of both species was confirmed by optical density and flow cytometry.
+ description: Each of three separate pairs containing the Z. mobilis ZMO0748 auxotroph and an E. coli proA, pheA
+ or ilvA auxotroph grew in unsupplemented ZMMG, where the individual auxotrophs did not. Optical density and
+ species-resolved flow cytometry support growth of both partners under those conditions. This does not establish
+ long-term community stability or the absence of additional beneficial or inhibitory exchanges.
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -223,6 +240,11 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: monitored by optical density for growth
explanation: Supports growth monitoring of the cocultures.
+ - reference: PMID:26885935
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: analyzed by flow cytometry to confirm high cell counts for each species
+ explanation: Species-resolved cell counts supplement bulk optical density.
environmental_factors:
- name: Auxotrophic mutant selection
value: Z. mobilis ZMO0748 auxotroph with E. coli proA, pheA, or ilvA auxotrophs
@@ -337,3 +359,32 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth extraction, cycling, or stress role was curated for this synthetic
obligate mutualism.
+discussions:
+- discussion_id: zymomonas_sulfur_identity_and_release_routes
+ prompt: Which sulfur species and cellular release/uptake routes mediate rescue in the live pairs?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ - ecological_interactions#E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ - ecological_interactions#Reciprocal Auxotroph Coculture Growth
+ rationale: 'Do not downgrade the positive spent-medium, supplementation and reciprocal-growth controls to mere
+ correlation. Distinguish those controls from exclusive glutathione necessity and active secretion: alternative
+ sulfur compounds and release by extracellular processing or lysis remain possible. The three pairs were tested
+ separately; longitudinal stability was outside the reported experiment.'
+ evidence:
+ - reference: PMID:26885935
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: identified glutathione related metabolites as potentially available for rescue
+ explanation: The abstract itself distinguishes candidate sulfur metabolites from the demonstrated growth phenotype.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T17:51:30Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain experimental amino-acid rescue and distinguish three alternative pairs.; Retain sulfur-rescue
+ controls while qualifying the exact transferred compound.; Retain condition-specific obligate growth and species-resolved
+ counts without long-term stability claims. Issue#1966; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ llm_assisted: true
diff --git a/kb/communities/hCom2_Complex_Gut_Microbiome.yaml b/kb/communities/hCom2_Complex_Gut_Microbiome.yaml
index 14d8a7504..123810f7c 100644
--- a/kb/communities/hCom2_Complex_Gut_Microbiome.yaml
+++ b/kb/communities/hCom2_Complex_Gut_Microbiome.yaml
@@ -53,10 +53,10 @@ taxonomy:
evidence:
- *id001
ecological_interactions:
-- name: Fecal-Challenge Open Niche Filling
- description: Species that engrafted after hCom1 fecal challenge were added to the defined gut consortium,
- filling open ecological niches to yield hCom2.
- interaction_type: COLONIZATION_FACILITATION
+- name: Fecal-Challenge-Guided Community Augmentation
+ description: Species identified after challenging hCom1-colonized mice with fecal communities informed the assembly
+ of hCom2. The intervention changes community membership; filling open niches is its ecological interpretation,
+ not a directly measured complete metabolic or spatial niche map.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: multi-organism process
@@ -65,17 +65,24 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: hCom2 Fecal-Challenge Stability
- description: Filling hCom1's open niches with engrafting gut species produced hCom2's higher stability
- when challenged again with human fecal microbiota.
+ description: 'Membership augmentation produced a community with greater fecal-challenge resilience in the tested
+ mice. PARTIAL mechanism: niche occupancy is a proposed explanation rather than a selectively measured mediator,
+ and unrelated donors expose residual invasibility.'
- target: hCom2 Escherichia coli Colonization Resistance
- description: Occupying the open gut niches left in hCom1 produced a more complete hCom2 consortium
- that resisted pathogenic Escherichia coli colonization.
+ description: 'HYPOTHESIZED mediation: broader niche occupancy could contribute to hCom2 resistance, but observing
+ resistance in hCom2 does not establish that the augmentation step or any added species is necessary. The study
+ does not resolve the protective strains or molecular pathway.'
evidence:
- - *id001
+ - reference: PMID:36070752
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: We identified new species that engrafted following fecal challenge and added them to hCom1, yielding
+ hCom2.
+ explanation: Supports the defined synthetic community design and represented community context.
- name: hCom2 Fecal-Challenge Stability
- description: The augmented hCom2 community remains more stable than hCom1 when challenged with a human
- fecal community in gnotobiotic mice.
- interaction_type: COLONIZATION_FACILITATION
+ description: In gnotobiotic mice, hCom2 was more resilient than hCom1 to fecal challenge. The primary study also
+ reports weaker resilience to unrelated fecal donors. Stability is therefore donor- and experiment-dependent,
+ not complete exclusion or universal human-microbiome equivalence.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: multi-organism process
@@ -83,11 +90,15 @@ ecological_interactions:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
evidence:
- - *id001
+ - reference: PMID:36070752
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: hCom2 exhibited increased stability to fecal challenge
+ explanation: Direct abstract evidence for the observed stability endpoint.
- name: hCom2 Escherichia coli Colonization Resistance
- description: The niche-filled hCom2 consortium provides robust colonization resistance against pathogenic
- Escherichia coli in gnotobiotic mice.
- interaction_type: COLONIZATION_FACILITATION
+ description: hCom2 conferred robust resistance to the tested pathogenic E. coli challenge in gnotobiotic mice.
+ The phenotype is community-level resistance, not facilitation of the invader and not proof that each bacterial
+ member is protective. The responsible strains and molecular mechanism remain unresolved.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: defense response to bacterium
@@ -95,7 +106,11 @@ ecological_interactions:
id: GO:0042742
label: defense response to bacterium
evidence:
- - *id001
+ - reference: PMID:36070752
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: robust colonization resistance against pathogenic Escherichia coli
+ explanation: Direct abstract evidence for the challenge phenotype; assembly alone is not outcome evidence.
cultivation_setup:
- cultivation_mode: BATCH
system_type: OTHER
@@ -212,7 +227,35 @@ curation_history:
- timestamp: '2026-09-13T00:56:50Z'
curator: codex
action: RECONCILE_PAYWALLED_EVIDENCE_REMOVAL
- changes: "Reapplied PR #766's 17 unsupported evidence removals onto current main, preserving its newer
- interaction curation; retained abstract-supported evidence. Re-evidencing debt remains tracked in
- #765."
+ changes: 'Reapplied PR #766''s 17 unsupported evidence removals onto current main, preserving its newer interaction
+ curation; retained abstract-supported evidence. Re-evidencing debt remains tracked in #765.'
+ llm_assisted: true
+- timestamp: '2026-10-08T17:51:31Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain augmentation while separating niche-filling interpretation from measurement.; Re-evidence the
+ stability endpoint and preserve unrelated-donor limits.; Re-evidence community resistance without facilitation
+ typing or strain-specific causality. Issue#1967; reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
llm_assisted: true
+discussions:
+- discussion_id: hcom_augmentation_vs_protective_mechanism
+ prompt: Which membership changes and ecological mechanisms cause the challenge phenotypes?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Fecal-Challenge-Guided Community Augmentation
+ - ecological_interactions#hCom2 Fecal-Challenge Stability
+ - ecological_interactions#hCom2 Escherichia coli Colonization Resistance
+ rationale: Preserve the augmented-community and pathogenic-challenge outcomes without assigning colonization-facilitation
+ labels. Phylum-dropout results narrow candidate explanations but do not identify a necessary individual strain
+ or distinguish direct protection from altered community architecture. Unrelated-donor invasion limits universal
+ stability. Existing non-graph re-evidencing debt remains under issue 765; no restricted article body is reintroduced
+ into the repository.
+ evidence:
+ - reference: PMID:36070752
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: robust colonization resistance against pathogenic Escherichia coli
+ explanation: Direct abstract evidence for the challenge phenotype; assembly alone is not outcome evidence.
+ posed_by: codex
+ posed_date: '2026-10-08'
diff --git a/references_cache/PMID_19114510.txt b/references_cache/PMID_19114510.txt
index be6c46da5..2405ab2fd 100644
--- a/references_cache/PMID_19114510.txt
+++ b/references_cache/PMID_19114510.txt
@@ -33,4 +33,12 @@ molecular clues for the understanding of their associative behavior.
DOI: 10.1128/AEM.01984-08
PMCID: PMC2663229
-PMID: 19114510 [Indexed for MEDLINE]
\ No newline at end of file
+PMID: 19114510 [Indexed for MEDLINE]
+
+## Primary-source excerpts
+Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC2663229/
+Section: Results, growth comparison. Retrieved 2026-10-08.
+License: Copyright ASM; short literal excerpt only.
+No full article or supplement imported.
+
+the coculture resulted in a threefold decrease of the final bacterial counts
diff --git a/references_cache/PMID_26885935.md b/references_cache/PMID_26885935.md
index 33d3d59a0..1f4faaee8 100644
--- a/references_cache/PMID_26885935.md
+++ b/references_cache/PMID_26885935.md
@@ -80,4 +80,14 @@ screening based methods and exometabolomics for both the selection of obligate
mutualism partners and elucidation of metabolites involved in auxotroph rescue.
DOI: 10.1021/acssynbio.5b00236
-PMID: 26885935 [Indexed for MEDLINE]
\ No newline at end of file
+PMID: 26885935 [Indexed for MEDLINE]
+
+## Primary-source excerpts
+Source: https://escholarship.org/content/qt2019585b/qt2019585b.pdf?t=on42ie
+Section: Accepted manuscript, rescue experiments in Results. Retrieved 2026-10-08.
+License: Repository manuscript: CC BY-NC-ND 4.0; unmodified short literal excerpts only.
+No full article or supplement imported.
+
+they all successfully grew in 50% spent medium and metabolite supplemented medium
+
+both cysteine and glutathione are capable of rescuing Z. mobilis
diff --git a/references_cache/PMID_41736479.txt b/references_cache/PMID_41736479.txt
new file mode 100644
index 000000000..b250a5526
--- /dev/null
+++ b/references_cache/PMID_41736479.txt
@@ -0,0 +1,41 @@
+1. Water Environ Res. 2026 Mar;98(3):e70318. doi: 10.1002/wer.70318.
+
+Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of
+1,2,3-Trichloropropane in Groundwater by a Non-Dehalogenimonas Consortium.
+
+Kong S(1)(2), Ning Z(1)(3), Chen Z(1), Zhang M(1)(3).
+
+Author information:
+(1)Institute of Hydrogeology and Environmental Geology, Chinese Academy of
+Geological Sciences, Shijiazhuang, China.
+(2)School of Resources and Environmental Engineering, Hefei University of
+Technology, Hefei, China.
+(3)Key Laboratory of Groundwater Remediation of Hebei Province & China
+Geological Survey, Zhengding, Hebei, China.
+
+1,2,3-Trichloropropane (TCP), a highly mobile chemical byproduct, has severely
+exacerbated groundwater environment deterioration. Due to the lack of effective
+natural attenuation pathways, TCP typically exhibits a fate of persistent
+retention within aquifers. To address this challenge, instead of relying on
+limited specific strains, this study focused on exploring broad-spectrum
+co-metabolic substrates to enhance the degradation efficiency of a
+non-Dehalogenimonas synergistic consortium optimized through long-term directed
+domestication. Results indicated that the average degradation rate of the
+domesticated consortium increased to 19.06 μmol L-1 d-1, achieving complete
+removal within 3.5 days, thereby effectively altering the environmental
+persistence of TCP. Microbial community and metagenomic analyses revealed that
+this transformation process was driven by a synergistic alliance comprising
+Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides, realized
+through a coupled metabolic module of "hydrogen production, cofactor synthesis,
+and reductive dechlorination". Crucially, the consortium demonstrated
+exceptional broad-spectrum adaptability to various co-metabolic substrates,
+where sodium acetate and lactate significantly enhanced the degradation
+efficiency. This study confirms that utilizing suitable co-metabolic substrates
+can effectively activate the non-Dehalogenimonas consortium to regulate the
+migration and fate of pollutants in complex groundwater environments, offering
+an efficient bioremediation strategy to arrest groundwater contamination.
+
+© 2026 Water Environment Federation.
+
+DOI: 10.1002/wer.70318
+PMID: 41736479 [Indexed for MEDLINE]
diff --git a/references_cache/PMID_42429207.txt b/references_cache/PMID_42429207.txt
index dc33c47d9..312925969 100644
--- a/references_cache/PMID_42429207.txt
+++ b/references_cache/PMID_42429207.txt
@@ -35,4 +35,12 @@ DOI: 10.1002/wer.70489
PMCID: PMC13352569
PMID: 42429207 [Indexed for MEDLINE]
-Conflict of interest statement: The authors declare no conflicts of interest.
\ No newline at end of file
+Conflict of interest statement: The authors declare no conflicts of interest.
+
+## Primary-source excerpts
+Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC13352569/
+Section: Results and Discussion, nitrogen-removal comparison. Retrieved 2026-10-08.
+License: Copyright 2026 Water Environment Federation; short literal excerpt only.
+No full article or supplement imported.
+
+phycoremediation using the AM–AB consortium delayed the removal of nitrogen compared to standalone activated C. vulgaris treatment
diff --git a/references_cache/doi_10.64898_2025.12.19.695487.md b/references_cache/doi_10.64898_2025.12.19.695487.md
index 4292558e3..89639936d 100644
--- a/references_cache/doi_10.64898_2025.12.19.695487.md
+++ b/references_cache/doi_10.64898_2025.12.19.695487.md
@@ -40,3 +40,14 @@ In co-culture experiments using a mixed substrate (glucose, cellobiose, and xylo
Overall, this study provides the first demonstration of a
Y. lipolytica
system capable of simultaneously utilizing cellulose- and hemicellulose-derived oligosaccharides. Moreover, benchmarking a division-of-labor consortium against a multifunctional monoculture highlights a robust strategy to enhance lipid biosynthesis and improve process resilience for LCB valorization.
+
+
+## Primary-source excerpts
+Source: https://www.biorxiv.org/content/early/2025/12/22/2025.12.19.695487.source.xml
+Section: Results, version 1 posted 2025-12-22. Retrieved 2026-10-08.
+License: All rights reserved; short literal excerpts only.
+No full article or supplement imported.
+
+the YBGL3 + YBXT-XR cocultures
+
+the 1:5 consortium ultimately reached a comparable lipid titer at 168 h
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index d82b1e97d..5bb8527f2 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`.
+## Batch124: Final Pending Records
+
+[Decisions](decisions/20261008-six-records-batch124.yaml),
+[provenance](cache-provenance-20261008-batch124.json),
+[validation](validation-20261008-batch124.json), and
+[self-adversarial review](adversarial-review-20261008-batch124.yaml) cover
+algae-MLSS, TCP groundwater, Yarrowia, yogurt, Zymomonas-E. coli and hCom2.
+All fifteen existing nodes and eight arrows remain, with six coherent renames.
+
+TCP retains amendment effects while distinguishing metagenomic inference.
+Yarrowia's lipid-fraction benefit is not a titer advantage or exclusive niches.
+Yogurt retains intervention outcomes with strain, growth-stage and recipient
+boundaries. Zymomonas retains rescue controls without exclusive glutathione
+mediation. hCom2 retains stability and resistance with direct outcome evidence,
+not colonization-facilitation labels or an established protective mechanism.
+Algae-only controls constrain a future algae-MLSS graph; its extension stays open.
+
+All 36 graph/discussion quotations match fresh primary artifacts and caches.
+The ledger records exact reading scope and access limitations, including
+abstract-bounded TCP and urease evidence. Four caches receive short attributed
+excerpts, and a missing TCP abstract is restored from an independently verified
+copy. The other 919 caches, 454 records and unrelated raw fields are unchanged.
+Six append-only histories record the work. One algae Edison dry run completed;
+there was no provider submission or spend.
+
+The inventory now has 405 reviewed records, zero pending and 55 requiring
+research. Zero pending is not completion of those research extensions.
+Repairs #1963-#1967 await protected-main merge. Graph extension #1968 and
+non-graph follow-ups #1969-#1971 and #765 remain open. This is source-based
+self-review, not independent approval; protected merge and branch deletion
+are still separate requirements.
+
## Batch123: Phenotypes And Inferred Mechanisms
[Decisions](decisions/20261008-four-records-batch123.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch124.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch124.yaml
new file mode 100644
index 000000000..c83a5c62f
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch124.yaml
@@ -0,0 +1,527 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 19010db53b3b5537d458727318921006e83e7ccb
+scope:
+- kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml
+- kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml
+- kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml
+- kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml
+- kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml
+- kb/communities/hCom2_Complex_Gut_Microbiome.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch124.json
+findings:
+- issue: 1963
+ severity: P2
+ finding: Qualify metagenome-inferred TCP coupling and retain amendment effects
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1964
+ severity: P2
+ finding: Separate Yarrowia lipid fraction from titer and hydrolysis from exclusive niches
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1965
+ severity: P2
+ finding: Preserve yogurt intervention results while separating strains and benefit recipients
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1966
+ severity: P2
+ finding: Re-evidence Zymomonas rescue controls without exclusive sulfur-mediator claims
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1967
+ severity: P2
+ finding: Re-evidence hCom2 resistance and remove colonization-facilitation misclassification
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1968
+ severity: P2
+ finding: Review AM-AB graph extension against algae-only controls
+ status: open_research_extension
+ disposition: Remain open until separately verified.
+- issue: 1969
+ severity: P2
+ finding: Curate available AM-AB wastewater and HRAP details without indoor-outdoor conflation
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1970
+ severity: P2
+ finding: Reconcile Yarrowia member labels and inoculum-dependent abundance metadata
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1971
+ severity: P2
+ finding: Align non-graph yogurt summary with strain-specific urease recipients
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- All15nodes and8arrows retained, six coherent renames, no new topology. Six canonical diffs and cache changes read.
+ TCP graph-owned YAML anchors preserved so unrelated media/ingredient blocks remain byte-identical. No dangling
+ targets or discussion anchors.
+- 'Algae-only controls bound a future AM-AB graph: early nitrogen removal is slower, phosphate detection limits
+ occur in both conditions, and BOD performance is not uniformly improved. Full Methods metadata is available, not
+ an ongoing abstract-access gap. Extension1968 and metadata1969 stay open.'
+- TCP metagenomic reconstruction is COMPUTATIONAL/PARTIAL, without invented tools, genus-specific roles or measured
+ transfer. Positive substrate amendments and culture-wide removal remain. Prior1108/1109 repairs preserved; no
+ new coupling-to-removal arrow.
+- Yarrowia exact YBGL3/YBXT-XR pair, shared glucose use and substrate succession are distinct from exclusive niches.34%
+ versus26.3% is a lipid-fraction comparison; best titer is comparable and1:2 performs worse. No polymer GO or demonstrated
+ burden-relief claims. Version1 preprint and metadata1970 limits remain.
+- Yogurt nutritional modeling, Nox perturbation and urease strain panels stay distinct. Positive interventions retained
+ with early/final and Streptococcus/Lactobacillus recipients separated. Nitrogen sufficiency and universal return-flow
+ mediation are not asserted. Both community-scoped outcomes name both original participants; metadata1971 remains.
+- Zymomonas spent-medium and individual-metabolite rescue remain positive, not mere correlation. Cysteine and glutathione
+ are sufficient alternatives; exact natural sulfur compound and release route remain unresolved. Three pairs remain
+ separate, with species-resolved counts and no long-term stability assertion.
+- hCom2 stability and resistance have direct endpoint evidence, not an assembly-only citation or colonization-facilitation
+ labels. Donor dependence and dropout architecture confounding limit mechanism/individual-strain claims. Non-graph
+ debt765 remains and no restricted full body is restored.
+- Thirteen focused tests and twelve targeted in-memory control/mutation/restored-control probes pass. Probes reject
+ specified scientific regressions, not every possible equivalent wording. Early test development failures included
+ an incorrect test taxon identifier, corrected to unchanged canonical NCBITaxon1585.
+- All30graph and6discussion quotes match fresh primary artifacts and caches. Four short excerpt appendices and one
+ independently matched missingTCPabstract;919originalcaches unchanged. Exact read scopes, failed retrievals and
+ successful alternatives recorded; no original figure-pixel,external-supplement,raw-data or code audit.
+- Zymomonas reference validation initially failed because its .md cache takes precedence over .txt. Move our exact
+ appendix to .md and restore our text-cache change; preserve failed/recovered logs. No validator changes, fabricated
+ content or weakened checks. EarlierTCPbaseline failure and24recovered checks also remain recorded. Correct algae
+ copyright holder to Water Environment Federation. Staged whitespace gate found trailing spaces in the newTCPcopy;
+ normalize only that copy and rerun affected checks, preserving the original user file and failed-check log.
+- Six sets of schema,strict,terms,references,snippets,rank/history checks pass.1187selected tests,lint,mypy and
+ deterministic render pass.57existing network warnings remain;zero structural defects. Exact456page/1359node/522arrow
+ descriptions verified,not screenshots or full Linux CI certification.
+- 454otherrecords,unrelated raw fields and all prior histories/decision artifacts unchanged. Census415community-level,137mixed,278community-only,1570taxa,1281sole-credit.
+ Yogurt adds two counted taxa but no sole credit;300participant-list users. Exact measured count bounds updated;
+ connectivity code and share guard unchanged.
+- 1963-1967 addressed pending protected-main merge;1968 extension,1969-1971 metadata and765 remain open. One algae
+ Edison dryrun, no provider submission or spend; priorRuegeria1883 configured-authentication blocker not retried
+ unchanged. Self-review is not independent approval.
+- Corpus405reviewed,zero pending,55needs_research across460records. Zero pending does not mean complete graphs or
+ a completed objective. Protected-root1836,actual exact-headCI,merge andbranchdeletion remain separate; postcommit
+ docs-current/publication not preasserted.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Erase algae-only nitrogen comparison
+ test: test_algal_extension_remains_open_and_control_bounded
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 23
+ assertion: assert "early nitrogen removal is slower" in gap["rationale"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/discussions/1/rationale
+ before: The primary study compares the combined culture with activated algae alone. Retain improved late
+ total-nitrogen removal, but early nitrogen removal is slower, phosphate reaches the detection limit in
+ both conditions, and BOD removal is not uniformly better. Biomass correlations do not establish a transfer
+ mechanism. New nodes require a separately authorized Edison causal-graph review; none were added in this
+ repair pass.
+ after: The primary study compares the combined culture with activated algae alone. Retain improved late
+ total-nitrogen removal, but early nitrogen removal is faster, phosphate reaches the detection limit in
+ both conditions, and BOD removal is not uniformly better. Biomass correlations do not establish a transfer
+ mechanism. New nodes require a separately authorized Edison causal-graph review; none were added in this
+ repair pass.
+ - mutation: Promote metagenome inference
+ test: test_tcp_reconstruction_is_not_measured_transfer
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 34
+ assertion: assert e["supports"] == "PARTIAL" and e["evidence_source"] == "COMPUTATIONAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/0/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Erase observed TCP removal rate
+ test: test_tcp_keeps_amendment_effects_and_shared_descriptors
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 45
+ assertion: assert "19.06" in b["description"] and "3.5 days" in b["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/description
+ before: Sodium acetate and lactate amendments enhanced TCP degradation in the domesticated consortium. The
+ abstract reports an overall average degradation rate of 19.06 umol L-1 d-1 and complete removal within
+ 3.5 days; those values are not separately assigned to each amendment or to an individual genus.
+ after: Sodium acetate and lactate amendments enhanced TCP degradation in the domesticated consortium. The
+ abstract reports an overall average degradation rate of 0 umol L-1 d-1 and complete removal within 3.5
+ days; those values are not separately assigned to each amendment or to an individual genus.
+ - mutation: Reassert exclusive Yarrowia niches
+ test: test_yarrowia_design_is_not_exclusive_niches_or_polymer_catalysis
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 54
+ assertion: assert "interaction_type" not in a and "biological_processes" not in a
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/0/interaction_type
+ before: null
+ after: NICHE_PARTITIONING
+ - mutation: Promote Yarrowia titer advantage
+ test: test_yarrowia_fraction_does_not_become_titer_advantage
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 64
+ assertion: assert "comparable lipid titers" in c["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/2/ecological_interactions/2/description
+ before: The nitrogen-limited 1:5 YBGL3:YBXT-XR consortium reached a lipid fraction of 34% versus 26.3% in
+ the multifunctional monoculture. The best consortium and monoculture reached comparable lipid titers,
+ while the 1:2 consortium performed worse. A higher lipid fraction is not a general increase in titer,
+ growth or productivity, nor evidence of lower metabolic burden.
+ after: The nitrogen-limited 1:5 YBGL3:YBXT-XR consortium reached a lipid fraction of 34% versus 26.3% in
+ the multifunctional monoculture. The best consortium and monoculture reached greater lipid titers, while
+ the 1:2 consortium performed worse. A higher lipid fraction is not a general increase in titer, growth
+ or productivity, nor evidence of lower metabolic burden.
+ - mutation: Promote yogurt return-flow mediation
+ test: test_yogurt_pairs_and_return_flow_remain_distinct
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 79
+ assertion: assert b["downstream"][0]["description"].startswith("HYPOTHESIZED mediation:")
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/1/downstream/0/description
+ before: 'HYPOTHESIZED mediation: nitrogen support can sustain S. thermophilus growth and hence potential
+ return metabolites. The cited strain-pair experiments do not selectively establish proteolysis as the
+ cause of formate/CO2 return flow; this is not a demonstrated universal feedback loop.'
+ after: Experimentally necessary universal return flow.
+ - mutation: Erase yogurt participant restriction
+ test: test_yogurt_urease_recipients_and_scopes_are_explicit
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 89
+ assertion: assert {t["term"]["id"] for t in node["participating_taxa"]} == {
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/2/participating_taxa
+ before:
+ - preferred_term: Streptococcus thermophilus
+ term:
+ id: NCBITaxon:1308
+ label: Streptococcus thermophilus
+ - preferred_term: Lactobacillus delbrueckii subsp. bulgaricus
+ term:
+ id: NCBITaxon:1585
+ label: Lactobacillus delbrueckii subsp. bulgaricus
+ after: []
+ - mutation: Erase Nox final-yield null
+ test: test_yogurt_nox_keeps_intervention_early_recipient_and_final_null
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 102
+ assertion: assert "final Streptococcus counts converged" in d["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/3/ecological_interactions/3/description
+ before: In the S. thermophilus 1131/L. bulgaricus 2038 pair, disrupting S. thermophilus nox reduced oxygen
+ removal and slowed skim-milk acidification. Pre-fermentation deoxygenation mainly accelerated early S.
+ thermophilus growth and formate/lactate accumulation, not L. bulgaricus growth; final Streptococcus counts
+ converged. This is a fermentation phenotype, not colonization facilitation. A direct Nox-to-Pfl mechanism
+ remains HYPOTHESIZED.
+ after: In the S. thermophilus 1131/L. bulgaricus 2038 pair, disrupting S. thermophilus nox reduced oxygen
+ removal and slowed skim-milk acidification. Pre-fermentation deoxygenation mainly accelerated early S.
+ thermophilus growth and formate/lactate accumulation, not L. bulgaricus growth; final Streptococcus counts
+ increased. This is a fermentation phenotype, not colonization facilitation. A direct Nox-to-Pfl mechanism
+ remains HYPOTHESIZED.
+ - mutation: Combine three separate mutualism pairs
+ test: test_zymomonas_rescue_is_positive_and_pairs_are_separate
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 112
+ assertion: assert "three separate pairs" in c["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/4/ecological_interactions/2/description
+ before: Each of three separate pairs containing the Z. mobilis ZMO0748 auxotroph and an E. coli proA, pheA
+ or ilvA auxotroph grew in unsupplemented ZMMG, where the individual auxotrophs did not. Optical density
+ and species-resolved flow cytometry support growth of both partners under those conditions. This does
+ not establish long-term community stability or the absence of additional beneficial or inhibitory exchanges.
+ after: Each of one four-member consortium containing the Z. mobilis ZMO0748 auxotroph and an E. coli proA,
+ pheA or ilvA auxotroph grew in unsupplemented ZMMG, where the individual auxotrophs did not. Optical density
+ and species-resolved flow cytometry support growth of both partners under those conditions. This does
+ not establish long-term community stability or the absence of additional beneficial or inhibitory exchanges.
+ - mutation: Erase alternative sulfur rescue
+ test: test_zymomonas_sulfur_rescue_is_not_exclusive_glutathione
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 121
+ assertion: '"Cysteine and glutathione supplementation independently supported rescue"'
+ restored_control: PASS
+ changed_values:
+ - path: records/4/ecological_interactions/1/description
+ before: E. coli spent medium rescued the Z. mobilis ZMO0748 cysteine-synthase-like mutant. Cysteine and
+ glutathione supplementation independently supported rescue. Glutathione-related compounds were detected
+ in spent medium, but free cysteine below detection was not excluded. Thus the phenotype is experimentally
+ supported while the exact naturally transferred sulfur compound and release/uptake route remain PARTIAL.
+ after: E. coli spent medium rescued the Z. mobilis ZMO0748 cysteine-synthase-like mutant. Only glutathione
+ could rescue growth. Glutathione-related compounds were detected in spent medium, but free cysteine below
+ detection was not excluded. Thus the phenotype is experimentally supported while the exact naturally transferred
+ sulfur compound and release/uptake route remain PARTIAL.
+ - mutation: Reclassify hCom resistance as facilitation
+ test: test_hcom_outcomes_have_direct_evidence_and_not_facilitation
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 133
+ assertion: assert all("interaction_type" not in n for n in [a, b, c])
+ restored_control: PASS
+ changed_values:
+ - path: records/5/ecological_interactions/2/interaction_type
+ before: null
+ after: COLONIZATION_FACILITATION
+ - mutation: Erase hCom donor dependence
+ test: test_hcom_donor_and_mediator_limits_remain
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 142
+ assertion: assert "weaker resilience to unrelated fecal donors" in b["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/5/ecological_interactions/1/description
+ before: In gnotobiotic mice, hCom2 was more resilient than hCom1 to fecal challenge. The primary study also
+ reports weaker resilience to unrelated fecal donors. Stability is therefore donor- and experiment-dependent,
+ not complete exclusion or universal human-microbiome equivalence.
+ after: In gnotobiotic mice, hCom2 was more resilient than hCom1 to fecal challenge. The primary study also
+ reports equal resilience to all fecal donors. Stability is therefore donor- and experiment-dependent,
+ not complete exclusion or universal human-microbiome equivalence.
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml: f3a69684e81df00ca791bfc61832141ad9048270f4b3ed476328b772d07604d2
+ kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml: ab6b0b9201bc3d3ca9c7b2cbd5395404b1ed071c064d2efb36351e4d72d6d02b
+ kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml: 2dbf53129f98e8df7edc68f7d3f2bc6ca7c748ac563d0e31abd1274a15ca051a
+ kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml: 693b023e694475fd4eeeb0fde9af92e56db2084b885af8b7bd5d1febe6140dcc
+ kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml: efc6e7b31f9bc7ebe11fe5a26f9f45e2a7b845684fd3a15c8b10e0d1994e6be6
+ kb/communities/hCom2_Complex_Gut_Microbiome.yaml: 84318d052c19431be7204a13f577dd246640b4786a6e7c4b863f01886e8746a7
+ tests/test_causal_review_batch124.py: 3cca5027c47066c2e9f9a0be7314fa3aa4d818dd64ff3a31ad429496ff1f2770
+ probe_script_sha256: c437189e4358f7efdb41d09b11961117ded0d6c6d1132ec7ff3e1535b771f63b
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch124/adversarial-regression-proof-targeted.json
+ sha256: 0d4e768d15d689cc8638808641d842bf9d789ca24507e46211e0524bb6be5522
+verification:
+ combined_regressions: 1187 passed in 353.41s (0:05:53)
+ new_regression_tests: 13
+ total_recorded_gate_outputs: 61
+ primary_graph_snippet_proof:
+ graph_quotations: 30
+ discussion_quotations: 6
+ fresh_primary_literal_matches: 36
+ all_cached_literal_matches: 36
+ retained_nodes: 15
+ removed_nodes: 0
+ renamed_nodes: 6
+ retained_arrows: 8
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml:
+ MATCH: 15
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/hCom2_Complex_Gut_Microbiome.yaml:
+ MATCH: 7
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9102
+ categories:
+ MATCH: 8971
+ RENDERING: 31
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 59
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 57
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml: ac925b5b57d1e2d173d9e515d8b371b300b885f3fc06c473570ddce7e3a07c87
+ tests/test_causal_review_batch124.py: 3cca5027c47066c2e9f9a0be7314fa3aa4d818dd64ff3a31ad429496ff1f2770
+ tests/test_participating_taxa.py: db84a4aedbbc553907c6ad35737d3f0f3900aa3ce50eb0aad61ef65b3855a8e7
+ tests/test_community_level_connectivity_credit.py: 0f02b8c5d89eed7a6578075899bfe4fa481f929515b4fd5b2641a61eedd4c88e
+ tests/test_causal_review_batch109.py: 6667be62a86cc92577f88b772c90c12541893e23e97e120a2f58bd0a5185aeea
+ tests/test_datamodel.py: f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25
+ reports/causal_graph_review/cache-provenance-20261008-batch124.json: 8875156f1920897cee5a7befb9ece8820ffa2e5d3c41b5f542bf577b53e2022c
+ kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml: f3a69684e81df00ca791bfc61832141ad9048270f4b3ed476328b772d07604d2
+ kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml: ab6b0b9201bc3d3ca9c7b2cbd5395404b1ed071c064d2efb36351e4d72d6d02b
+ kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml: 2dbf53129f98e8df7edc68f7d3f2bc6ca7c748ac563d0e31abd1274a15ca051a
+ kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml: 693b023e694475fd4eeeb0fde9af92e56db2084b885af8b7bd5d1febe6140dcc
+ kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml: efc6e7b31f9bc7ebe11fe5a26f9f45e2a7b845684fd3a15c8b10e0d1994e6be6
+ kb/communities/hCom2_Complex_Gut_Microbiome.yaml: 84318d052c19431be7204a13f577dd246640b4786a6e7c4b863f01886e8746a7
+ history_sha256:
+ history/records/AM_AB_Chlorella_MLSS_Wastewater_Consortium/2026-10-08T175132Z-codex-665b31.yaml: b38ec278e3b3a85d8ee7ca0d2b3f30dfe7cdf074fd2efad716e2fcf236bc7541
+ history/records/TCP_NonDehalogenimonas_Groundwater_Consortium/2026-10-08T175132Z-codex-e21077.yaml: 1a24a6a4a3e2c0f979ac91d4e87279e1ecb867b17030574faf36fa5f8a256741
+ history/records/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium/2026-10-08T175133Z-codex-bf87bc.yaml: 2b6780dd15a88d5d85f82b056baa608351cac9cd72be7138b36eae8a5ab9a588
+ history/records/Yogurt_TwoSpecies_Starter_Culture/2026-10-08T175133Z-codex-114f8d.yaml: a824d884702042318db809aa93f7f93649975781485c2118b3db94b628ba604a
+ history/records/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism/2026-10-08T175133Z-codex-2cd46c.yaml: ad7f00548befd400cc92f2a7487553dbdbf22ba90f952cbd7b686590068ae1d1
+ history/records/hCom2_Complex_Gut_Microbiome/2026-10-08T175134Z-codex-9059ef.yaml: c0acefe72e4ba1514d96db7897cf949b08a7c91ee55a0dd579f52e03334bcb92
+ unchanged_records: 454
+ unchanged_caches: 919
+ immutable_prior_history_and_decision_files: 909
+ cache_changes:
+ - path: references_cache/PMID_41736479.txt
+ before_sha256: null
+ after_sha256: 0f4e3719902f55ce45dfde9383042337bfd85897a53660e1d434f89a777be27e
+ action: Restore missing abstract from the existing main-checkout user file, independently match EuropePMC, add
+ final newline and strip trailing ASCII spaces/tabs for the staged whitespace gate. Original user file unchanged;
+ source words unchanged.
+ - path: references_cache/PMID_42429207.txt
+ before_sha256: 2a50d54a82547f7ddb7d1536dce9dbc5b7553c8769f1eec4b936db41ec973e8b
+ after_sha256: eb80e76d862305f4031055915eb45a832b8f32de2d0bfe042eb9142c314f4c7a
+ action: Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix.
+ - path: references_cache/doi_10.64898_2025.12.19.695487.md
+ before_sha256: b29827aa946f1564bd10177dfebab726689113664f122f4431bbfeb2ed7bfbd5
+ after_sha256: 561f7a1c054813f2b701c766fc4e69203400fe1ef88cd09dea41c522a1748e20
+ action: Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix.
+ - path: references_cache/PMID_19114510.txt
+ before_sha256: 27f1a2c09f8768aafe25638ffb75f83ede4920a0e2f02d7ae915f419e966daac
+ after_sha256: 5620d2ac074263119962e98e17f1d705a764c3f0b972328370c07a171da697cf
+ action: Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix.
+ - path: references_cache/PMID_26885935.md
+ before_sha256: 739cb68daf6d073e9057cfaa0a530869eb66b3c804241dcf9503e25153a080bc
+ after_sha256: 90b61b191addc52f9876cb1e93f1dfd729753ab5ffc2b22e9748c671198df777
+ action: Append the same short literal excerpts to the existing validator-preferred Markdown cache; original
+ bytes retained. Text-cache appendix moved here after a recorded precedence failure. Original abstract-only
+ frontmatter describes the retained base; the attributed appendix is not a full article.
+ edison:
+ required_for_existing_graph_repairs: false
+ required_for_algal_extension: true
+ dry_run_completed: true
+ dry_run_artifacts:
+ - /private/tmp/communitymech-batch124/edison-dry-run/AM_AB_Chlorella_MLSS_Wastewater_Consortium-edison-literature-causal-meta.yaml
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior authorized invocation;
+ no unchanged-state retry or broader spend.'
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 415
+ mixed: 137
+ community_level_only: 278
+ taxa: 1570
+ credited_solely_by_the_rule: 1281
+ delta_from_batch123:
+ records: 0
+ with_community_level: 1
+ mixed: 1
+ community_level_only: 0
+ taxa: 2
+ credited_solely_by_the_rule: 0
+ explanation: Yogurt urease/Nox are explicitly community-level with both original members, who remain pairwise-connected
+ by the two nutritional nodes.300participant-list users; two taxa newly counted in community-scoped records but
+ no new sole credit. Connectivity logic and share guard unchanged; measured count bounds updated by one.
+corpus:
+ records: 460
+ nodes: 1373
+ edges: 530
+ review_status_counts:
+ needs_research: 55
+ reviewed: 405
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Pre-source baseline covers460records,923caches,57existing warnings and zero structural defects. Six whole records
+ and15nodes/eight arrows reviewed; all retained,six renames,no new topology. Five existing graphs repaired; algae-MLSS
+ remains an empty-graph extension gap.
+- 'Fresh EuropePMC metadata/abstracts for eight PubMed papers and Crossref identities checked. Yarrowia bioRxivAPI
+ and version1 XML retrieved; not certified peer-reviewed. XML failures for four PMC articles did not imply absent
+ full text: their PMC HTML bodies were retrieved and read. TCP publisher403; only its abstract supports this review.'
+- Algae primary Methods2.1-2.9,Results/Discussion3.1-3.4,Conclusion andTables1-4 read. Algae-only controls bound
+ faster or universally better remediation; phosphate reaches detection limits in both and early nitrogen removal
+ is slower in AM-AB. Correlations and theoretical methane yield are not transfer or production measurements. Available
+ HRAP metadata deferred to1969; outdoor conditions must not inherit indoor stock settings.
+- Yarrowia full Methods,Results3.3-3.6,Discussion4.1-4.2 andConclusions read. Exact pair is YBGL3/YBXT-XR; shared
+ glucose use and lack of simultaneous glucose/xylose consumption rule out exclusive niches. Higher fraction in1:5
+ is not higher titer or all-ratio benefit. Methods/Results ratio ambiguity and existing member metadata remain1970.
+ Earlier enzyme-characterization Results not fully read.
+- Yogurt19114510 strain Methods,growth/nitrogen Results andBCAA/purine Discussion;20889781 strain/compound/metabolite
+ Methods,addition andnitrogen/CO2 Results/Table1 andDiscussion;24936380 main mechanism Results/Discussion andMethods;30594386
+ abstract read. Distinct pairs and stage-specific recipients kept separate. Positive knockout/supplementation outcomes
+ retained without flux or universal mutualism. Non-graph19395564 dataset not researched; urease summary deferred1971.
+- Zymomonas accepted manuscript abstract/introduction,Results andrescue controls throughpage8 andstrain Methods
+ start read via UCweb PDF extraction. Direct curl/urllib PDF downloads were empty and not evidence. Positive spent-medium,individual
+ metabolite andspecies-resolved growth results retained. Glutathione is not the exclusive necessary mediator; three
+ pairs are separate andlong-term stability untested. Remaining protocol Methods not fully read.
+- hCom2 construction,augmentation,resilience,architecture,EHECchallenge Results,Discussion/limitations and relevant
+ strain-preparation/augmentation/challenge Methods read. Donor dependence anddropout architecture confounding bound
+ niche-filling causality. Three facilitation labels removed andoutcomes re-evidenced with existing abstract text;
+ non-graph debt765 remains. No restricted full body restored.
+- All graph anddiscussion quotes checked against caches and fresh primary artifacts by normalized contiguous matching,not
+ entailment proof. Four caches gain short provenance-labeled excerpts; missingTCPabstract restored from an unchanged
+ user file andindependently matched.919originalcaches unchanged;924total. No full-body import,figure-pixel inspection,external-supplement/raw-data/code
+ audit or whole-record certification.
+- Initial TCPbaseline reference check failed due missingcache andnetworkDNS; originalfailure/log retained. Afterverifiedcache
+ restoration,24recovered targetbaseline checks passed. Fresh source retrieval logs retain failures as well as successful
+ alternative access routes.
+- Expanded all-state1196issue titles/bodies and178matchinghidden/ignored localpaths searched; ninepriorissue bodies
+ read. Credentials,.git,generateddocs/site andreferencecaches excluded from issue-dedup search;caches separately
+ inspected. No historicalPRcomment audit. Engineered gutaminoacid neighbor read as convention only,not transferred
+ evidence; no reusable target taxon files found in ignored-inclusive search.
+- Six guarded writes preserve454otherrecords,unrelated rawYAMLblocks andallpriorhistory/decision artifacts. Six
+ append-onlyhistories/events. Yogurturease/Nox endpoints nowcommunity-scoped withbothcanonicalparticipants; other
+ scopes/taxonomy preserved. Connectivity logic unchanged; census measured separately.
+- One-community algae Edison dryrun completed without provider submission orcredits. New extension requires separately
+ scoped spend authorization; priorRuegeria1883 configured-authentication blocker not retried unchanged. No credentials
+ inspected. Source-based self-adversarial review is notindependent approval.55researchrecords andprotectedmerge/branchdeletion
+ remain incomplete.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch124.json b/reports/causal_graph_review/cache-provenance-20261008-batch124.json
new file mode 100644
index 000000000..b99875c4b
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch124.json
@@ -0,0 +1,667 @@
+{
+ "changes": [
+ {
+ "path": "references_cache/PMID_41736479.txt",
+ "before_sha256": null,
+ "after_sha256": "0f4e3719902f55ce45dfde9383042337bfd85897a53660e1d434f89a777be27e",
+ "action": "Restore missing abstract from the existing main-checkout user file, independently match EuropePMC, add final newline and strip trailing ASCII spaces/tabs for the staged whitespace gate. Original user file unchanged; source words unchanged."
+ },
+ {
+ "path": "references_cache/PMID_42429207.txt",
+ "before_sha256": "2a50d54a82547f7ddb7d1536dce9dbc5b7553c8769f1eec4b936db41ec973e8b",
+ "after_sha256": "eb80e76d862305f4031055915eb45a832b8f32de2d0bfe042eb9142c314f4c7a",
+ "action": "Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix."
+ },
+ {
+ "path": "references_cache/doi_10.64898_2025.12.19.695487.md",
+ "before_sha256": "b29827aa946f1564bd10177dfebab726689113664f122f4431bbfeb2ed7bfbd5",
+ "after_sha256": "561f7a1c054813f2b701c766fc4e69203400fe1ef88cd09dea41c522a1748e20",
+ "action": "Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix."
+ },
+ {
+ "path": "references_cache/PMID_19114510.txt",
+ "before_sha256": "27f1a2c09f8768aafe25638ffb75f83ede4920a0e2f02d7ae915f419e966daac",
+ "after_sha256": "5620d2ac074263119962e98e17f1d705a764c3f0b972328370c07a171da697cf",
+ "action": "Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix."
+ },
+ {
+ "path": "references_cache/PMID_26885935.md",
+ "before_sha256": "739cb68daf6d073e9057cfaa0a530869eb66b3c804241dcf9503e25153a080bc",
+ "after_sha256": "90b61b191addc52f9876cb1e93f1dfd729753ab5ffc2b22e9748c671198df777",
+ "action": "Append the same short literal excerpts to the existing validator-preferred Markdown cache; original bytes retained. Text-cache appendix moved here after a recorded precedence failure. Original abstract-only frontmatter describes the retained base; the attributed appendix is not a full article."
+ }
+ ],
+ "unchanged_cache_files": 919,
+ "total_cache_files": 924,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch124/algal-abstract.txt": "2a545d760b407fb5402d0a655a8c2ef575d6c5bf639125098db4c6dea65ea3f8",
+ "/private/tmp/communitymech-batch124/algal-body.txt": "8732ad326220f65ce00fc61007eebc4e93aae6266aca6e2c5e5410c7b93e4eed",
+ "/private/tmp/communitymech-batch124/algal-crossref.json": "269b1296f173ede5f527e53a52c0a9ab5900e6a7a3f24e70beddaafa655b211e",
+ "/private/tmp/communitymech-batch124/algal-metadata.json": "1ff09935a8a5371ce87d56dfcdad001f5b685e763e30bf97dfc1a073b305a6af",
+ "/private/tmp/communitymech-batch124/algal-pmc.raw": "2e65b79dfbacc403a19da0617ec2f5ec5413480bed0aa6787625c60d44e24985",
+ "/private/tmp/communitymech-batch124/baseline.json": "e9ade8d2b84d5a41f39ed8c3957fc4d3fe885f611f7d04b9829d4a94284bd7f2",
+ "/private/tmp/communitymech-batch124/edison-dry-run/AM_AB_Chlorella_MLSS_Wastewater_Consortium-edison-literature-causal-meta.yaml": "f6bc64dcee804db9f19461a19b05fb8133f50839a87ab200dee4e895564f8d50",
+ "/private/tmp/communitymech-batch124/extra-sources.json": "f0eecbc1dcae423ea1f99a68698e4eb6891b6e105c5393e6c1000056ed9c7062",
+ "/private/tmp/communitymech-batch124/hcom-abstract.txt": "eeceb9e141b0f65642b15bc7a17eea8bf7dab84dd630dba0287b2995ba98c4e6",
+ "/private/tmp/communitymech-batch124/hcom-body.txt": "c4e132b44209d46378f67b887afabd1ca688f944dca9f2beb468356d668f79e0",
+ "/private/tmp/communitymech-batch124/hcom-crossref.json": "184aee7b68d0eeb4db7ac48b3e4783d8c472e8a40987214e940778bfd1e30514",
+ "/private/tmp/communitymech-batch124/hcom-metadata.json": "2a28bcf06f7100ff011e84576f637007abd38e7a0db425aebc7af8eee9ec1988",
+ "/private/tmp/communitymech-batch124/hcom-pmc.raw": "e7322c295efe2a250bf2047b42a44e3c2d34ff45a8f086286a187583798aa8c0",
+ "/private/tmp/communitymech-batch124/issue-dedup-current.json": "26af2cedf403df4ee06650c085069a750fba515913ed2c063a8f65aeba1f95a9",
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+ "timestamp": 1548979200000
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+ "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
+ },
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+ "timestamp": 1580515200000
+ },
+ "content-version": "vor",
+ "delay-in-days": 365,
+ "URL": "http://www.elsevier.com/open-access/userlicense/1.0/"
+ }
+ ]
+ }
+ },
+ "extra_retrievals": [
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+ "url": "https://api.biorxiv.org/details/biorxiv/10.64898/2025.12.19.695487",
+ "status": 200,
+ "final_url": "https://api.biorxiv.org/details/biorxiv/10.64898/2025.12.19.695487",
+ "content_type": "application/json",
+ "path": "/private/tmp/communitymech-batch124/yarrowia-api.raw",
+ "sha256": "35eaf5d8bc99868f621c1a0fd99e5b6dd5c298c005ed54a8727a50c1f7e69800"
+ },
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+ "status": 200,
+ "final_url": "https://api.crossref.org/works/10.64898/2025.12.19.695487",
+ "content_type": "application/json",
+ "path": "/private/tmp/communitymech-batch124/yarrowia-crossref.raw",
+ "sha256": "e24a6b7126a82589e4575ea64e1b12b58b0607f81e2450f205356fbdfb456938"
+ },
+ {
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+ "url": "https://www.biorxiv.org/content/10.64898/2025.12.19.695487v1.full",
+ "status": "failed",
+ "error": "HTTP Error 403: Forbidden"
+ },
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+ "status": 200,
+ "final_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13352569/",
+ "content_type": "text/html; charset=utf-8",
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+ "text": "/private/tmp/communitymech-batch124/algal-pmc.txt"
+ },
+ {
+ "key": "hcom-pmc",
+ "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9691261/",
+ "status": 200,
+ "final_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9691261/",
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+ "sha256": "e7322c295efe2a250bf2047b42a44e3c2d34ff45a8f086286a187583798aa8c0",
+ "text": "/private/tmp/communitymech-batch124/hcom-pmc.txt"
+ },
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+ "key": "yogurt-pmc",
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+ "status": 200,
+ "final_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC2663229/",
+ "content_type": "text/html; charset=utf-8",
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+ "sha256": "e2d5dd2b5672b4f1e8b7972678ec29f9dffd82cdc68529fcfffbd2de52919598",
+ "text": "/private/tmp/communitymech-batch124/yogurt-pmc.txt"
+ },
+ {
+ "key": "yogurt20889781-pmc",
+ "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC2988612/",
+ "status": 200,
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+ "content_type": "text/html; charset=utf-8",
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+ },
+ {
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+ "status": "failed",
+ "error": "HTTP Error 403: Forbidden"
+ },
+ {
+ "key": "zymomonas-osti",
+ "url": "https://www.osti.gov/pages/biblio/1429352",
+ "status": 200,
+ "final_url": "https://www.osti.gov/pages/biblio/1429352",
+ "content_type": "text/html;charset=UTF-8",
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+ },
+ {
+ "key": "zymomonas-osti-api",
+ "url": "https://www.osti.gov/api/v1/records/1429352",
+ "status": 200,
+ "final_url": "https://www.osti.gov/api/v1/records/1429352",
+ "content_type": "application/json",
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+ "sha256": "a9c7ff7fd216750f9dc024d8bf73584afb49b1a92af2a3dbef79977139bca2c2"
+ }
+ ],
+ "actual_read_scope": [
+ "Fresh EuropePMC metadata/abstracts for eight PubMed papers and Crossref identities checked. Yarrowia bioRxivAPI and version1 XML retrieved; not certified peer-reviewed. XML failures for four PMC articles did not imply absent full text: their PMC HTML bodies were retrieved and read. TCP publisher403; only its abstract supports this review.",
+ "Algae primary Methods2.1-2.9,Results/Discussion3.1-3.4,Conclusion andTables1-4 read. Algae-only controls bound faster or universally better remediation; phosphate reaches detection limits in both and early nitrogen removal is slower in AM-AB. Correlations and theoretical methane yield are not transfer or production measurements. Available HRAP metadata deferred to1969; outdoor conditions must not inherit indoor stock settings.",
+ "Yarrowia full Methods,Results3.3-3.6,Discussion4.1-4.2 andConclusions read. Exact pair is YBGL3/YBXT-XR; shared glucose use and lack of simultaneous glucose/xylose consumption rule out exclusive niches. Higher fraction in1:5 is not higher titer or all-ratio benefit. Methods/Results ratio ambiguity and existing member metadata remain1970. Earlier enzyme-characterization Results not fully read.",
+ "Yogurt19114510 strain Methods,growth/nitrogen Results andBCAA/purine Discussion;20889781 strain/compound/metabolite Methods,addition andnitrogen/CO2 Results/Table1 andDiscussion;24936380 main mechanism Results/Discussion andMethods;30594386 abstract read. Distinct pairs and stage-specific recipients kept separate. Positive knockout/supplementation outcomes retained without flux or universal mutualism. Non-graph19395564 dataset not researched; urease summary deferred1971.",
+ "Zymomonas accepted manuscript abstract/introduction,Results andrescue controls throughpage8 andstrain Methods start read via UCweb PDF extraction. Direct curl/urllib PDF downloads were empty and not evidence. Positive spent-medium,individual metabolite andspecies-resolved growth results retained. Glutathione is not the exclusive necessary mediator; three pairs are separate andlong-term stability untested. Remaining protocol Methods not fully read.",
+ "hCom2 construction,augmentation,resilience,architecture,EHECchallenge Results,Discussion/limitations and relevant strain-preparation/augmentation/challenge Methods read. Donor dependence anddropout architecture confounding bound niche-filling causality. Three facilitation labels removed andoutcomes re-evidenced with existing abstract text; non-graph debt765 remains. No restricted full body restored.",
+ "All graph anddiscussion quotes checked against caches and fresh primary artifacts by normalized contiguous matching,not entailment proof. Four caches gain short provenance-labeled excerpts; missingTCPabstract restored from an unchanged user file andindependently matched.919originalcaches unchanged;924total. No full-body import,figure-pixel inspection,external-supplement/raw-data/code audit or whole-record certification."
+ ]
+ },
+ "limitations": [
+ "Pre-source baseline covers460records,923caches,57existing warnings and zero structural defects. Six whole records and15nodes/eight arrows reviewed; all retained,six renames,no new topology. Five existing graphs repaired; algae-MLSS remains an empty-graph extension gap.",
+ "Fresh EuropePMC metadata/abstracts for eight PubMed papers and Crossref identities checked. Yarrowia bioRxivAPI and version1 XML retrieved; not certified peer-reviewed. XML failures for four PMC articles did not imply absent full text: their PMC HTML bodies were retrieved and read. TCP publisher403; only its abstract supports this review.",
+ "Algae primary Methods2.1-2.9,Results/Discussion3.1-3.4,Conclusion andTables1-4 read. Algae-only controls bound faster or universally better remediation; phosphate reaches detection limits in both and early nitrogen removal is slower in AM-AB. Correlations and theoretical methane yield are not transfer or production measurements. Available HRAP metadata deferred to1969; outdoor conditions must not inherit indoor stock settings.",
+ "Yarrowia full Methods,Results3.3-3.6,Discussion4.1-4.2 andConclusions read. Exact pair is YBGL3/YBXT-XR; shared glucose use and lack of simultaneous glucose/xylose consumption rule out exclusive niches. Higher fraction in1:5 is not higher titer or all-ratio benefit. Methods/Results ratio ambiguity and existing member metadata remain1970. Earlier enzyme-characterization Results not fully read.",
+ "Yogurt19114510 strain Methods,growth/nitrogen Results andBCAA/purine Discussion;20889781 strain/compound/metabolite Methods,addition andnitrogen/CO2 Results/Table1 andDiscussion;24936380 main mechanism Results/Discussion andMethods;30594386 abstract read. Distinct pairs and stage-specific recipients kept separate. Positive knockout/supplementation outcomes retained without flux or universal mutualism. Non-graph19395564 dataset not researched; urease summary deferred1971.",
+ "Zymomonas accepted manuscript abstract/introduction,Results andrescue controls throughpage8 andstrain Methods start read via UCweb PDF extraction. Direct curl/urllib PDF downloads were empty and not evidence. Positive spent-medium,individual metabolite andspecies-resolved growth results retained. Glutathione is not the exclusive necessary mediator; three pairs are separate andlong-term stability untested. Remaining protocol Methods not fully read.",
+ "hCom2 construction,augmentation,resilience,architecture,EHECchallenge Results,Discussion/limitations and relevant strain-preparation/augmentation/challenge Methods read. Donor dependence anddropout architecture confounding bound niche-filling causality. Three facilitation labels removed andoutcomes re-evidenced with existing abstract text; non-graph debt765 remains. No restricted full body restored.",
+ "All graph anddiscussion quotes checked against caches and fresh primary artifacts by normalized contiguous matching,not entailment proof. Four caches gain short provenance-labeled excerpts; missingTCPabstract restored from an unchanged user file andindependently matched.919originalcaches unchanged;924total. No full-body import,figure-pixel inspection,external-supplement/raw-data/code audit or whole-record certification.",
+ "Initial TCPbaseline reference check failed due missingcache andnetworkDNS; originalfailure/log retained. Afterverifiedcache restoration,24recovered targetbaseline checks passed. Fresh source retrieval logs retain failures as well as successful alternative access routes.",
+ "Expanded all-state1196issue titles/bodies and178matchinghidden/ignored localpaths searched; ninepriorissue bodies read. Credentials,.git,generateddocs/site andreferencecaches excluded from issue-dedup search;caches separately inspected. No historicalPRcomment audit. Engineered gutaminoacid neighbor read as convention only,not transferred evidence; no reusable target taxon files found in ignored-inclusive search.",
+ "Six guarded writes preserve454otherrecords,unrelated rawYAMLblocks andallpriorhistory/decision artifacts. Six append-onlyhistories/events. Yogurturease/Nox endpoints nowcommunity-scoped withbothcanonicalparticipants; other scopes/taxonomy preserved. Connectivity logic unchanged; census measured separately.",
+ "One-community algae Edison dryrun completed without provider submission orcredits. New extension requires separately scoped spend authorization; priorRuegeria1883 configured-authentication blocker not retried unchanged. No credentials inspected. Source-based self-adversarial review is notindependent approval.55researchrecords andprotectedmerge/branchdeletion remain incomplete."
+ ],
+ "cache_precedence_repair": {
+ "source": "references_cache/PMID_26885935.txt",
+ "destination": "references_cache/PMID_26885935.md",
+ "original_text_restored": true,
+ "retained_failure_log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-references.log",
+ "reason": "Reference fetcher 0.1.7 prefers .md; snippet audit combines both formats. No validator change or weakened gate."
+ },
+ "copyright_holder_correction": "Algae article copyright notice identifies Water Environment Federation, not publisher Wiley. Excerpt and scientific claims unchanged.",
+ "import_whitespace_normalization": {
+ "path": "references_cache/PMID_41736479.txt",
+ "before_sha256": "277a89b76cc003225388033aaf4e4f13ba3c836f17f16e99978ea7afbb074e46",
+ "after_sha256": "0f4e3719902f55ce45dfde9383042337bfd85897a53660e1d434f89a777be27e",
+ "failure_exit_code": 2,
+ "failure_log": "/private/tmp/communitymech-batch124/initial-staged-diff-check.log",
+ "failure_log_sha256": "eff4e386e2baddb56cc85eb8837fc85aa9900effedfcb29b3b68a7e6e7e49466",
+ "scope": "Final newline and trailing ASCII whitespace only; original user file untouched."
+ }
+}
diff --git a/reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml b/reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
new file mode 100644
index 000000000..fe9ddfea4
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
@@ -0,0 +1,1260 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 19010db53b3b5537d458727318921006e83e7ccb
+baseline_commit: 19010db53b3b5537d458727318921006e83e7ccb
+base_tree: e3628b1faedb3c6fc42392a051586a6a12536d27
+pre_source_baseline_sha256: e9ade8d2b84d5a41f39ed8c3957fc4d3fe885f611f7d04b9829d4a94284bd7f2
+issues:
+- 1968
+- 1963
+- 1964
+- 1965
+- 1966
+- 1967
+unresolved_research_issues:
+- 1968
+unresolved_non_graph_issues:
+- 1969
+- 1970
+- 1971
+- 765
+source_access:
+ retrieval_manifest:
+ algal:
+ pmid: '42429207'
+ doi: 10.1002/wer.70489
+ pmcid: PMC13352569
+ title: 'Activated Microalgae-Activated MLSS Bacteria Consortium Synergistically Improves Phycoremediation
+ Kinetics: A Parallel Bio-Activation Approach for Effective Wastewater Treatment and Biomass Production.'
+ metadata: /private/tmp/communitymech-batch124/algal-metadata.json
+ metadata_sha256: 1ff09935a8a5371ce87d56dfcdad001f5b685e763e30bf97dfc1a073b305a6af
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13352569/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch124/algal-abstract.txt
+ abstract_sha256: 2a545d760b407fb5402d0a655a8c2ef575d6c5bf639125098db4c6dea65ea3f8
+ crossref: /private/tmp/communitymech-batch124/algal-crossref.json
+ crossref_sha256: 269b1296f173ede5f527e53a52c0a9ab5900e6a7a3f24e70beddaafa655b211e
+ crossref_license:
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+ date-parts:
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+ timestamp: 1783641600000
+ content-version: vor
+ delay-in-days: 9
+ URL: http://onlinelibrary.wiley.com/termsAndConditions#vor
+ - start:
+ date-parts:
+ - - 2026
+ - 7
+ - 1
+ date-time: '2026-07-01T00:00:00Z'
+ timestamp: 1782864000000
+ content-version: tdm
+ delay-in-days: 0
+ URL: http://doi.wiley.com/10.1002/tdm_license_1.1
+ tcp:
+ pmid: '41736479'
+ doi: 10.1002/wer.70318
+ pmcid: null
+ title: Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of 1,2,3-Trichloropropane in Groundwater
+ by a Non-Dehalogenimonas Consortium.
+ metadata: /private/tmp/communitymech-batch124/tcp-metadata.json
+ metadata_sha256: e32ca67ee9e2c83f8f0ed64eeb3683820d8ecf2e7bf8bb307ce9f59269e7e287
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41736479+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ abstract: /private/tmp/communitymech-batch124/tcp-abstract.txt
+ abstract_sha256: 3a1aa5d913f92706a5ec31b5b34f12371fb9fa9e5dd0ebdfd0d9fe2e1d0a2ce0
+ crossref: /private/tmp/communitymech-batch124/tcp-crossref.json
+ crossref_sha256: bb9664ae15e56a71c6ddc140ca885ea5a2ce9afc5cb7c20604403b6a1e0f9c1e
+ crossref_license:
+ - start:
+ date-parts:
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+ - 2
+ - 24
+ date-time: '2026-02-24T00:00:00Z'
+ timestamp: 1771891200000
+ content-version: vor
+ delay-in-days: 0
+ URL: http://onlinelibrary.wiley.com/termsAndConditions#vor
+ - start:
+ date-parts:
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+ - 2
+ - 24
+ date-time: '2026-02-24T00:00:00Z'
+ timestamp: 1771891200000
+ content-version: tdm
+ delay-in-days: 0
+ URL: http://doi.wiley.com/10.1002/tdm_license_1.1
+ yogurt:
+ pmid: '19114510'
+ doi: 10.1128/aem.01984-08
+ pmcid: PMC2663229
+ title: 'Postgenomic analysis of streptococcus thermophilus cocultivated in milk with Lactobacillus delbrueckii
+ subsp. bulgaricus: involvement of nitrogen, purine, and iron metabolism.'
+ metadata: /private/tmp/communitymech-batch124/yogurt-metadata.json
+ metadata_sha256: f4317d3cb6e813d8414f388798cf052b6926e110eaa463c3e73125ddd30b2471
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A19114510+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2663229/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch124/yogurt-abstract.txt
+ abstract_sha256: 6f257e3c0f64ae07b5e3c8d7641aaf55881e372c7c7904f612d5346d7b1868c4
+ crossref: /private/tmp/communitymech-batch124/yogurt-crossref.json
+ crossref_sha256: 69f41c3aa024fe47e70e2f249867c0d2285116acf00e5c350f0526e0f888fed5
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2009
+ - 4
+ - 1
+ date-time: '2009-04-01T00:00:00Z'
+ timestamp: 1238544000000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ zymomonas:
+ pmid: '26885935'
+ doi: 10.1021/acssynbio.5b00236
+ pmcid: null
+ title: Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.
+ metadata: /private/tmp/communitymech-batch124/zymomonas-metadata.json
+ metadata_sha256: 674e8d70e46da8fe1ab72091a27fe767a16add29aab6b3109dfd6fa5209ae025
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A26885935+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ abstract: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ abstract_sha256: e3d54fff910d3f4457d39ef11220b652d6f3c25aa8940afee00cbb8730243988
+ crossref: /private/tmp/communitymech-batch124/zymomonas-crossref.json
+ crossref_sha256: a54175bb70a0e5616a216811b5b58975f3c512a5bad114b411575d06245e63c0
+ crossref_license: []
+ hcom:
+ pmid: '36070752'
+ doi: 10.1016/j.cell.2022.08.003
+ pmcid: PMC9691261
+ title: "Design, construction, and in\_vivo augmentation of a complex gut microbiome."
+ metadata: /private/tmp/communitymech-batch124/hcom-metadata.json
+ metadata_sha256: 2a28bcf06f7100ff011e84576f637007abd38e7a0db425aebc7af8eee9ec1988
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A36070752+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9691261/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch124/hcom-abstract.txt
+ abstract_sha256: eeceb9e141b0f65642b15bc7a17eea8bf7dab84dd630dba0287b2995ba98c4e6
+ crossref: /private/tmp/communitymech-batch124/hcom-crossref.json
+ crossref_sha256: 184aee7b68d0eeb4db7ac48b3e4783d8c472e8a40987214e940778bfd1e30514
+ crossref_license:
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+ content-version: tdm
+ delay-in-days: 0
+ URL: https://www.elsevier.com/legal/tdmrep-license
+ - start:
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+ date-time: '2023-10-07T00:00:00Z'
+ timestamp: 1696636800000
+ content-version: vor
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+ URL: http://www.elsevier.com/open-access/userlicense/1.0/
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+ timestamp: 1661990400000
+ content-version: stm-asf
+ delay-in-days: 0
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+ - start:
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+ yogurt20889781:
+ pmid: '20889781'
+ doi: 10.1128/aem.01122-10
+ pmcid: PMC2988612
+ title: Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus
+ thermophilus and Lactobacillus bulgaricus.
+ metadata: /private/tmp/communitymech-batch124/yogurt20889781-metadata.json
+ metadata_sha256: c20afdd0d27a499c9fb71e1f1414b7ff02f5c302ca19320b1b60ebcb4728d3ef
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2988612/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch124/yogurt20889781-abstract.txt
+ abstract_sha256: f3c38cb6afe64a6b14067e37b91cf0896df5a4c8ef41972738e5870064434f71
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+ crossref_sha256: 525d4782db396dd5c970445c3891ea7df0bca1bacdb8a780a572fb2adfde070b
+ crossref_license:
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+ timestamp: 1291161600000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://journals.asm.org/non-commercial-tdm-license
+ yogurt24936380:
+ pmid: '24936380'
+ doi: 10.12938/bmfh.33.31
+ pmcid: PMC4034325
+ title: NADH Oxidase of Streptococcus thermophilus 1131 is Required for the Effective Yogurt Fermentation with
+ Lactobacillus delbrueckii subsp. bulgaricus 2038.
+ metadata: /private/tmp/communitymech-batch124/yogurt24936380-metadata.json
+ metadata_sha256: f7e66f82d2cd0c9f56fd569fc046ae37672e89c6b305118b3ea54800992f59a1
+ retrievals:
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+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4034325/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch124/yogurt24936380-abstract.txt
+ abstract_sha256: efd8f9f6a68983e577273f33bad9d037005dacc2dc47bc0f0822f074b7fd61e6
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+ license:
+ - This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial
+ No Derivatives (by-nc-nd) License.
+ crossref: /private/tmp/communitymech-batch124/yogurt24936380-crossref.json
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+ crossref_license: []
+ yogurt30594386:
+ pmid: '30594386'
+ doi: 10.3168/jds.2018-15192
+ pmcid: null
+ title: The critical role of urease in yogurt fermentation with various combinations of Streptococcus thermophilus
+ and Lactobacillus delbrueckii ssp. bulgaricus.
+ metadata: /private/tmp/communitymech-batch124/yogurt30594386-metadata.json
+ metadata_sha256: 98bf0268c350257568d537b5ba0f0caf43ecac1f5f8db813ce0d02a71914d77e
+ retrievals:
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+ status: retrieved
+ abstract: /private/tmp/communitymech-batch124/yogurt30594386-abstract.txt
+ abstract_sha256: 7ccd9adb03c82f7c3da98cb3398bcee453765b92bbc80f3852fac06158a1253f
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+ content-version: tdm
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+ - start:
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+ timestamp: 1580515200000
+ content-version: vor
+ delay-in-days: 365
+ URL: http://www.elsevier.com/open-access/userlicense/1.0/
+ extra_retrievals:
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+ status: 200
+ final_url: https://api.crossref.org/works/10.64898/2025.12.19.695487
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+ - key: yarrowia-full
+ url: https://www.biorxiv.org/content/10.64898/2025.12.19.695487v1.full
+ status: failed
+ error: 'HTTP Error 403: Forbidden'
+ - key: algal-pmc
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC13352569/
+ status: 200
+ final_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC13352569/
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+ text: /private/tmp/communitymech-batch124/algal-pmc.txt
+ - key: hcom-pmc
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC9691261/
+ status: 200
+ final_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC9691261/
+ content_type: text/html; charset=utf-8
+ path: /private/tmp/communitymech-batch124/hcom-pmc.raw
+ sha256: e7322c295efe2a250bf2047b42a44e3c2d34ff45a8f086286a187583798aa8c0
+ text: /private/tmp/communitymech-batch124/hcom-pmc.txt
+ - key: yogurt-pmc
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC2663229/
+ status: 200
+ final_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC2663229/
+ content_type: text/html; charset=utf-8
+ path: /private/tmp/communitymech-batch124/yogurt-pmc.raw
+ sha256: e2d5dd2b5672b4f1e8b7972678ec29f9dffd82cdc68529fcfffbd2de52919598
+ text: /private/tmp/communitymech-batch124/yogurt-pmc.txt
+ - key: yogurt20889781-pmc
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC2988612/
+ status: 200
+ final_url: https://pmc.ncbi.nlm.nih.gov/articles/PMC2988612/
+ content_type: text/html; charset=utf-8
+ path: /private/tmp/communitymech-batch124/yogurt20889781-pmc.raw
+ sha256: bc0d91fd74e80dd2bbbe8aaade910f8f17a5d60fb02082ffbe304fa868f14b69
+ text: /private/tmp/communitymech-batch124/yogurt20889781-pmc.txt
+ - key: tcp-publisher
+ url: https://onlinelibrary.wiley.com/doi/full/10.1002/wer.70318
+ status: failed
+ error: 'HTTP Error 403: Forbidden'
+ - key: zymomonas-osti
+ url: https://www.osti.gov/pages/biblio/1429352
+ status: 200
+ final_url: https://www.osti.gov/pages/biblio/1429352
+ content_type: text/html;charset=UTF-8
+ path: /private/tmp/communitymech-batch124/zymomonas-osti.raw
+ sha256: 33ece9ce86ea63dccdaab2b182e54565af3e41b1c7447c1822112860f33763d7
+ text: /private/tmp/communitymech-batch124/zymomonas-osti.txt
+ - key: zymomonas-osti-api
+ url: https://www.osti.gov/api/v1/records/1429352
+ status: 200
+ final_url: https://www.osti.gov/api/v1/records/1429352
+ content_type: application/json
+ path: /private/tmp/communitymech-batch124/zymomonas-osti-api.raw
+ sha256: a9c7ff7fd216750f9dc024d8bf73584afb49b1a92af2a3dbef79977139bca2c2
+ actual_read_scope:
+ - 'Fresh EuropePMC metadata/abstracts for eight PubMed papers and Crossref identities checked. Yarrowia bioRxivAPI
+ and version1 XML retrieved; not certified peer-reviewed. XML failures for four PMC articles did not imply absent
+ full text: their PMC HTML bodies were retrieved and read. TCP publisher403; only its abstract supports this
+ review.'
+ - Algae primary Methods2.1-2.9,Results/Discussion3.1-3.4,Conclusion andTables1-4 read. Algae-only controls bound
+ faster or universally better remediation; phosphate reaches detection limits in both and early nitrogen removal
+ is slower in AM-AB. Correlations and theoretical methane yield are not transfer or production measurements.
+ Available HRAP metadata deferred to1969; outdoor conditions must not inherit indoor stock settings.
+ - Yarrowia full Methods,Results3.3-3.6,Discussion4.1-4.2 andConclusions read. Exact pair is YBGL3/YBXT-XR; shared
+ glucose use and lack of simultaneous glucose/xylose consumption rule out exclusive niches. Higher fraction in1:5
+ is not higher titer or all-ratio benefit. Methods/Results ratio ambiguity and existing member metadata remain1970.
+ Earlier enzyme-characterization Results not fully read.
+ - Yogurt19114510 strain Methods,growth/nitrogen Results andBCAA/purine Discussion;20889781 strain/compound/metabolite
+ Methods,addition andnitrogen/CO2 Results/Table1 andDiscussion;24936380 main mechanism Results/Discussion andMethods;30594386
+ abstract read. Distinct pairs and stage-specific recipients kept separate. Positive knockout/supplementation
+ outcomes retained without flux or universal mutualism. Non-graph19395564 dataset not researched; urease summary
+ deferred1971.
+ - Zymomonas accepted manuscript abstract/introduction,Results andrescue controls throughpage8 andstrain Methods
+ start read via UCweb PDF extraction. Direct curl/urllib PDF downloads were empty and not evidence. Positive
+ spent-medium,individual metabolite andspecies-resolved growth results retained. Glutathione is not the exclusive
+ necessary mediator; three pairs are separate andlong-term stability untested. Remaining protocol Methods not
+ fully read.
+ - hCom2 construction,augmentation,resilience,architecture,EHECchallenge Results,Discussion/limitations and relevant
+ strain-preparation/augmentation/challenge Methods read. Donor dependence anddropout architecture confounding
+ bound niche-filling causality. Three facilitation labels removed andoutcomes re-evidenced with existing abstract
+ text; non-graph debt765 remains. No restricted full body restored.
+ - All graph anddiscussion quotes checked against caches and fresh primary artifacts by normalized contiguous matching,not
+ entailment proof. Four caches gain short provenance-labeled excerpts; missingTCPabstract restored from an unchanged
+ user file andindependently matched.919originalcaches unchanged;924total. No full-body import,figure-pixel inspection,external-supplement/raw-data/code
+ audit or whole-record certification.
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+ node: Higher Lipid Fraction in the 1:5 Consortium
+ evidence_index: 0
+ reference: doi:10.64898/2025.12.19.695487
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yarrowia-api.raw
+ cache_artifact: references_cache/doi_10.64898_2025.12.19.695487.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium
+ node: Higher Lipid Fraction in the 1:5 Consortium
+ evidence_index: 1
+ reference: doi:10.64898/2025.12.19.695487
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yarrowia-body.txt
+ cache_artifact: references_cache/doi_10.64898_2025.12.19.695487.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Streptococcus Formate and Carbon Dioxide Support
+ evidence_index: 0
+ reference: PMID:20889781
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt20889781-abstract.txt
+ cache_artifact: references_cache/PMID_20889781.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Streptococcus Formate and Carbon Dioxide Support
+ evidence_index: 1
+ reference: PMID:20889781
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt20889781-abstract.txt
+ cache_artifact: references_cache/PMID_20889781.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Streptococcus Formate and Carbon Dioxide Support
+ evidence_index: 2
+ reference: PMID:24936380
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt24936380-abstract.txt
+ cache_artifact: references_cache/PMID_24936380.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Lactobacillus Proteolytic Nitrogen Support
+ evidence_index: 0
+ reference: PMID:20889781
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt20889781-abstract.txt
+ cache_artifact: references_cache/PMID_20889781.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Lactobacillus Proteolytic Nitrogen Support
+ evidence_index: 1
+ reference: PMID:19114510
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt-abstract.txt
+ cache_artifact: references_cache/PMID_19114510.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Urease-Dependent Acidification Acceleration
+ evidence_index: 0
+ reference: PMID:30594386
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt30594386-abstract.txt
+ cache_artifact: references_cache/PMID_30594386.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Urease-Dependent Acidification Acceleration
+ evidence_index: 1
+ reference: PMID:30594386
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt30594386-abstract.txt
+ cache_artifact: references_cache/PMID_30594386.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Streptococcus Nox-Dependent Milk Fermentation
+ evidence_index: 0
+ reference: PMID:24936380
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt24936380-abstract.txt
+ cache_artifact: references_cache/PMID_24936380.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Streptococcus Nox-Dependent Milk Fermentation
+ evidence_index: 1
+ reference: PMID:24936380
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt24936380-abstract.txt
+ cache_artifact: references_cache/PMID_24936380.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: Streptococcus Nox-Dependent Milk Fermentation
+ evidence_index: 2
+ reference: PMID:24936380
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt24936380-abstract.txt
+ cache_artifact: references_cache/PMID_24936380.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ evidence_index: 0
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ evidence_index: 1
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ evidence_index: 2
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-web-readable.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ evidence_index: 0
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ evidence_index: 1
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ evidence_index: 2
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-web-readable.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: Reciprocal Auxotroph Coculture Growth
+ evidence_index: 0
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: Reciprocal Auxotroph Coculture Growth
+ evidence_index: 1
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: Reciprocal Auxotroph Coculture Growth
+ evidence_index: 2
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: hCom2_Complex_Gut_Microbiome
+ node: Fecal-Challenge-Guided Community Augmentation
+ evidence_index: 0
+ reference: PMID:36070752
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/hcom-abstract.txt
+ cache_artifact: references_cache/PMID_36070752.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: hCom2_Complex_Gut_Microbiome
+ node: hCom2 Fecal-Challenge Stability
+ evidence_index: 0
+ reference: PMID:36070752
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/hcom-abstract.txt
+ cache_artifact: references_cache/PMID_36070752.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: hCom2_Complex_Gut_Microbiome
+ node: hCom2 Escherichia coli Colonization Resistance
+ evidence_index: 0
+ reference: PMID:36070752
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/hcom-abstract.txt
+ cache_artifact: references_cache/PMID_36070752.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+discussion_snippet_checks:
+- record: AM_AB_Chlorella_MLSS_Wastewater_Consortium
+ node: am_ab_control_bounded_graph_extension
+ evidence_index: 0
+ reference: PMID:42429207
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/algal-body.txt
+ cache_artifact: references_cache/PMID_42429207.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: TCP_NonDehalogenimonas_Groundwater_Consortium
+ node: tcp_module_mediation_vs_amendment_response
+ evidence_index: 0
+ reference: PMID:41736479
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/tcp-abstract.txt
+ cache_artifact: references_cache/PMID_41736479.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium
+ node: yarrowia_fraction_titer_and_competing_glucose_use
+ evidence_index: 0
+ reference: doi:10.64898/2025.12.19.695487
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yarrowia-body.txt
+ cache_artifact: references_cache/doi_10.64898_2025.12.19.695487.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Yogurt_TwoSpecies_Starter_Culture
+ node: yogurt_strain_stage_and_mediator_boundaries
+ evidence_index: 0
+ reference: PMID:19114510
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/yogurt-body.txt
+ cache_artifact: references_cache/PMID_19114510.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism
+ node: zymomonas_sulfur_identity_and_release_routes
+ evidence_index: 0
+ reference: PMID:26885935
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/zymomonas-abstract.txt
+ cache_artifact: references_cache/PMID_26885935.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: hCom2_Complex_Gut_Microbiome
+ node: hcom_augmentation_vs_protective_mechanism
+ evidence_index: 0
+ reference: PMID:36070752
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch124/hcom-abstract.txt
+ cache_artifact: references_cache/PMID_36070752.txt
+ scope: Normalized contiguous literal match, not entailment proof.
+cache_changes:
+- path: references_cache/PMID_41736479.txt
+ before_sha256: null
+ after_sha256: 0f4e3719902f55ce45dfde9383042337bfd85897a53660e1d434f89a777be27e
+ action: Restore missing abstract from the existing main-checkout user file, independently match EuropePMC, add
+ final newline and strip trailing ASCII spaces/tabs for the staged whitespace gate. Original user file unchanged;
+ source words unchanged.
+- path: references_cache/PMID_42429207.txt
+ before_sha256: 2a50d54a82547f7ddb7d1536dce9dbc5b7553c8769f1eec4b936db41ec973e8b
+ after_sha256: eb80e76d862305f4031055915eb45a832b8f32de2d0bfe042eb9142c314f4c7a
+ action: Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix.
+- path: references_cache/doi_10.64898_2025.12.19.695487.md
+ before_sha256: b29827aa946f1564bd10177dfebab726689113664f122f4431bbfeb2ed7bfbd5
+ after_sha256: 561f7a1c054813f2b701c766fc4e69203400fe1ef88cd09dea41c522a1748e20
+ action: Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix.
+- path: references_cache/PMID_19114510.txt
+ before_sha256: 27f1a2c09f8768aafe25638ffb75f83ede4920a0e2f02d7ae915f419e966daac
+ after_sha256: 5620d2ac074263119962e98e17f1d705a764c3f0b972328370c07a171da697cf
+ action: Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix.
+- path: references_cache/PMID_26885935.md
+ before_sha256: 739cb68daf6d073e9057cfaa0a530869eb66b3c804241dcf9503e25153a080bc
+ after_sha256: 90b61b191addc52f9876cb1e93f1dfd729753ab5ffc2b22e9748c671198df777
+ action: Append the same short literal excerpts to the existing validator-preferred Markdown cache; original bytes
+ retained. Text-cache appendix moved here after a recorded precedence failure. Original abstract-only frontmatter
+ describes the retained base; the attributed appendix is not a full article.
+edison:
+ required_for_existing_graph_repairs: false
+ required_for_algal_extension: true
+ dry_run_completed: true
+ dry_run_artifacts:
+ - /private/tmp/communitymech-batch124/edison-dry-run/AM_AB_Chlorella_MLSS_Wastewater_Consortium-edison-literature-causal-meta.yaml
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria1883: configured authentication unavailable in prior authorized invocation;
+ no unchanged-state retry or broader spend.'
+limitations:
+- Pre-source baseline covers460records,923caches,57existing warnings and zero structural defects. Six whole records
+ and15nodes/eight arrows reviewed; all retained,six renames,no new topology. Five existing graphs repaired; algae-MLSS
+ remains an empty-graph extension gap.
+- 'Fresh EuropePMC metadata/abstracts for eight PubMed papers and Crossref identities checked. Yarrowia bioRxivAPI
+ and version1 XML retrieved; not certified peer-reviewed. XML failures for four PMC articles did not imply absent
+ full text: their PMC HTML bodies were retrieved and read. TCP publisher403; only its abstract supports this review.'
+- Algae primary Methods2.1-2.9,Results/Discussion3.1-3.4,Conclusion andTables1-4 read. Algae-only controls bound
+ faster or universally better remediation; phosphate reaches detection limits in both and early nitrogen removal
+ is slower in AM-AB. Correlations and theoretical methane yield are not transfer or production measurements. Available
+ HRAP metadata deferred to1969; outdoor conditions must not inherit indoor stock settings.
+- Yarrowia full Methods,Results3.3-3.6,Discussion4.1-4.2 andConclusions read. Exact pair is YBGL3/YBXT-XR; shared
+ glucose use and lack of simultaneous glucose/xylose consumption rule out exclusive niches. Higher fraction in1:5
+ is not higher titer or all-ratio benefit. Methods/Results ratio ambiguity and existing member metadata remain1970.
+ Earlier enzyme-characterization Results not fully read.
+- Yogurt19114510 strain Methods,growth/nitrogen Results andBCAA/purine Discussion;20889781 strain/compound/metabolite
+ Methods,addition andnitrogen/CO2 Results/Table1 andDiscussion;24936380 main mechanism Results/Discussion andMethods;30594386
+ abstract read. Distinct pairs and stage-specific recipients kept separate. Positive knockout/supplementation outcomes
+ retained without flux or universal mutualism. Non-graph19395564 dataset not researched; urease summary deferred1971.
+- Zymomonas accepted manuscript abstract/introduction,Results andrescue controls throughpage8 andstrain Methods
+ start read via UCweb PDF extraction. Direct curl/urllib PDF downloads were empty and not evidence. Positive spent-medium,individual
+ metabolite andspecies-resolved growth results retained. Glutathione is not the exclusive necessary mediator; three
+ pairs are separate andlong-term stability untested. Remaining protocol Methods not fully read.
+- hCom2 construction,augmentation,resilience,architecture,EHECchallenge Results,Discussion/limitations and relevant
+ strain-preparation/augmentation/challenge Methods read. Donor dependence anddropout architecture confounding bound
+ niche-filling causality. Three facilitation labels removed andoutcomes re-evidenced with existing abstract text;
+ non-graph debt765 remains. No restricted full body restored.
+- All graph anddiscussion quotes checked against caches and fresh primary artifacts by normalized contiguous matching,not
+ entailment proof. Four caches gain short provenance-labeled excerpts; missingTCPabstract restored from an unchanged
+ user file andindependently matched.919originalcaches unchanged;924total. No full-body import,figure-pixel inspection,external-supplement/raw-data/code
+ audit or whole-record certification.
+- Initial TCPbaseline reference check failed due missingcache andnetworkDNS; originalfailure/log retained. Afterverifiedcache
+ restoration,24recovered targetbaseline checks passed. Fresh source retrieval logs retain failures as well as successful
+ alternative access routes.
+- Expanded all-state1196issue titles/bodies and178matchinghidden/ignored localpaths searched; ninepriorissue bodies
+ read. Credentials,.git,generateddocs/site andreferencecaches excluded from issue-dedup search;caches separately
+ inspected. No historicalPRcomment audit. Engineered gutaminoacid neighbor read as convention only,not transferred
+ evidence; no reusable target taxon files found in ignored-inclusive search.
+- Six guarded writes preserve454otherrecords,unrelated rawYAMLblocks andallpriorhistory/decision artifacts. Six
+ append-onlyhistories/events. Yogurturease/Nox endpoints nowcommunity-scoped withbothcanonicalparticipants; other
+ scopes/taxonomy preserved. Connectivity logic unchanged; census measured separately.
+- One-community algae Edison dryrun completed without provider submission orcredits. New extension requires separately
+ scoped spend authorization; priorRuegeria1883 configured-authentication blocker not retried unchanged. No credentials
+ inspected. Source-based self-adversarial review is notindependent approval.55researchrecords andprotectedmerge/branchdeletion
+ remain incomplete.
+records:
+- path: kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml
+ id: CommunityMech:000444
+ original_sha256: 1b8f102df55d246a4f8dd49e8b3e8d09ea2e7ac082cc829e2324109751889abb
+ record_sha256: f3a69684e81df00ca791bfc61832141ad9048270f4b3ed476328b772d07604d2
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ scope: Whole record and existing graph reviewed; existing-graph repair or documented empty-graph extension gap,
+ not whole-record certification.
+ summary: Review empty graph against full-text controls; retain a substantive extension gap without inventing nodes,
+ and update the stale abstract-access discussion.
+ node_decisions: []
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:42429207
+ issues:
+ - 1968
+ - 1969
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ curation_events_added: 1
+ history_files:
+ - history/records/AM_AB_Chlorella_MLSS_Wastewater_Consortium/2026-10-08T175132Z-codex-665b31.yaml
+- path: kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml
+ id: CommunityMech:000437
+ original_sha256: 0d96313dbd7866dd7d642e83eab9956ff03a6c7f6a867de6ffb91ce1a3796382
+ record_sha256: ab6b0b9201bc3d3ca9c7b2cbd5395404b1ed071c064d2efb36351e4d72d6d02b
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ scope: Whole record and existing graph reviewed; existing-graph repair or documented empty-graph extension gap,
+ not whole-record certification.
+ summary: Qualify reconstructed coupling and correct computational provenance without genus-specific functions.;
+ Retain positive amendment and removal endpoints without assigning culture-wide rates to each substrate.
+ node_decisions:
+ - node: Inferred Hydrogen Cofactor Reductive-Dechlorination Module
+ rationale: Qualify reconstructed coupling and correct computational provenance without genus-specific functions.
+ - node: Co-Metabolic Substrate Enhanced TCP Removal
+ rationale: Retain positive amendment and removal endpoints without assigning culture-wide rates to each substrate.
+ removed_node_decisions: []
+ renamed_nodes:
+ Hydrogen Cofactor Reductive-Dechlorination Module: Inferred Hydrogen Cofactor Reductive-Dechlorination Module
+ edges_before: []
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:41736479
+ issues:
+ - 1963
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/TCP_NonDehalogenimonas_Groundwater_Consortium/2026-10-08T175132Z-codex-e21077.yaml
+- path: kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml
+ id: CommunityMech:000354
+ original_sha256: 3f48f2b903eec6f6ac2e93c952821980eb066df571ec4e1a5519ac7c47293e7c
+ record_sha256: 2dbf53129f98e8df7edc68f7d3f2bc6ca7c748ac563d0e31abd1274a15ca051a
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ scope: Whole record and existing graph reviewed; existing-graph repair or documented empty-graph extension gap,
+ not whole-record certification.
+ summary: Retain engineered hydrolysis division without polymer-catabolism, exclusive-niche or burden-relief overclaims.;
+ Retain temporal succession while qualifying its mechanism.; Retain the condition-specific lipid-fraction benefit
+ and comparable-titer counterpoint.
+ node_decisions:
+ - node: Oligosaccharide Hydrolysis Division of Labor
+ rationale: Retain engineered hydrolysis division without polymer-catabolism, exclusive-niche or burden-relief
+ overclaims.
+ - node: Population Shift to YBXT-XR
+ rationale: Retain temporal succession while qualifying its mechanism.
+ - node: Higher Lipid Fraction in the 1:5 Consortium
+ rationale: Retain the condition-specific lipid-fraction benefit and comparable-titer counterpoint.
+ removed_node_decisions: []
+ renamed_nodes:
+ Cellobiose-Xylooligosaccharide Division of Labor: Oligosaccharide Hydrolysis Division of Labor
+ Enhanced Lipid Accumulation: Higher Lipid Fraction in the 1:5 Consortium
+ edges_before:
+ - &id001
+ source: Cellobiose-Xylooligosaccharide Division of Labor
+ target: Population Shift to YBXT-XR
+ description: Cellobiose depletion precedes enrichment of YBXT-XR and preferential use of the remaining xylooligosaccharides
+ for lipid synthesis.
+ - &id003
+ source: Cellobiose-Xylooligosaccharide Division of Labor
+ target: Enhanced Lipid Accumulation
+ description: Distributed oligosaccharide hydrolysis and assimilation yielded higher lipid accumulation than
+ the multifunctional monoculture benchmark.
+ edges_after:
+ - &id002
+ source: Oligosaccharide Hydrolysis Division of Labor
+ target: Population Shift to YBXT-XR
+ description: 'PARTIAL: Differential substrate capacities are consistent with the population shift after cellobiose
+ depletion. The time course supports temporal succession but does not isolate depletion from other changing
+ culture conditions.'
+ - &id004
+ source: Oligosaccharide Hydrolysis Division of Labor
+ target: Higher Lipid Fraction in the 1:5 Consortium
+ description: 'PARTIAL: The tested division-of-labor design yielded the higher final lipid fraction in the nitrogen-limited
+ 1:5 consortium. The comparison does not identify burden relief as mediator or establish superior titer or
+ performance at every inoculum ratio.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'PARTIAL: Differential substrate capacities are consistent with the population shift after cellobiose
+ depletion. The time course supports temporal succession but does not isolate depletion from other changing
+ culture conditions.'
+ - before: *id003
+ after: *id004
+ rationale: 'PARTIAL: The tested division-of-labor design yielded the higher final lipid fraction in the nitrogen-limited
+ 1:5 consortium. The comparison does not identify burden relief as mediator or establish superior titer or
+ performance at every inoculum ratio.'
+ removed_edge_decisions: []
+ references:
+ - doi:10.64898/2025.12.19.695487
+ issues:
+ - 1964
+ - 1970
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium/2026-10-08T175133Z-codex-bf87bc.yaml
+- path: kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml
+ id: CommunityMech:000164
+ original_sha256: 49f5a5749a60d2f6b314cd487f84c5c6c609d23657faf7342daad53833dc9ec2
+ record_sha256: 693b023e694475fd4eeeb0fde9af92e56db2084b885af8b7bd5d1febe6140dcc
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ scope: Whole record and existing graph reviewed; existing-graph repair or documented empty-graph extension gap,
+ not whole-record certification.
+ summary: Qualify the strain-specific formate/CO2 model.; Retain nitrogen support without nutritional sufficiency
+ or demonstrated return-flow mediation.; Represent the urease effect at culture level with distinct ammonia/CO2
+ recipients.; Preserve the Nox intervention and early-growth evidence without colonization or universal-recipient
+ claims.
+ node_decisions:
+ - node: Streptococcus Formate and Carbon Dioxide Support
+ rationale: Qualify the strain-specific formate/CO2 model.
+ - node: Lactobacillus Proteolytic Nitrogen Support
+ rationale: Retain nitrogen support without nutritional sufficiency or demonstrated return-flow mediation.
+ - node: Urease-Dependent Acidification Acceleration
+ rationale: Represent the urease effect at culture level with distinct ammonia/CO2 recipients.
+ - node: Streptococcus Nox-Dependent Milk Fermentation
+ rationale: Preserve the Nox intervention and early-growth evidence without colonization or universal-recipient
+ claims.
+ removed_node_decisions: []
+ renamed_nodes:
+ Oxygen Removal by Streptococcus Thermophilus: Streptococcus Nox-Dependent Milk Fermentation
+ edges_before:
+ - &id005
+ source: Lactobacillus Proteolytic Nitrogen Support
+ target: Streptococcus Formate and Carbon Dioxide Support
+ description: 'Proteolytic nitrogen released by L. delbrueckii supports S. thermophilus growth, enabling the
+ formate and carbon dioxide return flow that accelerates protocooperative acidification.
+
+ '
+ - &id007
+ source: Oxygen Removal by Streptococcus Thermophilus
+ target: Streptococcus Formate and Carbon Dioxide Support
+ description: S. thermophilus oxygen removal relieves dissolved-oxygen suppression of yogurt fermentation and
+ is associated with earlier formate accumulation during the two-species acidification process.
+ edges_after:
+ - &id006
+ source: Lactobacillus Proteolytic Nitrogen Support
+ target: Streptococcus Formate and Carbon Dioxide Support
+ description: 'HYPOTHESIZED mediation: nitrogen support can sustain S. thermophilus growth and hence potential
+ return metabolites. The cited strain-pair experiments do not selectively establish proteolysis as the cause
+ of formate/CO2 return flow; this is not a demonstrated universal feedback loop.'
+ - &id008
+ source: Streptococcus Nox-Dependent Milk Fermentation
+ target: Streptococcus Formate and Carbon Dioxide Support
+ description: 'PARTIAL: Oxygen removal promotes early formate accumulation in the 1131/2038 system, and the nox
+ mutant lacks detected formate in the tested monoculture. Protection of oxygen-sensitive Pfl is HYPOTHESIZED;
+ the study also considers other Nox functions and does not establish the CO2 branch or universal transfer to
+ L. bulgaricus.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: 'HYPOTHESIZED mediation: nitrogen support can sustain S. thermophilus growth and hence potential
+ return metabolites. The cited strain-pair experiments do not selectively establish proteolysis as the cause
+ of formate/CO2 return flow; this is not a demonstrated universal feedback loop.'
+ - before: *id007
+ after: *id008
+ rationale: 'PARTIAL: Oxygen removal promotes early formate accumulation in the 1131/2038 system, and the nox
+ mutant lacks detected formate in the tested monoculture. Protection of oxygen-sensitive Pfl is HYPOTHESIZED;
+ the study also considers other Nox functions and does not establish the CO2 branch or universal transfer to
+ L. bulgaricus.'
+ removed_edge_decisions: []
+ references:
+ - PMID:19114510
+ - PMID:20889781
+ - PMID:24936380
+ - PMID:30594386
+ issues:
+ - 1965
+ - 1971
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Yogurt_TwoSpecies_Starter_Culture/2026-10-08T175133Z-codex-114f8d.yaml
+- path: kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml
+ id: CommunityMech:000210
+ original_sha256: 5640166eed0e15b269178e292e4e63066adb88cd20d82e65b3dd05938ae49be3
+ record_sha256: efc6e7b31f9bc7ebe11fe5a26f9f45e2a7b845684fd3a15c8b10e0d1994e6be6
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ scope: Whole record and existing graph reviewed; existing-graph repair or documented empty-graph extension gap,
+ not whole-record certification.
+ summary: Retain experimental amino-acid rescue and distinguish three alternative pairs.; Retain sulfur-rescue
+ controls while qualifying the exact transferred compound.; Retain condition-specific obligate growth and species-resolved
+ counts without long-term stability claims.
+ node_decisions:
+ - node: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ rationale: Retain experimental amino-acid rescue and distinguish three alternative pairs.
+ - node: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ rationale: Retain sulfur-rescue controls while qualifying the exact transferred compound.
+ - node: Reciprocal Auxotroph Coculture Growth
+ rationale: Retain condition-specific obligate growth and species-resolved counts without long-term stability
+ claims.
+ removed_node_decisions: []
+ renamed_nodes:
+ E. coli Glutathione-Related Rescue of Zymomonas Auxotroph: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ edges_before:
+ - &id009
+ source: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ target: Reciprocal Auxotroph Coculture Growth
+ description: 'Z. mobilis amino acid exometabolites rescue E. coli amino acid auxotrophs selected for the validated
+ reciprocal cocultures.
+
+ '
+ - &id011
+ source: E. coli Glutathione-Related Rescue of Zymomonas Auxotroph
+ target: Reciprocal Auxotroph Coculture Growth
+ description: 'E. coli glutathione-related metabolites are candidate rescue compounds for the Z. mobilis ZMO0748
+ auxotroph used in the reciprocal cocultures.
+
+ '
+ edges_after:
+ - &id010
+ source: Zymomonas Amino Acid Rescue of E. coli Auxotrophs
+ target: Reciprocal Auxotroph Coculture Growth
+ description: Partner spent-medium and amino-acid rescue support the nutritional contribution to the three separately
+ tested reciprocal pairs. The molecular release route and all additional interactions are not resolved.
+ - &id012
+ source: E. coli Sulfur-Metabolite Rescue of Zymomonas Auxotroph
+ target: Reciprocal Auxotroph Coculture Growth
+ description: 'PARTIAL molecular assignment: sulfur-metabolite rescue supports the ZMO0748 contribution to reciprocal
+ growth, and glutathione is sufficient in supplementation. Its exclusive necessity in coculture and the exact
+ exchanged sulfur species were not established.'
+ retained_edge_decisions:
+ - before: *id009
+ after: *id010
+ rationale: Partner spent-medium and amino-acid rescue support the nutritional contribution to the three separately
+ tested reciprocal pairs. The molecular release route and all additional interactions are not resolved.
+ - before: *id011
+ after: *id012
+ rationale: 'PARTIAL molecular assignment: sulfur-metabolite rescue supports the ZMO0748 contribution to reciprocal
+ growth, and glutathione is sufficient in supplementation. Its exclusive necessity in coculture and the exact
+ exchanged sulfur species were not established.'
+ removed_edge_decisions: []
+ references:
+ - PMID:26885935
+ issues:
+ - 1966
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism/2026-10-08T175133Z-codex-2cd46c.yaml
+- path: kb/communities/hCom2_Complex_Gut_Microbiome.yaml
+ id: CommunityMech:000123
+ original_sha256: e707fdc5f03ae9a01cb7a71c7892d093e3211dbb99159cbbd9c57d25f921c036
+ record_sha256: 84318d052c19431be7204a13f577dd246640b4786a6e7c4b863f01886e8746a7
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml
+ scope: Whole record and existing graph reviewed; existing-graph repair or documented empty-graph extension gap,
+ not whole-record certification.
+ summary: Retain augmentation while separating niche-filling interpretation from measurement.; Re-evidence the
+ stability endpoint and preserve unrelated-donor limits.; Re-evidence community resistance without facilitation
+ typing or strain-specific causality.
+ node_decisions:
+ - node: Fecal-Challenge-Guided Community Augmentation
+ rationale: Retain augmentation while separating niche-filling interpretation from measurement.
+ - node: hCom2 Fecal-Challenge Stability
+ rationale: Re-evidence the stability endpoint and preserve unrelated-donor limits.
+ - node: hCom2 Escherichia coli Colonization Resistance
+ rationale: Re-evidence community resistance without facilitation typing or strain-specific causality.
+ removed_node_decisions: []
+ renamed_nodes:
+ Fecal-Challenge Open Niche Filling: Fecal-Challenge-Guided Community Augmentation
+ edges_before:
+ - &id013
+ source: Fecal-Challenge Open Niche Filling
+ target: hCom2 Fecal-Challenge Stability
+ description: Filling hCom1's open niches with engrafting gut species produced hCom2's higher stability when
+ challenged again with human fecal microbiota.
+ - &id015
+ source: Fecal-Challenge Open Niche Filling
+ target: hCom2 Escherichia coli Colonization Resistance
+ description: Occupying the open gut niches left in hCom1 produced a more complete hCom2 consortium that resisted
+ pathogenic Escherichia coli colonization.
+ edges_after:
+ - &id014
+ source: Fecal-Challenge-Guided Community Augmentation
+ target: hCom2 Fecal-Challenge Stability
+ description: 'Membership augmentation produced a community with greater fecal-challenge resilience in the tested
+ mice. PARTIAL mechanism: niche occupancy is a proposed explanation rather than a selectively measured mediator,
+ and unrelated donors expose residual invasibility.'
+ - &id016
+ source: Fecal-Challenge-Guided Community Augmentation
+ target: hCom2 Escherichia coli Colonization Resistance
+ description: 'HYPOTHESIZED mediation: broader niche occupancy could contribute to hCom2 resistance, but observing
+ resistance in hCom2 does not establish that the augmentation step or any added species is necessary. The study
+ does not resolve the protective strains or molecular pathway.'
+ retained_edge_decisions:
+ - before: *id013
+ after: *id014
+ rationale: 'Membership augmentation produced a community with greater fecal-challenge resilience in the tested
+ mice. PARTIAL mechanism: niche occupancy is a proposed explanation rather than a selectively measured mediator,
+ and unrelated donors expose residual invasibility.'
+ - before: *id015
+ after: *id016
+ rationale: 'HYPOTHESIZED mediation: broader niche occupancy could contribute to hCom2 resistance, but observing
+ resistance in hCom2 does not establish that the augmentation step or any added species is necessary. The study
+ does not resolve the protective strains or molecular pathway.'
+ removed_edge_decisions: []
+ references:
+ - PMID:36070752
+ issues:
+ - 1967
+ - 765
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/hCom2_Complex_Gut_Microbiome/2026-10-08T175134Z-codex-9059ef.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 26c1823c4..4e250266a 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -5,7 +5,7 @@ data/isolates/Chromobacterium_Gold_Biocyanidation.yaml CommunityMech:000273 6f85
data/isolates/Methylobacterium_REE_Ewaste_Platform.yaml CommunityMech:000322 70d9761a556a3e744eb81c26f1906bb0ce697b3d64be526ecaafddea7404f978 4 2 100.0 reports/causal_graph_review/decisions/20261005-six-records-batch3.yaml reviewed
kb/communities/AMD_Acidophile_Heterotroph_Network.yaml CommunityMech:000001 81fe29292038349e959041675b876ef4e351cdfb6884796989540185c6797834 5 1 80.0 reports/causal_graph_review/decisions/20261004-four-records.yaml reviewed
kb/communities/AMD_Nitrososphaerota_Archaeal.yaml CommunityMech:000002 4ec75078d1c9fcd32e5fbac218c3d4c48af25be5a0cb76887cc650c570c95e22 4 1 80.0 reports/causal_graph_review/decisions/20261005-seven-records.yaml reviewed
-kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml CommunityMech:000444 1b8f102df55d246a4f8dd49e8b3e8d09ea2e7ac082cc829e2324109751889abb 0 0 0.0 pending
+kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml CommunityMech:000444 f3a69684e81df00ca791bfc61832141ad9048270f4b3ed476328b772d07604d2 0 0 0.0 reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml needs_research
kb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml CommunityMech:000276 33b202bc07eceb38a47c560434734e8b21f1b251bf20433964af97aef3568b6b 3 2 100.0 reports/causal_graph_review/decisions/20261005-seven-records.yaml reviewed
kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml CommunityMech:000134 45dd6c7f42e725c1e51ec80e03b32e78235377a99d9dc56bafae6acccdeb7bb7 4 3 95.0 reports/causal_graph_review/decisions/20261004-four-records.yaml reviewed
kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml CommunityMech:000139 8b38b18b0519f17b387ecdd88334ea66438df128cd912a5c56da4f8c1f6d012d 4 3 91.2 reports/causal_graph_review/decisions/20261005-seven-records.yaml reviewed
@@ -414,7 +414,7 @@ kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Cocultu
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/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml CommunityMech:000437 ab6b0b9201bc3d3ca9c7b2cbd5395404b1ed071c064d2efb36351e4d72d6d02b 2 0 60.0 reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml reviewed
kb/communities/THOR_Rhizosphere_Model_Community.yaml CommunityMech:000079 1d75a279b70b1ece18d4453f8576a849996e712bfb2f4a0ea9542db2f22f0dca 3 2 90.0 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml CommunityMech:000072 a5c33db18b80a233099b80289b173c8c57e1420ced3a4f282ef99bb9100d0f11 4 4 92.5 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml CommunityMech:000100 d2b51e34f56530cb2992a40d195eae0f2395925e9d4f39b135d77a8822309320 4 2 87.5 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
@@ -454,8 +454,8 @@ kb/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml Commun
kb/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml CommunityMech:000438 ba42e79fb1133d49ce6280562566ffedd6bcf37306ce42b97473e7cfdc1b017f 3 0 63.3 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
kb/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml CommunityMech:000360 829d29dcebcb9ba30483df9d1ec71eafb945a6a3bf966539ee6a16d9abd9077d 2 0 57.5 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
kb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml CommunityMech:000404 06d15492c6e358b75deffe722b5299d7b5f86bf15090276db87fda690c6e639e 3 2 88.3 reports/causal_graph_review/decisions/20261008-four-records-batch123.yaml reviewed
-kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml CommunityMech:000354 3f48f2b903eec6f6ac2e93c952821980eb066df571ec4e1a5519ac7c47293e7c 3 2 100.0 pending
-kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml CommunityMech:000164 49f5a5749a60d2f6b314cd487f84c5c6c609d23657faf7342daad53833dc9ec2 4 2 100.0 pending
-kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml CommunityMech:000210 5640166eed0e15b269178e292e4e63066adb88cd20d82e65b3dd05938ae49be3 3 2 100.0 pending
-kb/communities/hCom2_Complex_Gut_Microbiome.yaml CommunityMech:000123 e707fdc5f03ae9a01cb7a71c7892d093e3211dbb99159cbbd9c57d25f921c036 3 2 100.0 pending
+kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml CommunityMech:000354 2dbf53129f98e8df7edc68f7d3f2bc6ca7c748ac563d0e31abd1274a15ca051a 3 2 93.3 reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml reviewed
+kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml CommunityMech:000164 693b023e694475fd4eeeb0fde9af92e56db2084b885af8b7bd5d1febe6140dcc 4 2 95.0 reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml reviewed
+kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml CommunityMech:000210 efc6e7b31f9bc7ebe11fe5a26f9f45e2a7b845684fd3a15c8b10e0d1994e6be6 3 2 100.0 reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml reviewed
+kb/communities/hCom2_Complex_Gut_Microbiome.yaml CommunityMech:000123 84318d052c19431be7204a13f577dd246640b4786a6e7c4b863f01886e8746a7 3 2 100.0 reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml reviewed
kb/communities/mCAFEs_Brachypodium_RCC.yaml CommunityMech:000078 273500dc8bec3a1e35cea5c32a9ac77be1c36ed5f5d01cd5f7861dfe65e40ecb 6 2 87.5 reports/causal_graph_review/decisions/20261008-four-records-batch119.yaml reviewed
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index d8094565b..a9cc7221a 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -7,9 +7,8 @@
"records_without_nodes": 10,
"records_without_edges": 189,
"review_status_counts": {
- "needs_research": 54,
- "pending": 6,
- "reviewed": 400
+ "needs_research": 55,
+ "reviewed": 405
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch124.json b/reports/causal_graph_review/validation-20261008-batch124.json
new file mode 100644
index 000000000..5a7adcafa
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch124.json
@@ -0,0 +1,1569 @@
+{
+ "base_commit": "19010db53b3b5537d458727318921006e83e7ccb",
+ "scope": [
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml",
+ "kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml",
+ "kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml",
+ "kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch124.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/focused.log",
+ "log_sha256": "2871d060c92d624d75af98a774e5d1a38fdef8d0a4631846a077f7ed71aae231",
+ "output_tail": "............. [100%]\n13 passed in 3.73s\n"
+ },
+ {
+ "check": "AM_AB_Chlorella_MLSS_Wastewater_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/AM_AB_Chlorella_MLSS_Wastewater_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "AM_AB_Chlorella_MLSS_Wastewater_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch124/AM_AB_Chlorella_MLSS_Wastewater_Consortium-strict.tsv",
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/AM_AB_Chlorella_MLSS_Wastewater_Consortium-strict.log",
+ "log_sha256": "27fc7f3c52f4b4ab43870163909b24eec649fffc73e2c834042193923fe6a484",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch124/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-batch124/AM_AB_Chlorella_MLSS_Wastewater_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "AM_AB_Chlorella_MLSS_Wastewater_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/AM_AB_Chlorella_MLSS_Wastewater_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "AM_AB_Chlorella_MLSS_Wastewater_Consortium-references",
+ "command": [
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+ "check": "AM_AB_Chlorella_MLSS_Wastewater_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "command": [
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+ "command": [
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+ "output_tail": "\u2705 Validation passed\n"
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+ "check": "Yogurt_TwoSpecies_Starter_Culture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Yogurt_TwoSpecies_Starter_Culture-references.log",
+ "log_sha256": "e1a3a780d95092ef3363e41024cbe076132fee8f51124cdc6b04e1143bdc18fb",
+ "output_tail": "Validating kb/communities/Yogurt_TwoSpecies_Starter_Culture.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/Yogurt_TwoSpecies_Starter_Culture.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": "Yogurt_TwoSpecies_Starter_Culture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Yogurt_TwoSpecies_Starter_Culture-snippets.log",
+ "log_sha256": "c72869c3cfa80d3275b80461e8b721727d9e301213f59836200303704b4482a6",
+ "output_tail": "# 27 evidence snippets scanned across 1 files\n MATCH 27\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": "Yogurt_TwoSpecies_Starter_Culture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Yogurt_TwoSpecies_Starter_Culture-rank.log",
+ "log_sha256": "c109a7aac36862384555152dac2041ddc843cda42674b75cc095bac2f5faaa84",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000164\",\n \"name\": \"Yogurt Two-Species Starter Culture\",\n \"score\": 95.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 10,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Yogurt_TwoSpecies_Starter_Culture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Yogurt_TwoSpecies_Starter_Culture/2026-10-08T175133Z-codex-114f8d.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Yogurt_TwoSpecies_Starter_Culture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch124/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-strict.tsv",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-strict.log",
+ "log_sha256": "2eda5ec480a979dfe0cf71f0125ffabd9ce7573d59a4e998b28f08c8fc93f853",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch124/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-batch124/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-strict.tsv\n"
+ },
+ {
+ "check": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-references-recovered.log",
+ "log_sha256": "2959646a27153905c732412e90e5d3d0e445109441808815f62b97b2a55a546e",
+ "output_tail": "Validating kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.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/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.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": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-snippets.log",
+ "log_sha256": "c72869c3cfa80d3275b80461e8b721727d9e301213f59836200303704b4482a6",
+ "output_tail": "# 27 evidence snippets scanned across 1 files\n MATCH 27\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": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-rank.log",
+ "log_sha256": "3ba1020239c9b74ec0c4a9ffa3251af83f6a081af7b71a720106f12a5ec8ad39",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000210\",\n \"name\": \"Zymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\",\n \"score\": 100.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 9,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism/2026-10-08T175133Z-codex-2cd46c.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "hCom2_Complex_Gut_Microbiome-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "hCom2_Complex_Gut_Microbiome-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch124/hCom2_Complex_Gut_Microbiome-strict.tsv",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-strict.log",
+ "log_sha256": "b46248c4c124fc6e1308b4beb21a04f53f6768945488a9d4d911b2e7dca8e556",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch124/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-batch124/hCom2_Complex_Gut_Microbiome-strict.tsv\n"
+ },
+ {
+ "check": "hCom2_Complex_Gut_Microbiome-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "hCom2_Complex_Gut_Microbiome-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-references.log",
+ "log_sha256": "2faebce8273e5a51cf2d07b598ad1d96fdde7ddbe6d0469b30c779d3eb759171",
+ "output_tail": "Validating kb/communities/hCom2_Complex_Gut_Microbiome.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/hCom2_Complex_Gut_Microbiome.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": "hCom2_Complex_Gut_Microbiome-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-snippets.log",
+ "log_sha256": "45007c108f9ec8bef530a5471e83cc9e84b78b05e90ad8c19de389a107ed4f60",
+ "output_tail": "# 7 evidence snippets scanned across 1 files\n MATCH 7\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": "hCom2_Complex_Gut_Microbiome-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-rank.log",
+ "log_sha256": "9175cf365e15823458af728b4be48b9a5ff4036f97b8ef156a6f57b9bc6ada74",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000123\",\n \"name\": \"hCom2 Complex Gut Microbiome\",\n \"score\": 100.0,\n \"taxonomy\": 1,\n \"connected_taxa\": 1,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/hCom2_Complex_Gut_Microbiome.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "hCom2_Complex_Gut_Microbiome-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/hCom2_Complex_Gut_Microbiome/2026-10-08T175134Z-codex-9059ef.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/hCom2_Complex_Gut_Microbiome-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-batch124/verification/inventory.log",
+ "log_sha256": "971f935046831fc273c41e59059a92bcbc4f08156b12d78d0a16ef104c75746b",
+ "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\": 1373,\n \"edges\": 530,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 189,\n \"review_status_counts\": {\n \"needs_research\": 55,\n \"reviewed\": 405\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-batch124/verification/network.log",
+ "log_sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9",
+ "output_tail": "\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 \"Tinto_River_Iron_Cycling_Community\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Basidiomycota\",\n \"taxon_id\": \"NCBITaxon:5204\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Basidiomycota\",\n \"term\": {\n \"id\": \"NCBITaxon:5204\",\n \"label\": \"Basidiomycota\"\n },\n \"gtdb_grounding_status\": \"NO_GTDB_EQUIVALENT\",\n \"notes\": \"Acidophilic fungi including Hortaea werneckii (black yeast) detected in Rio Tinto sediments and water. Fungi contribute to organic matter degradation, biofilm formation, and nutrient cycling through extracellular enzyme secretion.\\n\"\n },\n \"functional_role\": [\n \"PRIMARY_DEGRADER\"\n ],\n \"abundance_level\": \"RARE\",\n \"evidence\": [\n {\n \"reference\": \"PMID:25369810\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VIVO\",\n \"snippet\": \"Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons\",\n \"explanation\": \"Documents fungal presence\"\n }\n ]\n },\n \"message\": \"Taxon 'Basidiomycota' 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-batch124/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-batch124/verification/rank-all.log",
+ "log_sha256": "c4346ce632f867ee8f4ac7c28e0ef298f2df6ed5b7f810c9b7bf4d55af880955",
+ "output_tail": "ommunities/Cinnamate_Degradation_Consortium.yaml\tCommunityMech:000018\tCinnamate \u03b2-Oxidation Consortium\t3\t3\t0\t3\t2\t3\tinteraction_type\t0\t0\n406\t96.7\tkb/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.yaml\tCommunityMech:000172\tClostridium autoethanogenum-Clostridium kluyveri Syngas Coculture\t2\t2\t0\t3\t2\t8\tinteraction_type\t0\t0\n407\t96.7\tkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml\tCommunityMech:000266\tClostridium carboxidivorans-Clostridium kluyveri CO Chain-Elongation Coculture\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n408\t96.7\tkb/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.yaml\tCommunityMech:000174\tClostridium cellulovorans-Methanosarcina barkeri Cellulose Methane Coculture\t2\t2\t0\t3\t2\t8\tinteraction_type\t0\t0\n409\t96.7\tkb/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.yaml\tCommunityMech:000206\tClostridium-Saccharomyces Cellulose Ethanol Coculture\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n410\t96.7\tkb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml\tCommunityMech:000297\tDIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n411\t96.7\tkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml\tCommunityMech:000023\tDesulfovibrio-Methanococcus Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n412\t96.7\tkb/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.yaml\tCommunityMech:000340\tPelagerythrobacter-Salinicola PES Pyrene-Degradation SynCom\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n413\t96.7\tkb/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.yaml\tCommunityMech:000291\tPseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium\t2\t2\t0\t3\t2\t3\tinteraction_type\t0\t0\n414\t96.7\tkb/communities/SMutans_CAlbicans_ECC_Biofilm.yaml\tCommunityMech:000083\tStreptococcus mutans - Candida albicans ECC Biofilm Model\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n415\t96.7\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n416\t96.7\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t5\tinteraction_type\t0\t0\n417\t96.7\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\tinteraction_type\t0\t0\n418\t96.7\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t9\tinteraction_type\t0\t0\n419\t96.7\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t9\tinteraction_type\t0\t0\n420\t96.7\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\tinteraction_type\t0\t0\n421\t96.7\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t6\tinteraction_type\t0\t0\n422\t96.7\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\tinteraction_type\t0\t0\n423\t96.7\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t4\tinteraction_type\t0\t0\n424\t97.5\tkb/communities/Anammox_Granule_Metabolic_Interaction_Community.yaml\tCommunityMech:000146\tAnammox Granule Metabolic Interaction Community\t3\t3\t0\t4\t3\t5\tinteraction_type\t0\t0\n425\t97.5\tkb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml\tCommunityMech:000176\tORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community\t3\t3\t0\t4\t2\t8\tinteraction_type\t0\t0\n426\t97.5\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t8\tinteraction_type\t0\t0\n427\t97.5\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t8\tinteraction_type\t0\t0\n428\t97.9\tkb/communities/Maize_Drought_Response_SynCom.yaml\tCommunityMech:000103\tMaize Drought Response SynCom\t1\t1\t0\t7\t7\t8\tmetabolites_or_biological_processes\t0\t0\n429\t98.3\tkb/communities/Populus_Salt_Tolerant_SynComs.yaml\tCommunityMech:000090\tPopulus Salt-Tolerant Rhizosphere SynComs\t1\t1\t0\t3\t2\t3\tmetabolites_or_biological_processes\t0\t0\n430\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n431\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n432\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n433\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic Consortia\t6\t6\t0\t3\t2\t7\t\t0\t0\n434\t100.0\tkb/communities/Anabaena_MGS1_Anaerobic_Digestion_Methanogen_Consortium.yaml\tCommunityMech:000307\tAnabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium\t1\t1\t0\t5\t2\t7\t\t0\t0\n435\t100.0\tkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml\tCommunityMech:000245\tAvena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds\t1\t1\t0\t5\t2\t7\t\t0\t0\n436\t100.0\tkb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml\tCommunityMech:000142\tBacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism\t2\t2\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml\tCommunityMech:000012\tBioModels MODEL2405300001 Infant Gut HMO SynCom\t13\t13\t0\t3\t2\t6\t\t0\t0\n438\t100.0\tkb/communities/California_Grassland_Precipitation_Legacy_Soil_Community.yaml\tCommunityMech:000215\tCalifornia Grassland Precipitation Legacy Soil Community\t1\t1\t0\t3\t2\t6\t\t0\t0\n439\t100.0\tkb/communities/Cellulose_Methane_Quad_Culture_SynCom.yaml\tCommunityMech:000089\tCellulose-to-Methane Quad-Culture SynCom\t4\t4\t0\t6\t5\t9\t\t0\t0\n440\t100.0\tkb/communities/DVM_Triculture.yaml\tCommunityMech:000021\tDVM Tri-culture\t3\t3\t0\t4\t2\t7\t\t0\t0\n441\t100.0\tkb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\tCommunityMech:000301\tDehalococcoides mccartyi CWV2 Dechlorinating Consortium\t1\t1\t0\t5\t2\t6\t\t0\t0\n442\t100.0\tkb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml\tCommunityMech:000296\tEscherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture\t2\t2\t0\t3\t2\t6\t\t0\t0\n443\t100.0\tkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml\tCommunityMech:000350\tHigh-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment\t4\t4\t0\t3\t2\t6\t\t0\t0\n444\t100.0\tkb/communities/Honeybee_Core20_Defined_Microbiota.yaml\tCommunityMech:000124\tHoneybee Core-20 Defined Microbiota\t1\t1\t0\t3\t2\t3\t\t0\t0\n445\t100.0\tkb/communities/Microbacterium_Terrabacter_Sulfadiazine_CrossFeeding_Coculture.yaml\tCommunityMech:000462\tMicrobacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n446\t100.0\tkb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml\tCommunityMech:000157\tMicrocoleus-Massilia Cyanosphere Urea Mutualism\t2\t2\t0\t3\t2\t5\t\t0\t0\n447\t100.0\tkb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml\tCommunityMech:000119\tMultiomics Corn Straw Degradation SynCom\t1\t1\t0\t4\t3\t9\t\t0\t0\n448\t100.0\tkb/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.yaml\tCommunityMech:000156\tNeocallimastix-Methanobrevibacter Xylanolytic Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml\tCommunityMech:000190\tPelotomaculum-Methanocella Propionate RNA-Seq Coculture\t2\t2\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml\tCommunityMech:000052\tPelotomaculum-Methanothermobacter Syntrophic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n451\t100.0\tkb/communities/Phenol_Carboxylation_Consortium.yaml\tCommunityMech:000053\tPhenol Carboxylation Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n452\t100.0\tkb/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.yaml\tCommunityMech:000290\tPhosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture\t2\t2\t0\t3\t2\t4\t\t0\t0\n453\t100.0\tkb/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.yaml\tCommunityMech:000289\tPseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n454\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n455\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n456\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n457\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n458\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n459\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t9\t\t0\t0\n460\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/render.log",
+ "log_sha256": "2ac652c10e1fbbe68a20aef718580dfae0721a796c4f18baa4c9670c49ab67e8",
+ "output_tail": "unitymech-causal-batch124/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch124/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch124/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch124/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-batch124/verification/render-repeat.log",
+ "log_sha256": "2ac652c10e1fbbe68a20aef718580dfae0721a796c4f18baa4c9670c49ab67e8",
+ "output_tail": "unitymech-causal-batch124/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch124/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch124/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch124/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch124/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/connectivity-survey.log",
+ "log_sha256": "bb7f5b9d8e914cba29426a25d1e833ca8f024ab6d7df8602e2a4e0516ac13f0c",
+ "output_tail": "{\"records\": 460, \"with_community_level\": 415, \"mixed\": 137, \"community_level_only\": 278, \"taxa\": 1570, \"credited_solely_by_the_rule\": 1281}\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_batch113.py",
+ "tests/test_causal_review_batch114.py",
+ "tests/test_causal_review_batch115.py",
+ "tests/test_causal_review_batch116.py",
+ "tests/test_causal_review_batch117.py",
+ "tests/test_causal_review_batch118.py",
+ "tests/test_causal_review_batch119.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch120.py",
+ "tests/test_causal_review_batch121.py",
+ "tests/test_causal_review_batch122.py",
+ "tests/test_causal_review_batch123.py",
+ "tests/test_causal_review_batch124.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",
+ "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_network_palette.py",
+ "tests/test_datamodel.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-batch124/verification/regressions.log",
+ "log_sha256": "7dac59410f5ce31ffc2dc99e84b2536f10e5295b70991e00ef3cd84859abcb81",
+ "output_tail": "........................................................................ [ 6%]\n........................................................................ [ 12%]\n........................................................................ [ 18%]\n........................................................................ [ 24%]\n........................................................................ [ 30%]\n........................................................................ [ 36%]\n........................................................................ [ 42%]\n........................................................................ [ 48%]\n........................................................................ [ 54%]\n........................................................................ [ 60%]\n........................................................................ [ 66%]\n........................................................................ [ 72%]\n........................................................................ [ 78%]\n........................................................................ [ 84%]\n........................................................................ [ 90%]\n........................................................................ [ 97%]\n................................... [100%]\n1187 passed in 353.41s (0:05:53)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/just-lint.log",
+ "log_sha256": "31f4be531fdb65f5b6858d153213474f46a6ba865e3ae734f1f56d4a59fad407",
+ "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\n377 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-batch124/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-batch124/verification/audit-snippets-all.log",
+ "log_sha256": "f584d4aa5913a10afa8d3f8ab3d821edcc5fdf0e008d9c33eb4d5b13b12a593f",
+ "output_tail": "# 9102 evidence snippets scanned across 460 files\n MATCH 8971\n RENDERING 31\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 59\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-batch124/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ },
+ {
+ "check": "final-provenance-focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch124.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/final-provenance-focused.log",
+ "log_sha256": "a797b2d66be1d3489359b41b4c74e1ee7f965a93cc8f9504b5d9bd92a1bc3c39",
+ "output_tail": "............. [100%]\n13 passed in 4.30s\n"
+ },
+ {
+ "check": "final-provenance-algal-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/final-provenance-algal-references.log",
+ "log_sha256": "9867d329f0d9bbc1fe2508228fa9dc35b038c53a2c5bc3c43f02e04f06f86cca",
+ "output_tail": "Validating kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.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/AM_AB_Chlorella_MLSS_Wastewater_Consortium.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": "final-provenance-algal-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/final-provenance-algal-snippets.log",
+ "log_sha256": "759d12e7521dfe9481cc6bfd389f6d7f1b0390aedd3c0b5172914e5995d2699e",
+ "output_tail": "# 15 evidence snippets scanned across 1 files\n MATCH 15\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"
+ },
+ {
+ "check": "final-cache-focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch124.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/final-cache-focused.log",
+ "log_sha256": "493eb2c9cf42d82b3846ef2dc711723ab7c5455974c9f8909f6312943678e784",
+ "output_tail": "............. [100%]\n13 passed in 6.42s\n"
+ },
+ {
+ "check": "final-cache-tcp-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/final-cache-tcp-references.log",
+ "log_sha256": "9f855c4ca6aa02f2ace0c97dc34bce7ee9d6c668a846ec9b3b3939b2ce98393c",
+ "output_tail": "Validating kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.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/TCP_NonDehalogenimonas_Groundwater_Consortium.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": "final-cache-tcp-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/final-cache-tcp-snippets.log",
+ "log_sha256": "483cd650fb122ad2514b6743b44bf4d7472232907822d4b7c6dfdb404f6dbb29",
+ "output_tail": "# 18 evidence snippets scanned across 1 files\n MATCH 18\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"
+ }
+ ],
+ "limitations": [
+ "Pre-source baseline covers460records,923caches,57existing warnings and zero structural defects. Six whole records and15nodes/eight arrows reviewed; all retained,six renames,no new topology. Five existing graphs repaired; algae-MLSS remains an empty-graph extension gap.",
+ "Fresh EuropePMC metadata/abstracts for eight PubMed papers and Crossref identities checked. Yarrowia bioRxivAPI and version1 XML retrieved; not certified peer-reviewed. XML failures for four PMC articles did not imply absent full text: their PMC HTML bodies were retrieved and read. TCP publisher403; only its abstract supports this review.",
+ "Algae primary Methods2.1-2.9,Results/Discussion3.1-3.4,Conclusion andTables1-4 read. Algae-only controls bound faster or universally better remediation; phosphate reaches detection limits in both and early nitrogen removal is slower in AM-AB. Correlations and theoretical methane yield are not transfer or production measurements. Available HRAP metadata deferred to1969; outdoor conditions must not inherit indoor stock settings.",
+ "Yarrowia full Methods,Results3.3-3.6,Discussion4.1-4.2 andConclusions read. Exact pair is YBGL3/YBXT-XR; shared glucose use and lack of simultaneous glucose/xylose consumption rule out exclusive niches. Higher fraction in1:5 is not higher titer or all-ratio benefit. Methods/Results ratio ambiguity and existing member metadata remain1970. Earlier enzyme-characterization Results not fully read.",
+ "Yogurt19114510 strain Methods,growth/nitrogen Results andBCAA/purine Discussion;20889781 strain/compound/metabolite Methods,addition andnitrogen/CO2 Results/Table1 andDiscussion;24936380 main mechanism Results/Discussion andMethods;30594386 abstract read. Distinct pairs and stage-specific recipients kept separate. Positive knockout/supplementation outcomes retained without flux or universal mutualism. Non-graph19395564 dataset not researched; urease summary deferred1971.",
+ "Zymomonas accepted manuscript abstract/introduction,Results andrescue controls throughpage8 andstrain Methods start read via UCweb PDF extraction. Direct curl/urllib PDF downloads were empty and not evidence. Positive spent-medium,individual metabolite andspecies-resolved growth results retained. Glutathione is not the exclusive necessary mediator; three pairs are separate andlong-term stability untested. Remaining protocol Methods not fully read.",
+ "hCom2 construction,augmentation,resilience,architecture,EHECchallenge Results,Discussion/limitations and relevant strain-preparation/augmentation/challenge Methods read. Donor dependence anddropout architecture confounding bound niche-filling causality. Three facilitation labels removed andoutcomes re-evidenced with existing abstract text; non-graph debt765 remains. No restricted full body restored.",
+ "All graph anddiscussion quotes checked against caches and fresh primary artifacts by normalized contiguous matching,not entailment proof. Four caches gain short provenance-labeled excerpts; missingTCPabstract restored from an unchanged user file andindependently matched.919originalcaches unchanged;924total. No full-body import,figure-pixel inspection,external-supplement/raw-data/code audit or whole-record certification.",
+ "Initial TCPbaseline reference check failed due missingcache andnetworkDNS; originalfailure/log retained. Afterverifiedcache restoration,24recovered targetbaseline checks passed. Fresh source retrieval logs retain failures as well as successful alternative access routes.",
+ "Expanded all-state1196issue titles/bodies and178matchinghidden/ignored localpaths searched; ninepriorissue bodies read. Credentials,.git,generateddocs/site andreferencecaches excluded from issue-dedup search;caches separately inspected. No historicalPRcomment audit. Engineered gutaminoacid neighbor read as convention only,not transferred evidence; no reusable target taxon files found in ignored-inclusive search.",
+ "Six guarded writes preserve454otherrecords,unrelated rawYAMLblocks andallpriorhistory/decision artifacts. Six append-onlyhistories/events. Yogurturease/Nox endpoints nowcommunity-scoped withbothcanonicalparticipants; other scopes/taxonomy preserved. Connectivity logic unchanged; census measured separately.",
+ "One-community algae Edison dryrun completed without provider submission orcredits. New extension requires separately scoped spend authorization; priorRuegeria1883 configured-authentication blocker not retried unchanged. No credentials inspected. Source-based self-adversarial review is notindependent approval.55researchrecords andprotectedmerge/branchdeletion remain incomplete."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
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+ "MATCH": 15,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
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+ "MATCH": 18,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml": {
+ "MATCH": 18,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml": {
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+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml": {
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+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
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+ "NOCONTENT": 0
+ },
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml": {
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+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "failed_attempts": [
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+ "check": "Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch124/verification/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism-references.log",
+ "log_sha256": "fa64ea4921da246ee6713783fb04b046b337db5289c30eeb2c3d9731f78cb548",
+ "output_tail": "Validating kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (2):\n [ERROR] Text part not found as substring: 'they all successfully grew in 50% spent medium and metabolite supplemented medium' (note: only abstract available for PMID:26885935, full text may contain this excerpt)\n Location: ecological_interactions[0].evidence[2].snippet\n Reference: PMID:26885935\n [ERROR] Text part not found as substring: 'both cysteine and glutathione are capable of rescuing Z. mobilis' (note: only abstract available for PMID:26885935, full text may contain this excerpt)\n Location: ecological_interactions[1].evidence[2].snippet\n Reference: PMID:26885935\n\nValidation Summary:\n Total checks: 2\n Issues found: 2\n",
+ "explained_output_tail": "Validating kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Issues (2):\n [ERROR] Text part not found as substring: 'they all successfully grew in 50% spent medium and metabolite supplemented medium' (note: only the abstract is cached for PMID:26885935; try `just cache-fulltext PMID:26885935`)\n Location: ecological_interactions[0].evidence[2].snippet\n Reference: PMID:26885935\n [ERROR] Text part not found as substring: 'both cysteine and glutathione are capable of rescuing Z. mobilis' (note: only the abstract is cached for PMID:26885935; try `just cache-fulltext PMID:26885935`)\n Location: ecological_interactions[1].evidence[2].snippet\n Reference: PMID:26885935\n\nValidation Summary:\n Total checks: 2\n Issues found: 2\n\n[annotate] rewrote 2 misleading 'only abstract available' note(s) (#496)\n"
+ }
+ ],
+ "cache_precedence_recovery": "Move verified excerpts to existing preferred Markdown cache; preserve original failed output. No validator change or relaxed assertion.",
+ "unchanged_record_files": 454,
+ "unchanged_cache_files": 919,
+ "unchanged_raw_blocks": 93,
+ "cache_changes": [
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+ "before_sha256": null,
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+ },
+ {
+ "path": "references_cache/PMID_42429207.txt",
+ "before_sha256": "2a50d54a82547f7ddb7d1536dce9dbc5b7553c8769f1eec4b936db41ec973e8b",
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+ "action": "Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix."
+ },
+ {
+ "path": "references_cache/doi_10.64898_2025.12.19.695487.md",
+ "before_sha256": "b29827aa946f1564bd10177dfebab726689113664f122f4431bbfeb2ed7bfbd5",
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+ "action": "Append short literal primary excerpts with URL, section, date and license; preserve original cache prefix."
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+ "after_sha256": "90b61b191addc52f9876cb1e93f1dfd729753ab5ffc2b22e9748c671198df777",
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+ }
+ ],
+ "edison": {
+ "required_for_existing_graph_repairs": false,
+ "required_for_algal_extension": true,
+ "dry_run_completed": true,
+ "dry_run_artifacts": [
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+ "provider_submissions": 0,
+ "credits_spent": 0,
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+ "added_findings": {},
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+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1359,
+ "arrows": 522
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
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+ "community_level_only": 278,
+ "taxa": 1570,
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+ },
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
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+ "total": 9102,
+ "categories": {
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+ "MISMATCH": 40,
+ "NOCONTENT": 59
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+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
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+ "records_without_nodes": 10,
+ "records_without_edges": 189,
+ "review_status_counts": {
+ "needs_research": 55,
+ "reviewed": 405
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml": "ac925b5b57d1e2d173d9e515d8b371b300b885f3fc06c473570ddce7e3a07c87",
+ "tests/test_causal_review_batch124.py": "3cca5027c47066c2e9f9a0be7314fa3aa4d818dd64ff3a31ad429496ff1f2770",
+ "tests/test_participating_taxa.py": "db84a4aedbbc553907c6ad35737d3f0f3900aa3ce50eb0aad61ef65b3855a8e7",
+ "tests/test_community_level_connectivity_credit.py": "0f02b8c5d89eed7a6578075899bfe4fa481f929515b4fd5b2641a61eedd4c88e",
+ "tests/test_causal_review_batch109.py": "6667be62a86cc92577f88b772c90c12541893e23e97e120a2f58bd0a5185aeea",
+ "tests/test_datamodel.py": "f8d4750ad64eb4156857a86a8c6adf16dedefb09ca3c3da908f697e609a35f25",
+ "reports/causal_graph_review/cache-provenance-20261008-batch124.json": "8875156f1920897cee5a7befb9ece8820ffa2e5d3c41b5f542bf577b53e2022c",
+ "kb/communities/AM_AB_Chlorella_MLSS_Wastewater_Consortium.yaml": "f3a69684e81df00ca791bfc61832141ad9048270f4b3ed476328b772d07604d2",
+ "kb/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.yaml": "ab6b0b9201bc3d3ca9c7b2cbd5395404b1ed071c064d2efb36351e4d72d6d02b",
+ "kb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml": "2dbf53129f98e8df7edc68f7d3f2bc6ca7c748ac563d0e31abd1274a15ca051a",
+ "kb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml": "693b023e694475fd4eeeb0fde9af92e56db2084b885af8b7bd5d1febe6140dcc",
+ "kb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml": "efc6e7b31f9bc7ebe11fe5a26f9f45e2a7b845684fd3a15c8b10e0d1994e6be6",
+ "kb/communities/hCom2_Complex_Gut_Microbiome.yaml": "84318d052c19431be7204a13f577dd246640b4786a6e7c4b863f01886e8746a7"
+ },
+ "pre_research_baseline": {
+ "base_commit": "19010db53b3b5537d458727318921006e83e7ccb",
+ "base_tree": "e3628b1faedb3c6fc42392a051586a6a12536d27",
+ "research_worktree": "/private/tmp/communitymech-causal-batch124",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch124/baseline-rank.log",
+ "sha256": "3d040a2d8d4bcec43c8cffb25fc997ce03f11f9e8837fe19840d612d6bd45e74"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch124/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-batch124/baseline-network.log",
+ "sha256": "6a349ee70c3b3deb2e3171d0a85501f53c7faa0aca02351007a8296feed367e9"
+ },
+ {
+ "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-batch124/baseline-downstream.log",
+ "sha256": "9eae6adf6dc3a06dd3a965531e4f7b7edff368126d73abb7cfcc284c7c061e7e"
+ }
+ ],
+ "baseline_sha256": "e9ade8d2b84d5a41f39ed8c3957fc4d3fe885f611f7d04b9829d4a94284bd7f2"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs",
+ "total_recorded_gate_outputs": 61,
+ "provenance_finalization": "Corrected algae copyright holder from publisher Wiley to Water Environment Federation, as identified by primary notice. Excerpt, scientific claims, canonical records and tests unchanged; focused and affected reference/snippet checks rerun.",
+ "import_whitespace_normalization": {
+ "path": "references_cache/PMID_41736479.txt",
+ "before_sha256": "277a89b76cc003225388033aaf4e4f13ba3c836f17f16e99978ea7afbb074e46",
+ "after_sha256": "0f4e3719902f55ce45dfde9383042337bfd85897a53660e1d434f89a777be27e",
+ "failure_exit_code": 2,
+ "failure_log": "/private/tmp/communitymech-batch124/initial-staged-diff-check.log",
+ "failure_log_sha256": "eff4e386e2baddb56cc85eb8837fc85aa9900effedfcb29b3b68a7e6e7e49466",
+ "scope": "Final newline and trailing ASCII whitespace only; original user file untouched."
+ }
+}
diff --git a/tests/test_causal_review_batch109.py b/tests/test_causal_review_batch109.py
index 2130ea9b3..6d94c9b36 100644
--- a/tests/test_causal_review_batch109.py
+++ b/tests/test_causal_review_batch109.py
@@ -177,14 +177,15 @@ def test_hashes_histories_and_canonical_identity_only_scope_are_explicit():
def test_current_scope_census_tracks_later_source_bounded_repairs():
# Batch119 moves Bacillus protection to all three THOR members: one more sole credit.
+ # Batch124 adds yogurt's two named participants to mixed-scope records, not sole credit.
survey = runpy.run_path(str(ROOT / "tests/test_community_level_connectivity_credit.py"))[
"_survey"
]()
assert survey == {
"records": 460,
- "with_community_level": 414,
- "mixed": 136,
+ "with_community_level": 415,
+ "mixed": 137,
"community_level_only": 278,
- "taxa": 1568,
+ "taxa": 1570,
"credited_solely_by_the_rule": 1281,
}
diff --git a/tests/test_causal_review_batch124.py b/tests/test_causal_review_batch124.py
new file mode 100644
index 000000000..27f408b51
--- /dev/null
+++ b/tests/test_causal_review_batch124.py
@@ -0,0 +1,187 @@
+"""Retain measured outcomes while bounding cross-study and mediator claims."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-six-records-batch124.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_algal_extension_remains_open_and_control_bounded():
+ ledger, rows, docs = records()
+ assert not docs[0]["ecological_interactions"]
+ assert rows[0]["status"] == "needs_research"
+ gap = docs[0]["discussions"][-1]
+ assert "early nitrogen removal is slower" in gap["rationale"]
+ assert "BOD removal is not uniformly better" in gap["rationale"]
+ assert "no longer abstract-access gaps" in docs[0]["discussions"][0]["rationale"]
+ assert ledger["edison"]["dry_run_completed"]
+ assert ledger["edison"]["provider_submissions"] == 0
+
+
+def test_tcp_reconstruction_is_not_measured_transfer():
+ _, _, docs = records()
+ a, b = docs[1]["ecological_interactions"]
+ e = a["evidence"][0]
+ assert e["supports"] == "PARTIAL" and e["evidence_source"] == "COMPUTATIONAL"
+ assert e["computational_provenance"]["prediction_type"] == "OTHER"
+ assert "not measured intergenus" in a["description"]
+ assert not a.get("downstream") and not b.get("downstream")
+
+
+def test_tcp_keeps_amendment_effects_and_shared_descriptors():
+ _, _, docs = records()
+ doc = docs[1]
+ a, b = doc["ecological_interactions"]
+ assert "enhanced TCP degradation" in b["description"]
+ assert "19.06" in b["description"] and "3.5 days" in b["description"]
+ assert "not separately assigned" in b["description"]
+ assert a["metabolites"][1] is b["metabolites"][0]
+ assert doc["growth_media"][0]["composition"][0]["chebi_term"] is b["metabolites"][1]
+
+
+def test_yarrowia_design_is_not_exclusive_niches_or_polymer_catalysis():
+ _, _, docs = records()
+ a, _, _ = docs[2]["ecological_interactions"]
+ assert "interaction_type" not in a and "biological_processes" not in a
+ assert "Both can use glucose" in a["description"]
+ assert "not an interchangeable YBGL1" in a["description"]
+ assert "YBGL3 + YBXT-XR" in a["evidence"][-1]["snippet"]
+
+
+def test_yarrowia_fraction_does_not_become_titer_advantage():
+ _, _, docs = records()
+ a, b, c = docs[2]["ecological_interactions"]
+ assert "34% versus 26.3%" in c["description"]
+ assert "comparable lipid titers" in c["description"]
+ assert "1:2 consortium performed worse" in c["description"]
+ assert "interaction_type" not in c
+ assert "temporal succession" in b["description"]
+ assert all(e["description"].startswith("PARTIAL:") for e in a["downstream"])
+
+
+def test_yogurt_pairs_and_return_flow_remain_distinct():
+ _, _, docs = records()
+ a, b, _, _ = docs[3]["ecological_interactions"]
+ assert (
+ "CNRZ1066" in a["description"] and "not one universally beneficial pair" in a["description"]
+ )
+ assert all(e["supports"] == "PARTIAL" for e in a["evidence"])
+ assert "does not satisfy all" in b["description"]
+ assert b["downstream"][0]["description"].startswith("HYPOTHESIZED mediation:")
+
+
+def test_yogurt_urease_recipients_and_scopes_are_explicit():
+ _, _, docs = records()
+ c, d = docs[3]["ecological_interactions"][2:]
+ assert "Ammonia shortage mainly limits S. thermophilus" in c["description"]
+ assert "CO2 shortage affects responsive L. bulgaricus" in c["description"]
+ for node in [c, d]:
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert {t["term"]["id"] for t in node["participating_taxa"]} == {
+ "NCBITaxon:1308",
+ "NCBITaxon:1585",
+ }
+ assert not any(k in node for k in ["source_taxon", "target_taxon", "interaction_type"])
+
+
+def test_yogurt_nox_keeps_intervention_early_recipient_and_final_null():
+ _, _, docs = records()
+ d = docs[3]["ecological_interactions"][3]
+ assert "disrupting S. thermophilus nox" in d["description"]
+ assert "slowed skim-milk acidification" in d["description"]
+ assert "not L. bulgaricus growth" in d["description"]
+ assert "final Streptococcus counts converged" in d["description"]
+ assert "Pfl is HYPOTHESIZED" in d["downstream"][0]["description"]
+ assert "threefold decrease" in docs[3]["discussions"][-1]["evidence"][0]["snippet"]
+
+
+def test_zymomonas_rescue_is_positive_and_pairs_are_separate():
+ _, _, docs = records()
+ a, _, c = docs[4]["ecological_interactions"]
+ assert "spent medium and individual amino-acid supplementation rescued" in a["description"]
+ assert "not describe a four-member consortium" in a["description"]
+ assert "three separate pairs" in c["description"]
+ assert "species-resolved flow cytometry" in c["description"]
+ assert "does not establish long-term community stability" in c["description"]
+
+
+def test_zymomonas_sulfur_rescue_is_not_exclusive_glutathione():
+ _, _, docs = records()
+ b = docs[4]["ecological_interactions"][1]
+ assert (
+ "Cysteine and glutathione supplementation independently supported rescue"
+ in b["description"]
+ )
+ assert "free cysteine below detection was not excluded" in b["description"]
+ assert b["evidence"][0]["supports"] == "PARTIAL"
+ assert b["evidence"][-1]["supports"] == "SUPPORT"
+ assert "exclusive necessity" in b["downstream"][0]["description"]
+
+
+def test_hcom_outcomes_have_direct_evidence_and_not_facilitation():
+ _, _, docs = records()
+ a, b, c = docs[5]["ecological_interactions"]
+ assert all("interaction_type" not in n for n in [a, b, c])
+ assert "increased stability to fecal challenge" in b["evidence"][0]["snippet"]
+ assert "colonization resistance" in c["evidence"][0]["snippet"]
+ assert b["evidence"][0]["evidence_source"] == c["evidence"][0]["evidence_source"] == "IN_VIVO"
+
+
+def test_hcom_donor_and_mediator_limits_remain():
+ _, _, docs = records()
+ a, b, c = docs[5]["ecological_interactions"]
+ assert "weaker resilience to unrelated fecal donors" in b["description"]
+ assert "not proof that each bacterial member is protective" in c["description"]
+ assert "HYPOTHESIZED mediation:" in a["downstream"][1]["description"]
+ assert "necessary" in a["downstream"][1]["description"]
+ assert "issue 765" in docs[5]["discussions"][-1]["rationale"]
+
+
+def test_ledger_preserves_topology_history_and_limited_caches():
+ ledger, rows, docs = records()
+ counts = ledger["reviewed_counts"]
+ assert (counts["original_nodes"], counts["retained_nodes"], counts["removed_nodes"]) == (
+ 15,
+ 15,
+ 0,
+ )
+ assert (counts["original_arrows"], counts["retained_arrows"], counts["removed_arrows"]) == (
+ 8,
+ 8,
+ 0,
+ )
+ assert counts["renamed_nodes"] == 6 and counts["new_discussions"] == 6
+ assert not ledger["independent_approval"]
+ assert ledger["unresolved_research_issues"] == [1968]
+ assert ledger["unresolved_non_graph_issues"] == [1969, 1970, 1971, 765]
+ assert len(ledger["cache_changes"]) == 5
+ assert sum(c["before_sha256"] is None for c in ledger["cache_changes"]) == 1
+ for cache in ledger["cache_changes"]:
+ assert (
+ hashlib.sha256((ROOT / cache["path"]).read_bytes()).hexdigest() == cache["after_sha256"]
+ )
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1 and doc["curation_history"][-1]["llm_assisted"]
+ names = [n["name"] for n in doc["ecological_interactions"]]
+ assert [n["node"] for n in row["node_decisions"]] == names
+ assert all(
+ a.split("#", 1)[1] in names
+ for d in doc["discussions"]
+ for a in d["attaches_to"]
+ if a.startswith("ecological_interactions#")
+ )
+ assert all(
+ e["target"] in names
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ )
diff --git a/tests/test_community_level_connectivity_credit.py b/tests/test_community_level_connectivity_credit.py
index 0b934e459..222c01f4a 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -113,7 +113,8 @@ def test_most_records_carry_a_community_level_interaction(survey):
# #1893 makes pyrite roles/perturbations community-scoped; no invented exchange.
# #1901 scopes the E. coli product and equilibria; both members retain pairwise credit.
# #1910 narrows vitamin provision to the tested pair (415 -> 414).
- assert 130 <= survey["with_community_level"] <= 414, survey
+ # #1965 scopes yogurt fermentation outcomes to both already pairwise-connected members.
+ assert 130 <= survey["with_community_level"] <= 415, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
@@ -134,7 +135,8 @@ def test_the_mixed_records_are_where_the_coarseness_bites(survey):
# Batch112 adds two mixed-scope records and one community-only record.
# Batch114 adds one mixed record; no additional solely-credited taxa.
# Batch117 removes that record's community-wide claim (137 -> 136).
- assert 35 <= survey["mixed"] <= 136, survey
+ # Batch124 adds yogurt as one mixed record; no additional solely-credited taxa.
+ assert 35 <= survey["mixed"] <= 137, 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 318ea57b5..7e9d8e699 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -461,6 +461,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml",
"Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml",
"Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml",
+ "Yogurt_TwoSpecies_Starter_Culture.yaml",
"mCAFEs_Brachypodium_RCC.yaml",
}