diff --git a/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html b/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html
index 010d94dbd..4115cc65f 100644
--- a/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html
+++ b/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html
@@ -1020,7 +1020,7 @@ Ecological Interactions
Ecological interaction network for Sesame-flavor Baijiu Fuqu SynCom (13-genus)
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, mutualism, niche partitioning).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.
@@ -1028,18 +1028,8 @@
Ecological Interactions
-
-
-
-
@@ -1047,54 +1037,56 @@ Ecological Interactions
-
Pichia, Bacillus, Aspergillus, Saccharomyces, and Wickerhamomyces formed the five-genus SC1 base consortium because they are commonly used in Fuqu preparation and contribute to starch degradation, ethanol production, and flavor-compound formation.
+
The 13-genus SC3 had the highest flavor-compound diversity metric and 3-(methylthio)-1-propanal content among the three tested SynComs in simulated fermentation. The diversity metric was 0.45, 0.40 and 0.64 for SC1, SC2 and SC3, respectively; it is a chemical-content metric, not microbial richness. In large-scale production, SC3-derived Fuqu exceeded commercial Fuqu for the reported flavor metric and this sulfur-containing compound, while ethanol did not differ significantly. These are consortium-level outcomes, not demonstrated reciprocal microbial fitness, niche partitioning or a resolved exchange pathway.
Participating Taxa:
- Pichia,
+ Aspergillus,
Bacillus,
- Aspergillus,
+ Lactobacillus,
+
+ Leuconostoc,
+
+ Pediococcus,
+
+ Pichia,
Saccharomyces,
- Wickerhamomyces
+ Trichosporon,
-
+ Weissella,
+ Candida,
+ Torulaspora,
+ Clavispora,
+ Wickerhamomyces
-
Biological Processes:
-
+
-
- biological process involved in interspecies interaction between organisms
- (GO:0044419 )
-
-
+
Metabolites:
+
+ 3-(methylthio)-1-propanal
+ (CHEBI:49017 )
+
+
-
-
Downstream Effects:
-
-
→ Emergent flavor-compound co-production by the assembled SynCom
-
The Fuqu base guild supplies starch, ethanol, and flavor-production functions used as the SC1 foundation for the higher-performing SC3 SynCom.
-
-
@@ -1110,68 +1102,23 @@
Evidence
- SUPPORT (IN_VITRO)
"Pichia, Bacillus, Aspergillus, Saccharomyces, and Wickerhamomyces are microorganisms commonly used in the preparation of Fuqu"
+ "The resulting SynCom exhibited the highest flavor compound diversity (0.64) and 3-(methylthio)-1-propanal content (618.14 μg/kg) in simulative fermentation."
-
-
-
-
-
-
-
Lactobacillus, Leuconostoc, Weissella, and Pediococcus were added to the five-member SC1 base to test whether lactic-acid bacteria that make flavor compounds and precursors could enhance flavor-compound formation.
-
-
-
-
-
Participating Taxa:
-
- Lactobacillus,
-
- Leuconostoc,
-
- Weissella,
-
- Pediococcus
-
-
-
-
+
+
- Biological Processes:
-
+ "The diversity of flavor compounds in SC1, SC2, and SC3 was 0.45, 0.40, and 0.64, respectively."
-
- biological process involved in interspecies interaction between organisms
- (GO:0044419 )
-
-
-
-
-
-
Downstream Effects:
-
-
-
→ Emergent flavor-compound co-production by the assembled SynCom
-
The lactic-acid bacterial subguild expands the SC2 consortium with precursor-forming taxa that feed flavor-compound formation.
-
-
-
Evidence
-
-
@@ -1181,7 +1128,7 @@
Evidence
- SUPPORT (IN_VITRO)
- "SC2 was constructed by adding four lactic acid bacteria genera to the five microorganisms present in SC1, with the aim of enhancing the formation of flavor compounds."
+ "The ethanol content showed no significant difference between SC3"
@@ -1189,58 +1136,51 @@ Evidence
-
-
When the 13 core genera are assembled into a SynCom, the community exhibits emergent, community-level enhancement of flavor-compound production - the highest flavor-compound diversity and 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation, exceeding commercial Fuqu at large scale.
-
-
-
-
+
-
Metabolites:
+
- 3-(methylthio)-1-propanal
- (CHEBI:49017 )
+
+ Knowledge gaps & discussions (1)
-
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which interspecies mechanisms explain the SC3 flavor outcome?
+
+
The primary main text compares SC1, SC2 and SC3, then SC3-derived and commercial Fuqu. The five-genus base and addition of four LAB are assembly decisions supported by prior functional literature; they are not measured niche separation or metabolite transfer in this consortium. The source proposes fungal diversity and bacterial-fungal synergy as explanations. Retain that hypothesis and the positive flavor outcomes without assigning a specific donor, recipient or reciprocal growth benefit. No cultivation or optimization changes are made.
+
Attaches to: ecological_interactions#Flavor-compound outcomes of SC3 versus comparator starters
+
+ 1 evidence item(s)
+
+
+
IN_VITRO
+
PARTIAL
-
Evidence
-
-
-
+ the superior performance of SC3 may therefore be attributed to its higher fungal diversity, together with the synergistic interactions between its more diverse bacteria and fungi.
+ Source-proposed interpretation; exact interspecies mediation remains unresolved.
+
-
"The resulting SynCom exhibited the highest flavor compound diversity (0.64) and 3-(methylthio)-1-propanal content (618.14 μg/kg) in simulative fermentation."
-
-
+
-
Evidence
(function() {
var intId = "interaction:0";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
- var processes = [];
+ metabolites.push("3-(methylthio)-1-propanal");
- processes.push("biological process involved in interspecies interaction between organisms");
+ var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 3;
nodes.push({
id: intId,
- label: "Fuqu Starch Ethanol and Flavor Base Guild",
+ label: "Flavor-compound outcomes of SC3 versus comparator starters",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1502,60 +1442,31 @@ Evidence
var participantKeys = [
- "Pichia",
-
- "Bacillus",
-
"Aspergillus",
- "Saccharomyces",
-
- "Wickerhamomyces"
-
- ];
- participantKeys.forEach(function(key) {
- if (taxonNodeIds[key]) {
- links.push({ source: taxonNodeIds[key], target: intId });
- }
- });
-
- })();
-
- (function() {
- var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
- var metabolites = [];
-
- var processes = [];
-
-
- processes.push("biological process involved in interspecies interaction between organisms");
+ "Bacillus",
+ "Lactobacillus",
- var evidenceCount = 1;
+ "Leuconostoc",
- nodes.push({
- id: intId,
- label: "Lactic-Acid Bacteria Flavor-Precursor Guild",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
+ "Pediococcus",
+ "Pichia",
+ "Saccharomyces",
+ "Trichosporon",
- var participantKeys = [
+ "Weissella",
- "Lactobacillus",
+ "Candida",
- "Leuconostoc",
+ "Torulaspora",
- "Weissella",
+ "Clavispora",
- "Pediococcus"
+ "Wickerhamomyces"
];
participantKeys.forEach(function(key) {
@@ -1564,34 +1475,6 @@ Evidence
}
});
- })();
-
- (function() {
- var intId = "interaction:2";
- var intType = "MUTUALISM";
- var metabolites = [];
-
-
- metabolites.push("3-(methylthio)-1-propanal");
-
-
- var processes = [];
-
- var evidenceCount = 1;
-
- nodes.push({
- id: intId,
- label: "Emergent flavor-compound co-production by the assembled SynCom",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
- });
-
-
-
-
})();
@@ -1613,7 +1496,7 @@ Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 16;
+ var nodeCount = 14;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html b/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html
index b0a0b9354..7f06392fa 100644
--- a/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html
+++ b/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html
@@ -574,6 +574,11 @@ Ecological Interactions
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"> Mutualism
+
+
Ecological Interactions
Synergistic biofilm and EPS formation in co-culture
MUTUALISM
- Co-cultivation of the two strains synergistically enhances multispecies biofilm formation, extracellular polysaccharide (EPS) production, and metabolic activity relative to monocultures (measured, emergent).
+ Co-culture increased biofilm biomass, EPS and metabolic activity relative to monocultures. Species-specific qPCR also supported increased cell-equivalent abundance of both strains in the biofilm fraction, supporting reciprocal benefit in that assay. WB abundance did not increase in the planktonic fraction. This conditional biofilm mutualism is not proof of reciprocal metabolite delivery or of the same interaction operating on watermelon roots.
Source Taxon: Agrobacterium deltaense LSQ16
@@ -614,8 +619,7 @@ Synergistic biofilm and EPS formation in co-culture
→ SynCom Y Fusaric Acid and Wilt Resistance
-
The EPS-rich dual-species biofilm tolerated more fusaric acid than either monoculture and links the Agrobacterium-Bacillus biofilm synergy to pot-level watermelon Fusarium wilt suppression.
-
+
HYPOTHESIZED/PARTIAL: enhanced EPS-rich biofilm formation could contribute to fusaric-acid tolerance and the positive pot-level biocontrol outcome. Separate in-vitro and pot comparisons do not isolate biofilm mediation or establish that the in-vitro partnership occurs in the rhizosphere.
@@ -638,6 +642,19 @@ Evidence
+
+
+
+ "Quantitative PCR under co-culture conditions confirmed that mixed-species biofilm formation promotes the growth of both strains"
+
+
+
@@ -645,12 +662,19 @@ Evidence
-
SynCom Y biofilms showed higher resistance to fusaric acid than either monoculture and the two-strain inoculum reduced watermelon Fusarium wilt incidence more effectively than single-strain treatments in pots, connecting the cooperative biofilm to emergent biocontrol performance.
+
The two-strain biofilm tolerated fusaric-acid exposure better than either monoculture in vitro. Separately, SynCom Y reduced watermelon wilt in pots, with reported disease incidence 18.33% and control efficacy 79.13%. Preserve both positive outcomes without equating biofilm tolerance with pathogen killing or asserting that EPS, a specific exchanged metabolite or root colonization was experimentally isolated as the cause of disease suppression.
+
+
Participating Taxa:
+
+ Agrobacterium deltaense LSQ16,
+
+ Bacillus velezensis WB
+
+
@@ -664,17 +688,6 @@
SynCom Y Fusaric Acid and Wilt Resistance
-
Biological Processes:
-
-
@@ -717,7 +730,7 @@
Evidence
Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
CROSS_FEEDING
Genome-scale metabolic modeling predicts LSQ16 donates metabolites to WB (including L-ornithine, guanine, guanosine, malate, phosphate). Two predicted donations (L-ornithine, guanine) were experimentally confirmed to enhance WB biofilm; the remainder are model-only.
+ HYPOTHESIZED/PARTIAL: genome-scale models predict LSQ16-to-WB exchange of several metabolites. Exogenous L-ornithine and guanine increased WB biofilm biomass, and co-culture metabolite abundances were consistent with the proposed direction. Supplementation demonstrates a physiological response, not direct donor-to-recipient transfer. Malate and guanosine were also included in supplementation tests; the reported positive validation centers on ornithine and guanine. Other predicted exchanges are not established measured fluxes.
Source Taxon: Agrobacterium deltaense LSQ16
@@ -761,8 +774,7 @@ Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
→ Synergistic biofilm and EPS formation in co-culture
-
Experimentally validated L-ornithine and guanine additions connect the predicted LSQ16-to-WB donation route to enhanced B. velezensis biofilm formation in the measured co-culture synergy.
-
+
HYPOTHESIZED/PARTIAL: predicted LSQ16 provision of L-ornithine and guanine could contribute to WB biofilm enhancement, consistent with the positive additions and metabolite profiles. These results do not establish transfer, its necessity, or its quantitative contribution to the two-strain biofilm/EPS response.
@@ -778,7 +790,7 @@ Evidence
PMID:42125264
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"Moreover, exogenous supplementation of l-ornithine and guanine further enhanced the biofilm-forming capacity of B. velezensis WB."
@@ -791,10 +803,10 @@ Evidence
PMID:42125264
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
- "Predictive results indicated metabolite exchange between the two strains involved amino acids, purines, phosphates, and other compounds."
+ "A. deltaense LSQ16 may supply malate, O-acetylcarnitine, guanine, guanosine, l-ornithine, and phosphate to B. velezensis WB"
@@ -807,7 +819,7 @@ Evidence
Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
CROSS_FEEDING
- Genome-scale metabolic modeling predicts WB returns metabolites to LSQ16 (including L-serine, pyroglutamic acid, myristic acid, suberoylglycine). Model-only; no experimental validation reported for this direction.
+ HYPOTHESIZED/PARTIAL: models predict WB-to-LSQ16 return of L-serine, pyroglutamic acid, myristic acid and suberoylglycine. Metabolite abundance patterns are consistent with some predictions, but additions of tested reverse-direction candidates did not significantly enhance LSQ16 monoculture biofilm biomass. This negative endpoint does not prove that exchange is absent; it prevents describing a beneficial return flux as experimentally validated.
Source Taxon: Bacillus velezensis WB
@@ -841,10 +853,23 @@ Evidence
PMID:42125264
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
+
+
+ "which in turn provides suberoylglycine, myristic acid, l-serine, and pyroglutamic acid to A. deltaense LSQ16"
+
+
+
+
+
- "Predictive results indicated metabolite exchange between the two strains involved amino acids, purines, phosphates, and other compounds."
+ "the addition of l-serine, pyroglutamic acid, and other compounds did not result in a significant enhancement of the biofilm biomass in A. deltaense LSQ16 monocultures"
@@ -857,6 +882,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which predicted exchanges mediate biofilm synergy and the pot-level biocontrol outcome?
+
+
Preserve reciprocal biofilm-associated abundance, EPS, metabolic activity, FA tolerance and disease suppression. Forward additions are positive; tested reverse additions did not significantly enhance LSQ16 biofilm. Neither result directly measures interspecies transfer. The primary discussion explicitly leaves rhizosphere synergy unverified. Modeling methods name CarveMe, Cobra toolbox and FBA but do not state versions or genome input accessions; the cited SRA range belongs to RNA-seq. Main text and captions were read, not separate supplementary data or raw datasets.
+
+
Attaches to: ecological_interactions#Synergistic biofilm and EPS formation in co-culture, ecological_interactions#SynCom Y Fusaric Acid and Wilt Resistance, ecological_interactions#Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB, ecological_interactions#Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
Whether the two strains form a synergistic relationship in the rhizosphere still requires validation via root colonization assays.
+
Explicit limitation separating in-vitro biofilm findings from rhizosphere mechanism.
+
+
+
+
@@ -1043,7 +1107,7 @@ Evidence
processes.push("biofilm formation");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1072,7 +1136,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1081,10 +1145,6 @@ Evidence
var processes = [];
-
- processes.push("symbiotic process");
-
-
var evidenceCount = 2;
nodes.push({
@@ -1100,6 +1160,19 @@ Evidence
+ var participantKeys = [
+
+ "Agrobacterium deltaense LSQ16",
+
+ "Bacillus velezensis WB"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
@@ -1159,7 +1232,7 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html b/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html
index 9c001ac77..66a5792b2 100644
--- a/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html
+++ b/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html
@@ -599,6 +599,11 @@ Ecological Interactions
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"> Mutualism
+
+
@@ -608,7 +613,7 @@ Ecological Interactions
Photosynthetic Sucrose Transfer To Azotobacter
CROSS_FEEDING
- Engineered S. elongatus PCC 7942 cscB fixes inorganic carbon under illumination and exports sucrose that supports A. vinelandii growth when fixed carbon is absent.
+ The engineered cscB S. elongatus/AV3 A. vinelandii coculture required a sucrose-exporting cyanobacterium and grew without added fixed carbon or nitrogen. This supports the existing photosynthetic carbon-supply direction. The initial glutamate-supplemented experiments are a distinct context; the reviewed abstract does not resolve transfer rates or detailed transport.
Source Taxon: Synechococcus elongatus PCC 7942 cscB
@@ -657,8 +662,7 @@ Photosynthetic Sucrose Transfer To Azotobacter
→ Light-Driven PHB Production
-
Sucrose exported by engineered S. elongatus supplies the fixed carbon used by A. vinelandii in the light-driven coculture that produced PHB.
-
+
HYPOTHESIZED/PARTIAL: cyanobacterial carbon supply supports the productive coculture and is proposed to provide carbon for PHB. The abstract establishes exporter-dependent growth and PHB production, not direct carbon tracing into PHB or isolated control of its yield.
@@ -703,7 +707,7 @@ Evidence
Diazotrophic Nitrogen Support
MUTUALISM
- A. vinelandii provides biological nitrogen fixation capacity in the mutualism, enabling coculture growth in the absence of added fixed nitrogen.
+ The diazotrophic AV3 partner provides nitrogen-fixation capacity in the engineered mutualism that grows without added fixed carbon or nitrogen, whereas neither member grows alone under that omission. Preserve this growth-context mutualism without specifying an unreported exported nitrogen compound, transfer rate or nitrogen-dependent change in PHB yield.
Source Taxon: Azotobacter vinelandii AV3
@@ -742,8 +746,7 @@ Diazotrophic Nitrogen Support
→ Light-Driven PHB Production
-
Diazotrophic nitrogen fixation by A. vinelandii enables coculture growth without added fixed nitrogen in the same mutualism that produced PHB.
-
+
HYPOTHESIZED/PARTIAL: diazotrophic support could enable growth of the PHB-producing coculture under fixed-nitrogen omission. The abstract does not isolate nitrogen supply as the mediator of a PHB-production change or establish the exact PHB assay conditions.
@@ -786,16 +789,19 @@ Evidence
-
The designed mutualism produced polyhydroxybutyrate, linking photosynthetic carbon capture and diazotrophic growth support to biopolymer production.
+
The designed coculture was demonstrated to produce PHB. This is a productive community endpoint, not independent evidence of reciprocal fitness or direct photosynthetic flux. The abstract names alginate as a potential product, not demonstrated production, and does not supply the PHB assay conditions or quantify carbon/nitrogen mediation.
-
Source Taxon: Synechococcus elongatus PCC 7942 cscB
+
Participating Taxa:
-
Target Taxon: Azotobacter vinelandii AV3
+ Synechococcus elongatus PCC 7942 cscB,
+
+ Azotobacter vinelandii AV3
+
+
@@ -809,17 +815,6 @@
Light-Driven PHB Production
-
Biological Processes:
-
-
@@ -840,28 +835,54 @@
Evidence
-
-
- - SUPPORT (IN_VITRO)
- "industrially relevant products, such as polyhydroxybutyrate (PHB) and alginate"
+
-
+
-
+
+ Knowledge gaps & discussions (1)
-
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How do carbon and nitrogen provision contribute to the demonstrated PHB outcome?
+
+
The independently retrieved primary abstract distinguishes initial glutamate studies from the engineered carbon/nitrogen-omission mutualism. It supports exporter-dependent growth, failure of either partner alone under omission and PHB production. It does not specify a transferred nitrogen species, fluxes or the precise PHB assay conditions. Full article and supplements were not retrieved in this bounded review; no absence claim is made. Alginate remains a proposed capability, not a measured product.
+
Attaches to: ecological_interactions#Photosynthetic Sucrose Transfer To Azotobacter, ecological_interactions#Diazotrophic Nitrogen Support, ecological_interactions#Light-Driven PHB Production
-
-
+
+ 1 evidence item(s)
+
+
+
+
From initial studies of the coculture grown in media with glutamate, we proposed a model of cross-feeding between these organisms.
+
Initial supplemented-condition model must not be conflated with the later engineered omission experiment.
+
+
+
+
@@ -1372,7 +1393,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1381,11 +1402,7 @@ Evidence
var processes = [];
-
- processes.push("photosynthesis");
-
-
- var evidenceCount = 2;
+ var evidenceCount = 1;
nodes.push({
id: intId,
@@ -1398,17 +1415,20 @@ Evidence
});
- var srcKey = "Synechococcus elongatus PCC 7942 cscB";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Azotobacter vinelandii AV3";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Synechococcus elongatus PCC 7942 cscB",
+
+ "Azotobacter vinelandii AV3"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/docs/communities/Synechococcus_Bacillus_SPC.html b/docs/communities/Synechococcus_Bacillus_SPC.html
index c9e551f7a..7d2c13826 100644
--- a/docs/communities/Synechococcus_Bacillus_SPC.html
+++ b/docs/communities/Synechococcus_Bacillus_SPC.html
@@ -559,7 +559,7 @@ Ecological Interactions
Ecological interaction network for Synechococcus-Bacillus Synthetic Photosynthetic Consortium
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, mutualism).
+ Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).
@@ -572,8 +572,8 @@
Ecological Interactions
@@ -584,7 +584,7 @@ Ecological Interactions
CO2 Fixation and Sucrose Production
CROSS_FEEDING
- Engineered Synechococcus elongatus PCC 7942 cscB+ fixes CO2 photosynthetically and secretes the bulk of that fixed carbon as sucrose, providing the carbohydrate feedstock for Bacillus subtilis 168.
+ Engineered cscB+ S. elongatus provides photosynthetic carbon, including exported sucrose, to Bacillus-containing cocultures. This record names B. subtilis 168, used in the alpha-amylase demonstration; several growth and perturbation experiments instead used 3610. Preserve carbon support without transferring all 3610 results to strain 168.
Source Taxon: Synechococcus elongatus PCC 7942 cscB+
@@ -629,7 +629,7 @@ CO2 Fixation and Sucrose Production
→ Sucrose Uptake and Heterotrophic Growth
-
Secreted cyanobacterial photosynthate is taken up as the sucrose carbon source that lets the heterotrophic partner grow in the light-driven coculture.
+
PARTIAL: cyanobacterial sucrose export is the proposed carbon supply for the existing heterotrophic-growth node. Sucrose-dependent Bacillus growth and the 168-specific production assay support this route, but exact growth kinetics must remain strain-specific.
@@ -659,14 +659,17 @@ Evidence
-
Bacillus subtilis 168 grows heterotrophically on the sucrose-rich photosynthate secreted by engineered Synechococcus, making heterotroph growth dependent on the cyanobacterial carbon-export module.
+
PARTIAL: photosynthate supported Bacillus cocultures, with initial growth followed by declining viability in batch assays. B. subtilis 168 was explicitly used for active alpha-amylase production, which increased with induced cyanobacterial sucrose secretion. That positive result does not establish weeks-to-months persistence of strain 168 or justify assigning 3610 perturbation results to it.
+
-
Source Taxon: Bacillus subtilis 168
+
Participating Taxa:
+ Bacillus subtilis 168
+
+
@@ -693,16 +696,6 @@
Sucrose Uptake and Heterotrophic Growth
-
-
Downstream Effects:
-
-
-
→ Sucrose-Dependent Long-Term Consortium Stabilization
-
Heterotrophic sucrose utilization is the positive carbon-flow process that counterbalances destabilizing non-sucrose byproducts and lets both members persist for weeks to months.
-
-
-
-
Evidence
@@ -714,103 +707,75 @@
Evidence
PMID:28127397
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"We observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair"
-
-
-
-
-
-
-
Robustness of the autotroph-heterotroph coculture depends on heterotroph sucrose utilization together with species-independent interactions, allowing both members to persist under long-term culture and perturbation.
-
-
-
Source Taxon: Bacillus subtilis 168
-
+
+
+
PMID:28127397
-
Target Taxon: Synechococcus elongatus PCC 7942 cscB+
+ - PARTIAL (IN_VITRO)
+
"In consortia with S. elongatus, B. subtilis 168 produces alpha-amylase after 24 hours in constant light"
+
-
Metabolites:
+
- sucrose
- (CHEBI:17992 )
+
Biological Processes:
-
+
+ Knowledge gaps & discussions (1)
-
- sucrose catabolic process
- (GO:0005987 )
-
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which strain- and condition-specific interactions explain growth and persistence in this dyad?
+
+
The source combines batch, continuous, density-dependent and production assays. Keep their positive results without treating every partner or strain as persistent for weeks to months. Cyanobacterial growth stimulation is observed, but metabolite return and byproduct absorption remain hypotheses. Light-associated inhibition is supported without identifying oxygen as the exclusive cause. For Bacillus, the canonical168 production assay is distinct from 3610 perturbation experiments. For E. coli, the early non-sucrose inference differs from later sucrose-sensitive production; for yeast, W303Clump is not parental W303. No new causal node, direction, cultivation protocol or strain optimization is added.
-
- photosynthesis
- (GO:0015979 )
-
+
Attaches to: ecological_interactions#CO2 Fixation and Sucrose Production, ecological_interactions#Sucrose Uptake and Heterotrophic Growth
-
+
+ 1 evidence item(s)
+
+
+
IN_VITRO
+
PARTIAL
-
Evidence
-
-
-
+ we hypothesize that these benefits arise from emergent cross-feeding of metabolite(s) and/or absorption of byproducts
+ Source-explicit proposed mediator of cyanobacterial stimulation, not a measured transfer mechanism.
+
-
"Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization"
-
-
-
-
-
-
- "inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures"
-
-
+
-
Evidence
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1041,7 +1006,7 @@ Evidence
processes.push("sucrose catabolic process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1054,57 +1019,19 @@ Evidence
});
- var srcKey = "Bacillus subtilis 168";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- })();
-
- (function() {
- var intId = "interaction:2";
- var intType = "MUTUALISM";
- var metabolites = [];
-
-
- metabolites.push("sucrose");
+ "Bacillus subtilis 168"
-
- var processes = [];
-
-
- processes.push("sucrose catabolic process");
-
- processes.push("photosynthesis");
-
-
- var evidenceCount = 2;
-
- nodes.push({
- id: intId,
- label: "Sucrose-Dependent Long-Term Consortium Stabilization",
- type: "interaction",
- interactionType: intType,
- metabolites: metabolites,
- processes: processes,
- evidenceCount: evidenceCount
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
});
-
- var srcKey = "Bacillus subtilis 168";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
-
-
-
- var tgtKey = "Synechococcus elongatus PCC 7942 cscB+";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
-
})();
@@ -1126,7 +1053,7 @@ Evidence
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
- var nodeCount = 5;
+ var nodeCount = 4;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);
diff --git a/docs/communities/Synechococcus_Ecoli_SPC.html b/docs/communities/Synechococcus_Ecoli_SPC.html
index 53fae9144..6dcc45a5a 100644
--- a/docs/communities/Synechococcus_Ecoli_SPC.html
+++ b/docs/communities/Synechococcus_Ecoli_SPC.html
@@ -575,23 +575,29 @@ Ecological Interactions
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"> Mutualism
+
-
Synechococcus elongatus fixes atmospheric CO2 through photosynthesis and converts the fixed carbon into sucrose. The CscB transporter enables export of sucrose to the extracellular environment when induced with IPTG in the presence of osmotic pressure (NaCl).
-
+
CscB+ S. elongatus fixes carbon and exports sucrose, but E. coli W and W delta-cscR grew during early batch coculture independently of induced sucrose export. The source infers substantial use of other photosynthates at that stage; their identities, including the proposed extracellular polymers, were not resolved. The earlier 85% carbon-export capability is not a concentration or a measurement of this dyad.
Source Taxon: Synechococcus elongatus PCC 7942 cscB+
+
Target Taxon: Escherichia coli W delta-cscR
+
Metabolites:
@@ -627,8 +633,8 @@
CO2 Fixation and Sucrose Production
Downstream Effects:
-
→ Sucrose Uptake and Heterotrophic Growth
-
Secreted sucrose supports E. coli growth
+
→ E. coli growth on cyanobacterial photosynthate
+
Cyanobacterial photosynthate supports E. coli growth. PARTIAL for sucrose-specific mediation: early growth was insensitive to export induction, so that phase cannot be attributed solely to sucrose; later productive cocultures show a sucrose contribution.
Evidence
+
+
+
+ "E. coli strains cannot utilize sucrose effectively and dominantly depend on other metabolites from S. elongatus"
+
+
+
-
E. coli utilizes the sucrose secreted by Synechococcus elongatus as its carbon and energy source for heterotrophic growth. This establishes a stable syntrophic relationship where the phototroph provides fixed carbon and the heterotroph benefits without needing to fix CO2.
-
+
E. coli W delta-cscR grew on cyanobacterial photosynthate and maintained viability in continuous coculture for more than two weeks. Early batch growth was not primarily attributable to sucrose export; improved sucrose utilization contributed to later PHB production in separately functionalized strains. No product-removal feedback mechanism establishing syntrophy is shown by carbon feeding alone.
-
Source Taxon: Escherichia coli W delta-cscR
+
Participating Taxa:
+
+ Escherichia coli W delta-cscR
+
+
@@ -698,7 +719,7 @@
Sucrose Uptake and Heterotrophic Growth
→ E. coli Stimulation of Cyanobacterial Growth
-
E. coli W delta-cscR growth on Synechococcus-derived photosynthate establishes the reciprocal dyad in which the heterotroph increases cyanobacterial growth relative to axenic controls.
+
HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend on culture context.
Evidence
- SUPPORT (IN_VITRO)
- "Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads"
+ "we determined that co-cultures maintain stable ratios for more than two weeks"
@@ -730,7 +751,7 @@ Evidence
E. coli Stimulation of Cyanobacterial Growth
MUTUALISM
- E. coli W delta-cscR persists on cyanobacterial photosynthate and stimulates cscB+ Synechococcus elongatus growth relative to axenic cyanobacterial controls in the synthetic photosynthetic coculture platform.
+ The tested heterotrophic partner increased cyanobacterial abundance relative to axenic controls in low-density cocultures. Together with photosynthate-supported heterotroph growth, this supports conditional reciprocal benefit. It is not universal stability: dense illuminated cyanobacteria could inhibit heterotroph viability. The source proposes metabolite return or byproduct absorption as possible explanations for stimulation, without resolving the mediator; respiratory CO2 alone was considered questionable.
Source Taxon: Escherichia coli W delta-cscR
@@ -797,6 +818,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which strain- and condition-specific interactions explain growth and persistence in this dyad?
+
+
The source combines batch, continuous, density-dependent and production assays. Keep their positive results without treating every partner or strain as persistent for weeks to months. Cyanobacterial growth stimulation is observed, but metabolite return and byproduct absorption remain hypotheses. Light-associated inhibition is supported without identifying oxygen as the exclusive cause. For Bacillus, the canonical168 production assay is distinct from 3610 perturbation experiments. For E. coli, the early non-sucrose inference differs from later sucrose-sensitive production; for yeast, W303Clump is not parental W303. No new causal node, direction, cultivation protocol or strain optimization is added.
+
+
Attaches to: ecological_interactions#Photosynthetic carbon supply to E. coli, ecological_interactions#E. coli growth on cyanobacterial photosynthate, ecological_interactions#E. coli Stimulation of Cyanobacterial Growth
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
we hypothesize that these benefits arise from emergent cross-feeding of metabolite(s) and/or absorption of byproducts
+
Source-explicit proposed mediator of cyanobacterial stimulation, not a measured transfer mechanism.
+
+
+
+
@@ -1082,11 +1142,11 @@ Evidence
processes.push("sucrose biosynthetic process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "CO2 Fixation and Sucrose Production",
+ label: "Photosynthetic carbon supply to E. coli",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1102,11 +1162,16 @@ Evidence
+ var tgtKey = "Escherichia coli W delta-cscR";
+ if (taxonNodeIds[tgtKey]) {
+ links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+ }
+
})();
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1123,7 +1188,7 @@ Evidence
nodes.push({
id: intId,
- label: "Sucrose Uptake and Heterotrophic Growth",
+ label: "E. coli growth on cyanobacterial photosynthate",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1132,12 +1197,18 @@ Evidence
});
- var srcKey = "Escherichia coli W delta-cscR";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Escherichia coli W delta-cscR"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/docs/communities/Synechococcus_Saccharomyces_SPC.html b/docs/communities/Synechococcus_Saccharomyces_SPC.html
index 481e94335..bee558446 100644
--- a/docs/communities/Synechococcus_Saccharomyces_SPC.html
+++ b/docs/communities/Synechococcus_Saccharomyces_SPC.html
@@ -597,6 +597,11 @@ Ecological Interactions
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"> Mutualism
+
+
@@ -606,13 +611,15 @@ Ecological Interactions
CO2 Fixation and Sucrose Production
CROSS_FEEDING
- Engineered Synechococcus elongatus PCC 7942 fixes carbon dioxide under light and exports sucrose through the cscB+ transporter, making fixed carbon available to a heterotrophic partner.
+ CscB+ S. elongatus fixes carbon and exports sucrose that supports the evolved S. cerevisiae W303Clump partner. The parental W303 did not grow in the tested cocultures; the positive carbon-supply result is specific to W303Clump and the tested conditions.
Source Taxon: Synechococcus elongatus PCC 7942 cscB+
+ Target Taxon: Saccharomyces cerevisiae W303Clump
+
Metabolites:
@@ -679,15 +686,17 @@
Evidence
-
The yeast grows on the sucrose the cyanobacterium secretes. The paper reports no product formation for this dyad -- its photoproduction demonstrations use B. subtilis (alpha-amylase) and E. coli (polyhydroxybutyrate) -- so nothing beyond sucrose catabolism is claimed here.
-
+
W303Clump utilized cyanobacterial sucrose and persisted for more than two months in continuous coculture. Separate continuous experiments demonstrated persistence during light-dark cycling; the two-month duration is not assigned to that diurnal assay. Initial growth followed by declining viability in batch culture is a distinct result. Parental W303 did not grow in the tested coculture; the study does not demonstrate a bioproduct for this yeast dyad.
-
Source Taxon: Saccharomyces cerevisiae W303Clump
+
Participating Taxa:
+
+ Saccharomyces cerevisiae W303Clump
+
+
@@ -719,8 +728,7 @@
Sucrose Utilization by the Heterotrophic Partner
→ Yeast Stimulation of Cyanobacterial Growth
-
Sucrose utilization sustains W303Clump in the light-driven dyad, and the presence of each tested heterotroph, including the yeast partner, reciprocally increased S. elongatus growth.
-
+
HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend on culture context.
Evidence
- SUPPORT (IN_VITRO)
- "Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads"
+ "S. cerevisiae W303Clump maintains viability in continuous culture with sucrose-secreting S. elongatus for greater than two months"
@@ -752,8 +760,7 @@ Evidence
Yeast Stimulation of Cyanobacterial Growth
MUTUALISM
- Saccharomyces cerevisiae W303Clump persists on cyanobacterially derived sucrose and, as one of the heterotrophs in this dyad series, stimulates cscB+ S. elongatus growth relative to axenic cyanobacterial controls.
-
+ The tested heterotrophic partner increased cyanobacterial abundance relative to axenic controls in low-density cocultures. Together with photosynthate-supported heterotroph growth, this supports conditional reciprocal benefit. It is not universal stability: dense illuminated cyanobacteria could inhibit heterotroph viability. The source proposes metabolite return or byproduct absorption as possible explanations for stimulation, without resolving the mediator; respiratory CO2 alone was considered questionable.
Source Taxon: Saccharomyces cerevisiae W303Clump
@@ -820,6 +827,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which strain- and condition-specific interactions explain growth and persistence in this dyad?
+
+
The source combines batch, continuous, density-dependent and production assays. Keep their positive results without treating every partner or strain as persistent for weeks to months. Cyanobacterial growth stimulation is observed, but metabolite return and byproduct absorption remain hypotheses. Light-associated inhibition is supported without identifying oxygen as the exclusive cause. For Bacillus, the canonical168 production assay is distinct from 3610 perturbation experiments. For E. coli, the early non-sucrose inference differs from later sucrose-sensitive production; for yeast, W303Clump is not parental W303. No new causal node, direction, cultivation protocol or strain optimization is added.
+
+
Attaches to: ecological_interactions#CO2 Fixation and Sucrose Production, ecological_interactions#Sucrose Utilization by the Heterotrophic Partner, ecological_interactions#Yeast Stimulation of Cyanobacterial Growth
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
we hypothesize that these benefits arise from emergent cross-feeding of metabolite(s) and/or absorption of byproducts
+
Source-explicit proposed mediator of cyanobacterial stimulation, not a measured transfer mechanism.
+
+
+
+
@@ -1024,11 +1070,16 @@ Evidence
+ var tgtKey = "Saccharomyces cerevisiae W303Clump";
+ if (taxonNodeIds[tgtKey]) {
+ links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+ }
+
})();
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1054,12 +1105,18 @@ Evidence
});
- var srcKey = "Saccharomyces cerevisiae W303Clump";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Saccharomyces cerevisiae W303Clump"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/history/records/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus/2026-10-08T045942Z-codex-f64ce1.yaml b/history/records/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus/2026-10-08T045942Z-codex-f64ce1.yaml
new file mode 100644
index 000000000..275cc83ba
--- /dev/null
+++ b/history/records/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus/2026-10-08T045942Z-codex-f64ce1.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml
+ slug: SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus
+session:
+ id: 2026-10-08T045942Z-codex-f64ce1
+ timestamp: '2026-10-08T04:59:42Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1849
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain comparator-specific chemical outcomes; remove construction nodes, unsupported
+ interaction types and two design-order arrows.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
diff --git a/history/records/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture/2026-10-08T045943Z-codex-deec92.yaml b/history/records/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture/2026-10-08T045943Z-codex-deec92.yaml
new file mode 100644
index 000000000..625892ab5
--- /dev/null
+++ b/history/records/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture/2026-10-08T045943Z-codex-deec92.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
+ slug: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+session:
+ id: 2026-10-08T045943Z-codex-deec92
+ timestamp: '2026-10-08T04:59:43Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1850
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain assay-specific reciprocal biofilm growth and qualify its proposed downstream
+ mediation.; Retain measured FA tolerance and pot biocontrol as community outcomes, not
+ a second mutualism.; Separate positive supplementation from transfer and correct modeling
+ input/version provenance.; Retain predicted return with the reported negative supplementation
+ endpoint and corrected provenance.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
diff --git a/history/records/Synechococcus_Azotobacter_Photoproduction_Mutualism/2026-10-08T045943Z-codex-31bb19.yaml b/history/records/Synechococcus_Azotobacter_Photoproduction_Mutualism/2026-10-08T045943Z-codex-31bb19.yaml
new file mode 100644
index 000000000..75b1c65d3
--- /dev/null
+++ b/history/records/Synechococcus_Azotobacter_Photoproduction_Mutualism/2026-10-08T045943Z-codex-31bb19.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml
+ slug: Synechococcus_Azotobacter_Photoproduction_Mutualism
+session:
+ id: 2026-10-08T045943Z-codex-31bb19
+ timestamp: '2026-10-08T04:59:43Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1851
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain exporter-dependent carbon support without transport-rate or PHB-tracing
+ claims.; Retain omission-context mutualism; qualify nitrogen-to-PHB mediation and substrate
+ role.; Retain PHB production as a community endpoint and distinguish potential alginate
+ production.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
diff --git a/history/records/Synechococcus_Bacillus_SPC/2026-10-08T045943Z-codex-9d0c0c.yaml b/history/records/Synechococcus_Bacillus_SPC/2026-10-08T045943Z-codex-9d0c0c.yaml
new file mode 100644
index 000000000..5f7c6201b
--- /dev/null
+++ b/history/records/Synechococcus_Bacillus_SPC/2026-10-08T045943Z-codex-9d0c0c.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Bacillus_SPC.yaml
+ slug: Synechococcus_Bacillus_SPC
+session:
+ id: 2026-10-08T045943Z-codex-9d0c0c
+ timestamp: '2026-10-08T04:59:43Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1852
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain cyanobacterial carbon support with explicit 168-versus-3610 scope.; Retain
+ bounded Bacillus growth support and the positive168 assay; remove unestablished long-term
+ stability.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
diff --git a/history/records/Synechococcus_Ecoli_SPC/2026-10-08T045944Z-codex-9a70f9.yaml b/history/records/Synechococcus_Ecoli_SPC/2026-10-08T045944Z-codex-9a70f9.yaml
new file mode 100644
index 000000000..1e2c388e1
--- /dev/null
+++ b/history/records/Synechococcus_Ecoli_SPC/2026-10-08T045944Z-codex-9a70f9.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Ecoli_SPC.yaml
+ slug: Synechococcus_Ecoli_SPC
+session:
+ id: 2026-10-08T045944Z-codex-9a70f9
+ timestamp: '2026-10-08T04:59:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1853
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain carbon supply while distinguishing early non-sucrose dependence and removing
+ the invalid concentration.; Retain strain-specific growth/persistence, not sucrose-exclusive
+ growth or syntrophy.; Retain conditional reciprocal growth benefit; mediator of cyanobacterial
+ stimulation is unresolved.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
diff --git a/history/records/Synechococcus_Saccharomyces_SPC/2026-10-08T045944Z-codex-a56048.yaml b/history/records/Synechococcus_Saccharomyces_SPC/2026-10-08T045944Z-codex-a56048.yaml
new file mode 100644
index 000000000..4d116cef2
--- /dev/null
+++ b/history/records/Synechococcus_Saccharomyces_SPC/2026-10-08T045944Z-codex-a56048.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Synechococcus_Saccharomyces_SPC.yaml
+ slug: Synechococcus_Saccharomyces_SPC
+session:
+ id: 2026-10-08T045944Z-codex-a56048
+ timestamp: '2026-10-08T04:59:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1854
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain donor-to-W303Clump sucrose provision, not a generic yeast claim.; Retain
+ long-term continuous persistence separately from batch decline and the negative parental
+ control.; Retain conditional reciprocal growth benefit; qualify the proposed contribution
+ of sucrose-supported yeast.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
diff --git a/kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml b/kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml
index a6466d1b5..c60a0ea62 100644
--- a/kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml
+++ b/kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml
@@ -306,57 +306,46 @@ taxonomy:
core microbiota involved in the production of those flavor compounds
explanation: Identifies Wickerhamomyces as a core member genus of the Fuqu SynCom.
ecological_interactions:
-- name: Fuqu Starch Ethanol and Flavor Base Guild
- description: Pichia, Bacillus, Aspergillus, Saccharomyces, and Wickerhamomyces
- formed the five-genus SC1 base consortium because they are commonly used
- in Fuqu preparation and contribute to starch degradation, ethanol production,
- and flavor-compound formation.
- interaction_type: NICHE_PARTITIONING
+- name: Flavor-compound outcomes of SC3 versus comparator starters
+ description: The 13-genus SC3 had the highest flavor-compound diversity metric and 3-(methylthio)-1-propanal content
+ among the three tested SynComs in simulated fermentation. The diversity metric was 0.45, 0.40 and 0.64 for SC1,
+ SC2 and SC3, respectively; it is a chemical-content metric, not microbial richness. In large-scale production,
+ SC3-derived Fuqu exceeded commercial Fuqu for the reported flavor metric and this sulfur-containing compound,
+ while ethanol did not differ significantly. These are consortium-level outcomes, not demonstrated reciprocal
+ microbial fitness, niche partitioning or a resolved exchange pathway.
scope: COMMUNITY_LEVEL
- participating_taxa:
- - preferred_term: Pichia
- term:
- id: NCBITaxon:4919
- label: Pichia
- - preferred_term: Bacillus
- term:
- id: NCBITaxon:1386
- label: Bacillus
- - preferred_term: Aspergillus
- term:
- id: NCBITaxon:5052
- label: Aspergillus
- - preferred_term: Saccharomyces
- term:
- id: NCBITaxon:4930
- label: Saccharomyces
- - preferred_term: Wickerhamomyces
- term:
- id: NCBITaxon:599737
- label: Wickerhamomyces
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
+ metabolites:
+ - preferred_term: 3-(methylthio)-1-propanal
term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Emergent flavor-compound co-production by the assembled SynCom
- description: The Fuqu base guild supplies starch, ethanol, and flavor-production
- functions used as the SC1 foundation for the higher-performing SC3 SynCom.
+ id: CHEBI:49017
+ label: 3-methylthiopropanal
evidence:
- reference: PMID:42121419
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Pichia, Bacillus, Aspergillus, Saccharomyces, and Wickerhamomyces
- are microorganisms commonly used in the preparation of Fuqu
- explanation: Supports the five core Fuqu genera as a functional base guild.
-- name: Lactic-Acid Bacteria Flavor-Precursor Guild
- description: Lactobacillus, Leuconostoc, Weissella, and Pediococcus were added
- to the five-member SC1 base to test whether lactic-acid bacteria that make
- flavor compounds and precursors could enhance flavor-compound formation.
- interaction_type: CROSS_FEEDING
- scope: COMMUNITY_LEVEL
+ snippet: The resulting SynCom exhibited the highest flavor compound diversity (0.64) and 3-(methylthio)-1-propanal
+ content (618.14 μg/kg) in simulative fermentation.
+ explanation: Supports the measured SC3 flavor outcomes, not reciprocal benefit or a donor-to-recipient mechanism.
+ - reference: PMID:42121419
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The diversity of flavor compounds in SC1, SC2, and SC3 was 0.45, 0.40, and 0.64, respectively.
+ explanation: The intermediate LAB-containing consortium did not monotonically increase the diversity metric.
+ - reference: PMID:42121419
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: The ethanol content showed no significant difference between SC3
+ explanation: Large-scale SC3 versus commercial-Fuqu ethanol comparison; not a general increase in all fermentation
+ endpoints.
participating_taxa:
+ - preferred_term: Aspergillus
+ term:
+ id: NCBITaxon:5052
+ label: Aspergillus
+ - preferred_term: Bacillus
+ term:
+ id: NCBITaxon:1386
+ label: Bacillus
- preferred_term: Lactobacillus
term:
id: NCBITaxon:1578
@@ -365,53 +354,42 @@ ecological_interactions:
term:
id: NCBITaxon:1243
label: Leuconostoc
+ - preferred_term: Pediococcus
+ term:
+ id: NCBITaxon:1253
+ label: Pediococcus
+ - preferred_term: Pichia
+ term:
+ id: NCBITaxon:4919
+ label: Pichia
+ - preferred_term: Saccharomyces
+ term:
+ id: NCBITaxon:4930
+ label: Saccharomyces
+ - preferred_term: Trichosporon
+ term:
+ id: NCBITaxon:5552
+ label: Trichosporon
- preferred_term: Weissella
term:
id: NCBITaxon:46255
label: Weissella
- - preferred_term: Pediococcus
+ - preferred_term: Candida
term:
- id: NCBITaxon:1253
- label: Pediococcus
- biological_processes:
- - preferred_term: biological process involved in interspecies interaction between organisms
+ id: NCBITaxon:5475
+ label: Candida
+ - preferred_term: Torulaspora
term:
- id: GO:0044419
- label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: Emergent flavor-compound co-production by the assembled SynCom
- description: The lactic-acid bacterial subguild expands the SC2 consortium
- with precursor-forming taxa that feed flavor-compound formation.
- evidence:
- - reference: PMID:42121419
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: SC2 was constructed by adding four lactic acid bacteria genera to
- the five microorganisms present in SC1, with the aim of enhancing the
- formation of flavor compounds.
- explanation: Supports the four lactic-acid bacterial genera as a flavor-precursor
- expansion of the SC1 Fuqu guild.
-- name: Emergent flavor-compound co-production by the assembled SynCom
- description: When the 13 core genera are assembled into a SynCom, the community exhibits emergent,
- community-level enhancement of flavor-compound production - the highest flavor-compound diversity and
- 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation,
- exceeding commercial Fuqu at large scale.
- interaction_type: MUTUALISM
- scope: COMMUNITY_LEVEL
- metabolites:
- - preferred_term: 3-(methylthio)-1-propanal
+ id: NCBITaxon:4948
+ label: Torulaspora
+ - preferred_term: Clavispora
term:
- id: CHEBI:49017
- label: 3-methylthiopropanal
- evidence:
- - reference: PMID:42121419
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: The resulting SynCom exhibited the highest flavor compound diversity
- (0.64) and 3-(methylthio)-1-propanal content (618.14 μg/kg) in simulative
- fermentation.
- explanation: Community-level emergent enhancement of flavor-compound diversity and the key sulfur
- flavor compound 3-(methylthio)-1-propanal by the assembled SynCom.
+ id: NCBITaxon:36910
+ label: Clavispora
+ - preferred_term: Wickerhamomyces
+ term:
+ id: NCBITaxon:599737
+ label: Wickerhamomyces
growth_media:
- name: sorghum extract medium (simulated fermentation)
temperature_range: '30-37'
@@ -468,3 +446,30 @@ cultivation_setup:
evidence_source: IN_VITRO
snippet: Each strain in the SynComs was mixed at an equal concentration of 1 × 105
CFU/mL
+discussions:
+- discussion_id: fuqu-comparator-outcomes-versus-exchange
+ prompt: Which interspecies mechanisms explain the SC3 flavor outcome?
+ rationale: The primary main text compares SC1, SC2 and SC3, then SC3-derived and commercial Fuqu. The five-genus
+ base and addition of four LAB are assembly decisions supported by prior functional literature; they are not
+ measured niche separation or metabolite transfer in this consortium. The source proposes fungal diversity and
+ bacterial-fungal synergy as explanations. Retain that hypothesis and the positive flavor outcomes without assigning
+ a specific donor, recipient or reciprocal growth benefit. No cultivation or optimization changes are made.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Flavor-compound outcomes of SC3 versus comparator starters
+ evidence:
+ - reference: PMID:42121419
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: the superior performance of SC3 may therefore be attributed to its higher fungal diversity, together
+ with the synergistic interactions between its more diverse bacteria and fungi.
+ explanation: Source-proposed interpretation; exact interspecies mediation remains unresolved.
+curation_history:
+- timestamp: '2026-10-08T04:59:39Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain comparator-specific chemical outcomes; remove construction nodes, unsupported interaction types
+ and two design-order arrows. Issue#1849; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ llm_assisted: true
diff --git a/kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml b/kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
index 6bb48d573..125c22ff6 100644
--- a/kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
+++ b/kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
@@ -76,9 +76,11 @@ taxonomy:
explanation: Identifies B. velezensis WB as a member strain of the co-culture.
ecological_interactions:
- name: Synergistic biofilm and EPS formation in co-culture
- description: Co-cultivation of the two strains synergistically enhances multispecies biofilm
- formation, extracellular polysaccharide (EPS) production, and metabolic activity relative to
- monocultures (measured, emergent).
+ description: Co-culture increased biofilm biomass, EPS and metabolic activity relative to monocultures. Species-specific
+ qPCR also supported increased cell-equivalent abundance of both strains in the biofilm fraction, supporting
+ reciprocal benefit in that assay. WB abundance did not increase in the planktonic fraction. This conditional
+ biofilm mutualism is not proof of reciprocal metabolite delivery or of the same interaction operating on watermelon
+ roots.
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -98,56 +100,63 @@ ecological_interactions:
label: biofilm formation
downstream:
- target: SynCom Y Fusaric Acid and Wilt Resistance
- description: >
- The EPS-rich dual-species biofilm tolerated more fusaric acid than either
- monoculture and links the Agrobacterium-Bacillus biofilm synergy to pot-level
- watermelon Fusarium wilt suppression.
+ description: 'HYPOTHESIZED/PARTIAL: enhanced EPS-rich biofilm formation could contribute to fusaric-acid tolerance
+ and the positive pot-level biocontrol outcome. Separate in-vitro and pot comparisons do not isolate biofilm
+ mediation or establish that the in-vitro partnership occurs in the rhizosphere.'
evidence:
- reference: PMID:42125264
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Compared with monocultures, co-cultivation also markedly increased extracellular
- polysaccharide production and metabolic activity.
+ snippet: Compared with monocultures, co-cultivation also markedly increased extracellular polysaccharide production
+ and metabolic activity.
explanation: Measured emergent synergy (biofilm, EPS, metabolic activity) in co-culture vs monocultures.
- confidence_score: 0.9
+ - reference: PMID:42125264
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: Quantitative PCR under co-culture conditions confirmed that mixed-species biofilm formation promotes
+ the growth of both strains
+ explanation: Supports reciprocal biofilm-associated growth, distinct from merely observing more total community
+ biomass.
- name: SynCom Y Fusaric Acid and Wilt Resistance
- description: SynCom Y biofilms showed higher resistance to fusaric acid than either monoculture
- and the two-strain inoculum reduced watermelon Fusarium wilt incidence more effectively than
- single-strain treatments in pots, connecting the cooperative biofilm to emergent biocontrol
- performance.
- interaction_type: MUTUALISM
+ description: The two-strain biofilm tolerated fusaric-acid exposure better than either monoculture in vitro. Separately,
+ SynCom Y reduced watermelon wilt in pots, with reported disease incidence 18.33% and control efficacy 79.13%.
+ Preserve both positive outcomes without equating biofilm tolerance with pathogen killing or asserting that EPS,
+ a specific exchanged metabolite or root colonization was experimentally isolated as the cause of disease suppression.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: fusaric acid
term:
id: CHEBI:5199
label: Fusaric acid
- biological_processes:
- - preferred_term: symbiotic process
- term:
- id: GO:0044403
- label: biological process involved in symbiotic interaction
evidence:
- reference: PMID:42125264
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: The two-strain biofilm showed a notable biomass decrease at 17 μg/mL FA, indicating
- enhanced resistance to FA compared with single-species biofilms
- explanation: SynCom Y tolerated higher fusaric acid before biofilm biomass decreased than either
- single-species biofilm.
- confidence_score: 0.85
+ snippet: The two-strain biofilm showed a notable biomass decrease at 17 μg/mL FA, indicating enhanced resistance
+ to FA compared with single-species biofilms
+ explanation: SynCom Y tolerated higher fusaric acid before biofilm biomass decreased than either single-species
+ biofilm.
- reference: PMID:42125264
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: The SynCom Y, composed of A. deltaense LSQ16 and B. velezensis WB, exhibited a disease
- incidence of 18.33% and a control efficacy of 79.13%
- explanation: Watermelon pot trials showed stronger Fusarium wilt control by SynCom Y than by
- single-strain treatments.
- confidence_score: 0.85
+ snippet: The SynCom Y, composed of A. deltaense LSQ16 and B. velezensis WB, exhibited a disease incidence of
+ 18.33% and a control efficacy of 79.13%
+ explanation: Watermelon pot trials showed stronger Fusarium wilt control by SynCom Y than by single-strain treatments.
+ participating_taxa:
+ - preferred_term: Agrobacterium deltaense LSQ16
+ term:
+ id: NCBITaxon:1183412
+ label: Agrobacterium deltae
+ - preferred_term: Bacillus velezensis WB
+ term:
+ id: NCBITaxon:492670
+ label: Bacillus velezensis
- name: Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
- description: Genome-scale metabolic modeling predicts LSQ16 donates metabolites to WB (including
- L-ornithine, guanine, guanosine, malate, phosphate). Two predicted donations (L-ornithine,
- guanine) were experimentally confirmed to enhance WB biofilm; the remainder are model-only.
+ description: 'HYPOTHESIZED/PARTIAL: genome-scale models predict LSQ16-to-WB exchange of several metabolites. Exogenous
+ L-ornithine and guanine increased WB biofilm biomass, and co-culture metabolite abundances were consistent with
+ the proposed direction. Supplementation demonstrates a physiological response, not direct donor-to-recipient
+ transfer. Malate and guanosine were also included in supplementation tests; the reported positive validation
+ centers on ornithine and guanine. Other predicted exchanges are not established measured fluxes.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -183,26 +192,23 @@ ecological_interactions:
label: phosphate
downstream:
- target: Synergistic biofilm and EPS formation in co-culture
- description: >
- Experimentally validated L-ornithine and guanine additions connect the
- predicted LSQ16-to-WB donation route to enhanced B. velezensis biofilm
- formation in the measured co-culture synergy.
+ description: 'HYPOTHESIZED/PARTIAL: predicted LSQ16 provision of L-ornithine and guanine could contribute to
+ WB biofilm enhancement, consistent with the positive additions and metabolite profiles. These results do not
+ establish transfer, its necessity, or its quantitative contribution to the two-strain biofilm/EPS response.'
evidence:
- reference: PMID:42125264
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: Moreover, exogenous supplementation of l-ornithine and guanine further enhanced the
- biofilm-forming capacity of B. velezensis WB.
- explanation: Experimental validation that two predicted LSQ16->WB donations (L-ornithine, guanine)
- enhance WB biofilm formation.
- confidence_score: 0.9
+ snippet: Moreover, exogenous supplementation of l-ornithine and guanine further enhanced the biofilm-forming
+ capacity of B. velezensis WB.
+ explanation: Positive exogenous additions support biofilm responsiveness, not experimentally confirmed donation
+ by LSQ16.
- reference: PMID:42125264
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: Predictive results indicated metabolite exchange between the two strains involved amino
- acids, purines, phosphates, and other compounds.
- explanation: Model-predicted (not measured) donations; guanosine, malate and phosphate are model-only.
- confidence_score: 0.4
+ snippet: A. deltaense LSQ16 may supply malate, O-acetylcarnitine, guanine, guanosine, l-ornithine, and phosphate
+ to B. velezensis WB
+ explanation: Explicit model-predicted forward direction; measured transfer is not established.
computational_provenance:
prediction_type: FLUX_BALANCE_ANALYSIS
tools:
@@ -210,22 +216,22 @@ ecological_interactions:
tool_reference: PMID:30192979
role: draft genome-scale metabolic model reconstruction
- tool_name: COBRA Toolbox
- tool_version: '3.0'
tool_reference: PMID:30787451
role: model refinement and validation
- tool_name: Flux Balance Analysis (FBA)
tool_reference: PMID:20212490
role: prediction of exchangeable metabolites
- model_source: de-novo draft genome-scale metabolic models reconstructed from the two strain
- genomes (no published model identifier)
- input_accession: SRA:SRR33382738-SRR33382752
+ model_source: Draft strain-specific genome-scale models reconstructed with CarveMe; genome input accessions
+ are not specified in the reviewed main-text modeling section.
simulated_medium: LBGM
- parameters: FBA to identify all potentially exchangeable metabolites in the two-species consortium;
- CarveMe version not reported in source.
+ parameters: FBA assessed potential exchanges in LBGM; software versions are not specified in the reviewed
+ methods. SRR33382738-SRR33382752 identifies RNA-seq, not verified genome inputs.
- name: Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
- description: Genome-scale metabolic modeling predicts WB returns metabolites to LSQ16 (including
- L-serine, pyroglutamic acid, myristic acid, suberoylglycine). Model-only; no experimental
- validation reported for this direction.
+ description: 'HYPOTHESIZED/PARTIAL: models predict WB-to-LSQ16 return of L-serine, pyroglutamic acid, myristic
+ acid and suberoylglycine. Metabolite abundance patterns are consistent with some predictions, but additions
+ of tested reverse-direction candidates did not significantly enhance LSQ16 monoculture biofilm biomass. This
+ negative endpoint does not prove that exchange is absent; it prevents describing a beneficial return flux as
+ experimentally validated.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -245,13 +251,11 @@ ecological_interactions:
label: L-serine
evidence:
- reference: PMID:42125264
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: Predictive results indicated metabolite exchange between the two strains involved amino
- acids, purines, phosphates, and other compounds.
- explanation: Model-predicted WB->LSQ16 return fluxes (L-serine and others); no experimental
- validation reported for this direction.
- confidence_score: 0.3
+ snippet: which in turn provides suberoylglycine, myristic acid, l-serine, and pyroglutamic acid to A. deltaense
+ LSQ16
+ explanation: Explicit model-predicted reverse direction, not an observed beneficial return flux.
computational_provenance:
prediction_type: FLUX_BALANCE_ANALYSIS
tools:
@@ -259,18 +263,23 @@ ecological_interactions:
tool_reference: PMID:30192979
role: draft genome-scale metabolic model reconstruction
- tool_name: COBRA Toolbox
- tool_version: '3.0'
tool_reference: PMID:30787451
role: model refinement and validation
- tool_name: Flux Balance Analysis (FBA)
tool_reference: PMID:20212490
role: prediction of exchangeable metabolites
- model_source: de-novo draft genome-scale metabolic models reconstructed from the two strain
- genomes (no published model identifier)
- input_accession: SRA:SRR33382738-SRR33382752
+ model_source: Draft strain-specific genome-scale models reconstructed with CarveMe; genome input accessions
+ are not specified in the reviewed main-text modeling section.
simulated_medium: LBGM
- parameters: FBA to identify all potentially exchangeable metabolites in the two-species consortium;
- CarveMe version not reported in source.
+ parameters: FBA assessed potential exchanges in LBGM; software versions are not specified in the reviewed
+ methods. SRR33382738-SRR33382752 identifies RNA-seq, not verified genome inputs.
+ - reference: PMID:42125264
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: the addition of l-serine, pyroglutamic acid, and other compounds did not result in a significant enhancement
+ of the biofilm biomass in A. deltaense LSQ16 monocultures
+ explanation: Negative supplementation endpoint limits the proposed biofilm benefit without refuting all possible
+ exchange.
growth_media:
- name: LBGM
temperature: '30'
@@ -325,3 +334,36 @@ cultivation_setup:
strainer (Biologix) placed in each well. Each well was supplemented with 10 mL
TSB medium and 100 μL bacterial suspension and incubated statically at 30 °C for
24, 48, and 72 h to allow biofilm formation
+discussions:
+- discussion_id: syncom-y-growth-versus-transfer-and-biocontrol
+ prompt: Which predicted exchanges mediate biofilm synergy and the pot-level biocontrol outcome?
+ rationale: Preserve reciprocal biofilm-associated abundance, EPS, metabolic activity, FA tolerance and disease
+ suppression. Forward additions are positive; tested reverse additions did not significantly enhance LSQ16 biofilm.
+ Neither result directly measures interspecies transfer. The primary discussion explicitly leaves rhizosphere
+ synergy unverified. Modeling methods name CarveMe, Cobra toolbox and FBA but do not state versions or genome
+ input accessions; the cited SRA range belongs to RNA-seq. Main text and captions were read, not separate supplementary
+ data or raw datasets.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Synergistic biofilm and EPS formation in co-culture
+ - ecological_interactions#SynCom Y Fusaric Acid and Wilt Resistance
+ - ecological_interactions#Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
+ - ecological_interactions#Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
+ evidence:
+ - reference: PMID:42125264
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Whether the two strains form a synergistic relationship in the rhizosphere still requires validation
+ via root colonization assays.
+ explanation: Explicit limitation separating in-vitro biofilm findings from rhizosphere mechanism.
+curation_history:
+- timestamp: '2026-10-08T04:59:40Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain assay-specific reciprocal biofilm growth and qualify its proposed downstream mediation.; Retain
+ measured FA tolerance and pot biocontrol as community outcomes, not a second mutualism.; Separate positive supplementation
+ from transfer and correct modeling input/version provenance.; Retain predicted return with the reported negative
+ supplementation endpoint and corrected provenance. Issue#1850; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ llm_assisted: true
diff --git a/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml b/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml
index 2cba91316..30b9c5580 100644
--- a/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml
+++ b/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml
@@ -116,8 +116,10 @@ taxonomy:
explanation: Supports the nitrogen-fixing functional role of A. vinelandii in the coculture design.
ecological_interactions:
- name: Photosynthetic Sucrose Transfer To Azotobacter
- description: Engineered S. elongatus PCC 7942 cscB fixes inorganic carbon under illumination and exports
- sucrose that supports A. vinelandii growth when fixed carbon is absent.
+ description: The engineered cscB S. elongatus/AV3 A. vinelandii coculture required a sucrose-exporting cyanobacterium
+ and grew without added fixed carbon or nitrogen. This supports the existing photosynthetic carbon-supply direction.
+ The initial glutamate-supplemented experiments are a distinct context; the reviewed abstract does not resolve
+ transfer rates or detailed transport.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -135,6 +137,7 @@ ecological_interactions:
term:
id: CHEBI:16526
label: carbon dioxide
+ notes: Carbon-fixation substrate, not the exchanged organic carbon species.
- preferred_term: sucrose
term:
id: CHEBI:17992
@@ -150,9 +153,9 @@ ecological_interactions:
label: sucrose biosynthetic process
downstream:
- target: Light-Driven PHB Production
- description: >
- Sucrose exported by engineered S. elongatus supplies the fixed carbon used
- by A. vinelandii in the light-driven coculture that produced PHB.
+ description: 'HYPOTHESIZED/PARTIAL: cyanobacterial carbon supply supports the productive coculture and is proposed
+ to provide carbon for PHB. The abstract establishes exporter-dependent growth and PHB production, not direct
+ carbon tracing into PHB or isolated control of its yield.'
evidence:
- reference: PMID:27232890
supports: SUPPORT
@@ -165,8 +168,10 @@ ecological_interactions:
snippet: We investigate the growth of a photosynthetic cyanobacterium
explanation: Supports the photosynthetic role of the cyanobacterial member.
- name: Diazotrophic Nitrogen Support
- description: A. vinelandii provides biological nitrogen fixation capacity in the mutualism, enabling
- coculture growth in the absence of added fixed nitrogen.
+ description: The diazotrophic AV3 partner provides nitrogen-fixation capacity in the engineered mutualism that
+ grows without added fixed carbon or nitrogen, whereas neither member grows alone under that omission. Preserve
+ this growth-context mutualism without specifying an unreported exported nitrogen compound, transfer rate or
+ nitrogen-dependent change in PHB yield.
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -184,6 +189,7 @@ ecological_interactions:
term:
id: CHEBI:17997
label: dinitrogen
+ notes: Dinitrogen is the fixation substrate, not a claimed donor-to-recipient transfer product.
biological_processes:
- preferred_term: nitrogen fixation
term:
@@ -191,9 +197,9 @@ ecological_interactions:
label: nitrogen fixation
downstream:
- target: Light-Driven PHB Production
- description: >
- Diazotrophic nitrogen fixation by A. vinelandii enables coculture growth
- without added fixed nitrogen in the same mutualism that produced PHB.
+ description: 'HYPOTHESIZED/PARTIAL: diazotrophic support could enable growth of the PHB-producing coculture
+ under fixed-nitrogen omission. The abstract does not isolate nitrogen supply as the mediator of a PHB-production
+ change or establish the exact PHB assay conditions.'
evidence:
- reference: PMID:27232890
supports: SUPPORT
@@ -206,41 +212,31 @@ ecological_interactions:
snippet: neither organism can grow alone without fixed carbon or nitrogen
explanation: Supports mutual dependence under fixed-carbon and fixed-nitrogen omission.
- name: Light-Driven PHB Production
- description: The designed mutualism produced polyhydroxybutyrate, linking photosynthetic carbon capture
- and diazotrophic growth support to biopolymer production.
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Synechococcus elongatus PCC 7942 cscB
- term:
- id: NCBITaxon:1140
- label: Synechococcus elongatus PCC 7942 = FACHB-805
- target_taxon:
- preferred_term: Azotobacter vinelandii AV3
- term:
- id: NCBITaxon:354
- label: Azotobacter vinelandii
+ description: The designed coculture was demonstrated to produce PHB. This is a productive community endpoint,
+ not independent evidence of reciprocal fitness or direct photosynthetic flux. The abstract names alginate as
+ a potential product, not demonstrated production, and does not supply the PHB assay conditions or quantify carbon/nitrogen
+ mediation.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: poly(3-hydroxybutyrate)
term:
id: CHEBI:53389
label: poly(3-hydroxybutyrate)
- biological_processes:
- - preferred_term: photosynthesis
- term:
- id: GO:0015979
- label: photosynthesis
evidence:
- reference: PMID:27232890
supports: SUPPORT
evidence_source: IN_VITRO
snippet: We demonstrate the ability of the coculture to produce PHB in this work.
explanation: Supports PHB production by the designed coculture.
- - reference: PMID:27232890
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: industrially relevant products, such as polyhydroxybutyrate (PHB) and alginate
- explanation: Supports the bioproduct relevance of PHB and alginate in the designed system.
+ participating_taxa:
+ - preferred_term: Synechococcus elongatus PCC 7942 cscB
+ term:
+ id: NCBITaxon:1140
+ label: Synechococcus elongatus PCC 7942 = FACHB-805
+ - preferred_term: Azotobacter vinelandii AV3
+ term:
+ id: NCBITaxon:354
+ label: Azotobacter vinelandii
environmental_factors:
- name: Illumination
value: sunlight or laboratory illumination
@@ -411,3 +407,33 @@ rare_earth_elements_present: []
metal_relevance: INCIDENTAL
metal_notes: Trace metals are reported as inorganic inputs in the photoproduction concept, but no
specific metal species or metal-cycling mechanism is curated from the available abstract.
+discussions:
+- discussion_id: azotobacter-growth-context-and-phb-mediation
+ prompt: How do carbon and nitrogen provision contribute to the demonstrated PHB outcome?
+ rationale: The independently retrieved primary abstract distinguishes initial glutamate studies from the engineered
+ carbon/nitrogen-omission mutualism. It supports exporter-dependent growth, failure of either partner alone under
+ omission and PHB production. It does not specify a transferred nitrogen species, fluxes or the precise PHB assay
+ conditions. Full article and supplements were not retrieved in this bounded review; no absence claim is made.
+ Alginate remains a proposed capability, not a measured product.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Photosynthetic Sucrose Transfer To Azotobacter
+ - ecological_interactions#Diazotrophic Nitrogen Support
+ - ecological_interactions#Light-Driven PHB Production
+ evidence:
+ - reference: PMID:27232890
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: From initial studies of the coculture grown in media with glutamate, we proposed a model of cross-feeding
+ between these organisms.
+ explanation: Initial supplemented-condition model must not be conflated with the later engineered omission experiment.
+curation_history:
+- timestamp: '2026-10-08T04:59:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain exporter-dependent carbon support without transport-rate or PHB-tracing claims.; Retain omission-context
+ mutualism; qualify nitrogen-to-PHB mediation and substrate role.; Retain PHB production as a community endpoint
+ and distinguish potential alginate production. Issue#1851; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ llm_assisted: true
diff --git a/kb/communities/Synechococcus_Bacillus_SPC.yaml b/kb/communities/Synechococcus_Bacillus_SPC.yaml
index 425b6777e..b3c3a6f11 100644
--- a/kb/communities/Synechococcus_Bacillus_SPC.yaml
+++ b/kb/communities/Synechococcus_Bacillus_SPC.yaml
@@ -88,9 +88,9 @@ taxonomy:
Bacillus subtilis, Escherichia coli, or Saccharomyces cerevisiae'
ecological_interactions:
- name: CO2 Fixation and Sucrose Production
- description: Engineered Synechococcus elongatus PCC 7942 cscB+ fixes CO2
- photosynthetically and secretes the bulk of that fixed carbon as sucrose,
- providing the carbohydrate feedstock for Bacillus subtilis 168.
+ description: Engineered cscB+ S. elongatus provides photosynthetic carbon, including exported sucrose, to Bacillus-containing
+ cocultures. This record names B. subtilis 168, used in the alpha-amylase demonstration; several growth and perturbation
+ experiments instead used 3610. Preserve carbon support without transferring all 3610 results to strain 168.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -119,93 +119,51 @@ ecological_interactions:
label: sucrose biosynthetic process
downstream:
- target: Sucrose Uptake and Heterotrophic Growth
- description: Secreted cyanobacterial photosynthate is taken up as the sucrose
- carbon source that lets the heterotrophic partner grow in the light-driven
- coculture.
+ description: 'PARTIAL: cyanobacterial sucrose export is the proposed carbon supply for the existing heterotrophic-growth
+ node. Sucrose-dependent Bacillus growth and the 168-specific production assay support this route, but exact
+ growth kinetics must remain strain-specific.'
evidence:
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete
- the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes
+ snippet: We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk
+ of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes
+ explanation: Supports the engineered sucrose-export capacity; exact partner growth and condition boundaries
+ are recorded separately.
- name: Sucrose Uptake and Heterotrophic Growth
- description: Bacillus subtilis 168 grows heterotrophically on the sucrose-rich
- photosynthate secreted by engineered Synechococcus, making heterotroph growth
- dependent on the cyanobacterial carbon-export module.
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
- preferred_term: Bacillus subtilis 168
- term:
- id: NCBITaxon:1423
- label: Bacillus subtilis
+ description: 'PARTIAL: photosynthate supported Bacillus cocultures, with initial growth followed by declining
+ viability in batch assays. B. subtilis 168 was explicitly used for active alpha-amylase production, which increased
+ with induced cyanobacterial sucrose secretion. That positive result does not establish weeks-to-months persistence
+ of strain 168 or justify assigning 3610 perturbation results to it.'
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: sucrose
term:
id: CHEBI:17992
label: sucrose
- biological_processes:
- - preferred_term: sucrose catabolic process
- term:
- id: GO:0005987
- label: sucrose catabolic process
- downstream:
- - target: Sucrose-Dependent Long-Term Consortium Stabilization
- description: Heterotrophic sucrose utilization is the positive carbon-flow
- process that counterbalances destabilizing non-sucrose byproducts and lets
- both members persist for weeks to months.
evidence:
- reference: PMID:28127397
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
- snippet: We observed heterotrophic growth dependent upon cyanobacterial photosynthate in
- each co-culture pair
- explanation: Supports heterotrophic growth on Synechococcus-derived photosynthate.
-- name: Sucrose-Dependent Long-Term Consortium Stabilization
- description: Robustness of the autotroph-heterotroph coculture depends on
- heterotroph sucrose utilization together with species-independent interactions,
- allowing both members to persist under long-term culture and perturbation.
- interaction_type: MUTUALISM
- scope: PAIRWISE
- source_taxon:
- preferred_term: Bacillus subtilis 168
+ snippet: We observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair
+ explanation: Abstract-level Bacillus growth result; several detailed assays use 3610 rather than canonical strain168.
+ - reference: PMID:28127397
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: In consortia with S. elongatus, B. subtilis 168 produces alpha-amylase after 24 hours in constant light
+ explanation: Direct 168-specific production evidence supports a productive coculture, not a long-term growth
+ trajectory.
+ participating_taxa:
+ - preferred_term: Bacillus subtilis 168
term:
id: NCBITaxon:1423
label: Bacillus subtilis
- target_taxon:
- preferred_term: Synechococcus elongatus PCC 7942 cscB+
- term:
- id: NCBITaxon:32046
- label: Synechococcus elongatus
- metabolites:
- - preferred_term: sucrose
- term:
- id: CHEBI:17992
- label: sucrose
biological_processes:
- preferred_term: sucrose catabolic process
term:
id: GO:0005987
label: sucrose catabolic process
- - preferred_term: photosynthesis
- term:
- id: GO:0015979
- label: photosynthesis
- evidence:
- - reference: PMID:28127397
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: Stability and productivity of autotroph/heterotroph co-cultures was dependent
- on heterotroph sucrose utilization
- explanation: Supports sucrose utilization as a stability determinant of the
- photosynthetic cocultures.
- - reference: PMID:28127397
- supports: SUPPORT
- evidence_source: IN_VITRO
- snippet: inoculation of each heterotrophic species enhanced cyanobacterial growth in
- comparison to axenic cultures
- explanation: Supports the reciprocal growth benefit supplied by heterotrophs
- to Synechococcus in the sucrose-secreting consortia.
+ notes: Capacity and condition-dependent utilization; not an exclusive explanation of all coculture growth.
related_ingredients:
- preferred_term: sucrose
chebi_term:
@@ -280,3 +238,33 @@ cultivation_setup:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Data for growth rate was collected from 25 mL flask
+discussions:
+- discussion_id: spc-bacillus-assay-and-mediator-boundaries
+ prompt: Which strain- and condition-specific interactions explain growth and persistence in this dyad?
+ rationale: The source combines batch, continuous, density-dependent and production assays. Keep their positive
+ results without treating every partner or strain as persistent for weeks to months. Cyanobacterial growth stimulation
+ is observed, but metabolite return and byproduct absorption remain hypotheses. Light-associated inhibition is
+ supported without identifying oxygen as the exclusive cause. For Bacillus, the canonical168 production assay
+ is distinct from 3610 perturbation experiments. For E. coli, the early non-sucrose inference differs from later
+ sucrose-sensitive production; for yeast, W303Clump is not parental W303. No new causal node, direction, cultivation
+ protocol or strain optimization is added.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#CO2 Fixation and Sucrose Production
+ - ecological_interactions#Sucrose Uptake and Heterotrophic Growth
+ evidence:
+ - reference: PMID:28127397
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: we hypothesize that these benefits arise from emergent cross-feeding of metabolite(s) and/or absorption
+ of byproducts
+ explanation: Source-explicit proposed mediator of cyanobacterial stimulation, not a measured transfer mechanism.
+curation_history:
+- timestamp: '2026-10-08T04:59:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain cyanobacterial carbon support with explicit 168-versus-3610 scope.; Retain bounded Bacillus growth
+ support and the positive168 assay; remove unestablished long-term stability. Issue#1852; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ llm_assisted: true
diff --git a/kb/communities/Synechococcus_Ecoli_SPC.yaml b/kb/communities/Synechococcus_Ecoli_SPC.yaml
index 90f6c9554..f9654a819 100644
--- a/kb/communities/Synechococcus_Ecoli_SPC.yaml
+++ b/kb/communities/Synechococcus_Ecoli_SPC.yaml
@@ -104,12 +104,11 @@ taxonomy:
explanation: Identifies the sucrose-improved E. coli W derivative used in
the Synechococcus/E. coli dyad.
ecological_interactions:
-- name: CO2 Fixation and Sucrose Production
- description: 'Synechococcus elongatus fixes atmospheric CO2 through photosynthesis and converts the
- fixed carbon into sucrose. The CscB transporter enables export of sucrose to the extracellular environment
- when induced with IPTG in the presence of osmotic pressure (NaCl).
-
- '
+- name: Photosynthetic carbon supply to E. coli
+ description: CscB+ S. elongatus fixes carbon and exports sucrose, but E. coli W and W delta-cscR grew during early
+ batch coculture independently of induced sucrose export. The source infers substantial use of other photosynthates
+ at that stage; their identities, including the proposed extracellular polymers, were not resolved. The earlier
+ 85% carbon-export capability is not a concentration or a measurement of this dyad.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -122,7 +121,6 @@ ecological_interactions:
term:
id: CHEBI:17992
label: sucrose
- concentration: Up to 85% of fixed carbon
biological_processes:
- preferred_term: photosynthesis
term:
@@ -133,55 +131,71 @@ ecological_interactions:
id: GO:0005986
label: sucrose biosynthetic process
downstream:
- - target: Sucrose Uptake and Heterotrophic Growth
- description: Secreted sucrose supports E. coli growth
+ - target: E. coli growth on cyanobacterial photosynthate
+ description: 'Cyanobacterial photosynthate supports E. coli growth. PARTIAL for sucrose-specific mediation:
+ early growth was insensitive to export induction, so that phase cannot be attributed solely to sucrose; later
+ productive cocultures show a sucrose contribution.'
evidence:
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete
- the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes
- explanation: Demonstrates the core cross-feeding interaction
-- name: Sucrose Uptake and Heterotrophic Growth
- description: 'E. coli utilizes the sucrose secreted by Synechococcus elongatus as its carbon and energy
- source for heterotrophic growth. This establishes a stable syntrophic relationship where the phototroph
- provides fixed carbon and the heterotroph benefits without needing to fix CO2.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
+ snippet: We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk
+ of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes
+ explanation: Supports the engineered sucrose-export capacity; exact partner growth and condition boundaries
+ are recorded separately.
+ - reference: PMID:28127397
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: E. coli strains cannot utilize sucrose effectively and dominantly depend on other metabolites from
+ S. elongatus
+ explanation: Source inference for early low-sucrose growth; does not identify a measured alternative carbon
+ species.
+ target_taxon:
preferred_term: Escherichia coli W delta-cscR
term:
id: NCBITaxon:562
label: Escherichia coli
+- name: E. coli growth on cyanobacterial photosynthate
+ description: E. coli W delta-cscR grew on cyanobacterial photosynthate and maintained viability in continuous
+ coculture for more than two weeks. Early batch growth was not primarily attributable to sucrose export; improved
+ sucrose utilization contributed to later PHB production in separately functionalized strains. No product-removal
+ feedback mechanism establishing syntrophy is shown by carbon feeding alone.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: sucrose
term:
id: CHEBI:17992
label: sucrose
- biological_processes:
- - preferred_term: sucrose catabolic process
- term:
- id: GO:0005987
- label: sucrose catabolic process
downstream:
- target: E. coli Stimulation of Cyanobacterial Growth
- description: E. coli W delta-cscR growth on Synechococcus-derived
- photosynthate establishes the reciprocal dyad in which the heterotroph
- increases cyanobacterial growth relative to axenic controls.
+ description: 'HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed
+ cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate
+ sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend
+ on culture context.'
evidence:
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph
- sucrose utilization, as well as other species-independent interactions that we observed across all
- dyads
- explanation: Demonstrates stable, long-term growth of the consortium
+ snippet: we determined that co-cultures maintain stable ratios for more than two weeks
+ explanation: Primary Results identifies these continuous cultures as W delta-cscR paired with cscB+ S. elongatus,
+ not every E. coli background.
+ participating_taxa:
+ - preferred_term: Escherichia coli W delta-cscR
+ term:
+ id: NCBITaxon:562
+ label: Escherichia coli
+ biological_processes:
+ - preferred_term: sucrose catabolic process
+ term:
+ id: GO:0005987
+ label: sucrose catabolic process
+ notes: Capacity and condition-dependent utilization; not an exclusive explanation of all coculture growth.
- name: E. coli Stimulation of Cyanobacterial Growth
- description: E. coli W delta-cscR persists on cyanobacterial photosynthate and
- stimulates cscB+ Synechococcus elongatus growth relative to axenic
- cyanobacterial controls in the synthetic photosynthetic coculture platform.
+ description: 'The tested heterotrophic partner increased cyanobacterial abundance relative to axenic controls
+ in low-density cocultures. Together with photosynthate-supported heterotroph growth, this supports conditional
+ reciprocal benefit. It is not universal stability: dense illuminated cyanobacteria could inhibit heterotroph
+ viability. The source proposes metabolite return or byproduct absorption as possible explanations for stimulation,
+ without resolving the mediator; respiratory CO2 alone was considered questionable.'
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -204,16 +218,17 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: inoculation of each heterotrophic species enhanced cyanobacterial growth
- explanation: Supports stimulation of S. elongatus growth by the tested
- heterotrophic partners, including the E. coli W delta-cscR dyad.
+ explanation: Supports the measured heterotroph-associated cyanobacterial growth increase, not its exact mediator
+ or unconditional mutualism.
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- all three evolutionarily unrelated heterotrophs can significantly
- increase cyanobacterial growth under a range of growth conditions
- explanation: Supports the reverse positive interaction from the E. coli
- heterotroph to cscB+ S. elongatus.
+ snippet: 'all three evolutionarily unrelated heterotrophs can significantly increase cyanobacterial growth under
+ a range of growth conditions
+
+ '
+ explanation: Supports the measured heterotroph-associated cyanobacterial growth increase, not its exact mediator
+ or unconditional mutualism.
environmental_factors:
- name: Light
value: Continuous illumination
@@ -338,3 +353,35 @@ cultivation_setup:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Data for growth rate was collected from 25 mL flask
+discussions:
+- discussion_id: spc-ecoli-assay-and-mediator-boundaries
+ prompt: Which strain- and condition-specific interactions explain growth and persistence in this dyad?
+ rationale: The source combines batch, continuous, density-dependent and production assays. Keep their positive
+ results without treating every partner or strain as persistent for weeks to months. Cyanobacterial growth stimulation
+ is observed, but metabolite return and byproduct absorption remain hypotheses. Light-associated inhibition is
+ supported without identifying oxygen as the exclusive cause. For Bacillus, the canonical168 production assay
+ is distinct from 3610 perturbation experiments. For E. coli, the early non-sucrose inference differs from later
+ sucrose-sensitive production; for yeast, W303Clump is not parental W303. No new causal node, direction, cultivation
+ protocol or strain optimization is added.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#Photosynthetic carbon supply to E. coli
+ - ecological_interactions#E. coli growth on cyanobacterial photosynthate
+ - ecological_interactions#E. coli Stimulation of Cyanobacterial Growth
+ evidence:
+ - reference: PMID:28127397
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: we hypothesize that these benefits arise from emergent cross-feeding of metabolite(s) and/or absorption
+ of byproducts
+ explanation: Source-explicit proposed mediator of cyanobacterial stimulation, not a measured transfer mechanism.
+curation_history:
+- timestamp: '2026-10-08T04:59:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain carbon supply while distinguishing early non-sucrose dependence and removing the invalid concentration.;
+ Retain strain-specific growth/persistence, not sucrose-exclusive growth or syntrophy.; Retain conditional reciprocal
+ growth benefit; mediator of cyanobacterial stimulation is unresolved. Issue#1853; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ llm_assisted: true
diff --git a/kb/communities/Synechococcus_Saccharomyces_SPC.yaml b/kb/communities/Synechococcus_Saccharomyces_SPC.yaml
index 4d5623602..3f3f076ee 100644
--- a/kb/communities/Synechococcus_Saccharomyces_SPC.yaml
+++ b/kb/communities/Synechococcus_Saccharomyces_SPC.yaml
@@ -99,9 +99,9 @@ taxonomy:
explanation: Records that the parental strain is NOT a member; only the evolved W303Clump is.
ecological_interactions:
- name: CO2 Fixation and Sucrose Production
- description: Engineered Synechococcus elongatus PCC 7942 fixes carbon dioxide
- under light and exports sucrose through the cscB+ transporter, making fixed
- carbon available to a heterotrophic partner.
+ description: CscB+ S. elongatus fixes carbon and exports sucrose that supports the evolved S. cerevisiae W303Clump
+ partner. The parental W303 did not grow in the tested cocultures; the positive carbon-supply result is specific
+ to W303Clump and the tested conditions.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -125,57 +125,63 @@ ecological_interactions:
label: sucrose biosynthetic process
downstream:
- target: Sucrose Utilization by the Heterotrophic Partner
- description: The sucrose exported by engineered S. elongatus is the fixed
- carbon source that supports the evolved Saccharomyces cerevisiae
- W303Clump partner in continuous coculture.
+ description: The sucrose exported by engineered S. elongatus is the fixed carbon source that supports the evolved
+ Saccharomyces cerevisiae W303Clump partner in continuous coculture.
evidence:
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete
- the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes
-- name: Sucrose Utilization by the Heterotrophic Partner
- description: 'The yeast grows on the sucrose the cyanobacterium secretes. The paper reports no
- product formation for this dyad -- its photoproduction demonstrations use B. subtilis
- (alpha-amylase) and E. coli (polyhydroxybutyrate) -- so nothing beyond sucrose catabolism is
- claimed here.
-
- '
- interaction_type: CROSS_FEEDING
- scope: PAIRWISE
- source_taxon:
+ snippet: We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk
+ of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes
+ explanation: Supports the engineered sucrose-export capacity; exact partner growth and condition boundaries
+ are recorded separately.
+ target_taxon:
preferred_term: Saccharomyces cerevisiae W303Clump
term:
id: NCBITaxon:4932
label: Saccharomyces cerevisiae
+- name: Sucrose Utilization by the Heterotrophic Partner
+ description: W303Clump utilized cyanobacterial sucrose and persisted for more than two months in continuous coculture.
+ Separate continuous experiments demonstrated persistence during light-dark cycling; the two-month duration is
+ not assigned to that diurnal assay. Initial growth followed by declining viability in batch culture is a distinct
+ result. Parental W303 did not grow in the tested coculture; the study does not demonstrate a bioproduct for
+ this yeast dyad.
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: sucrose
term:
id: CHEBI:17992
label: sucrose
- biological_processes:
- - preferred_term: sucrose catabolic process
- term:
- id: GO:0005987
- label: sucrose catabolic process
downstream:
- target: Yeast Stimulation of Cyanobacterial Growth
- description: >
- Sucrose utilization sustains W303Clump in the light-driven dyad, and the
- presence of each tested heterotroph, including the yeast partner,
- reciprocally increased S. elongatus growth.
+ description: 'HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed
+ cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate
+ sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend
+ on culture context.'
evidence:
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph
- sucrose utilization, as well as other species-independent interactions that we observed across all
- dyads
+ snippet: S. cerevisiae W303Clump maintains viability in continuous culture with sucrose-secreting S. elongatus
+ for greater than two months
+ explanation: Exact yeast/continuous-culture persistence, not persistence of every strain or batch condition.
+ participating_taxa:
+ - preferred_term: Saccharomyces cerevisiae W303Clump
+ term:
+ id: NCBITaxon:4932
+ label: Saccharomyces cerevisiae
+ biological_processes:
+ - preferred_term: sucrose catabolic process
+ term:
+ id: GO:0005987
+ label: sucrose catabolic process
+ notes: Capacity and condition-dependent utilization; not an exclusive explanation of all coculture growth.
- name: Yeast Stimulation of Cyanobacterial Growth
- description: >
- Saccharomyces cerevisiae W303Clump persists on cyanobacterially derived
- sucrose and, as one of the heterotrophs in this dyad series, stimulates
- cscB+ S. elongatus growth relative to axenic cyanobacterial controls.
+ description: 'The tested heterotrophic partner increased cyanobacterial abundance relative to axenic controls
+ in low-density cocultures. Together with photosynthate-supported heterotroph growth, this supports conditional
+ reciprocal benefit. It is not universal stability: dense illuminated cyanobacteria could inhibit heterotroph
+ viability. The source proposes metabolite return or byproduct absorption as possible explanations for stimulation,
+ without resolving the mediator; respiratory CO2 alone was considered questionable.'
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -198,16 +204,17 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: inoculation of each heterotrophic species enhanced cyanobacterial growth
- explanation: Supports stimulation of S. elongatus growth by the tested
- heterotrophic partners, including the W303Clump yeast dyad.
+ explanation: Supports the measured heterotroph-associated cyanobacterial growth increase, not its exact mediator
+ or unconditional mutualism.
- reference: PMID:28127397
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: >
- all three evolutionarily unrelated heterotrophs can significantly
- increase cyanobacterial growth under a range of growth conditions
- explanation: Supports the reverse positive interaction from the yeast
- heterotroph to cscB+ S. elongatus.
+ snippet: 'all three evolutionarily unrelated heterotrophs can significantly increase cyanobacterial growth under
+ a range of growth conditions
+
+ '
+ explanation: Supports the measured heterotroph-associated cyanobacterial growth increase, not its exact mediator
+ or unconditional mutualism.
related_ingredients:
- preferred_term: sucrose
chebi_term:
@@ -253,3 +260,35 @@ growth_media:
snippet: S. elongatus was propagated in BG-11 (Sigma-Aldrich) plus 1 g/L HEPES, pH 8 in constant
light at 35 °C
explanation: Base medium and maintenance conditions for the cyanobacterial primary producer.
+discussions:
+- discussion_id: spc-yeast-assay-and-mediator-boundaries
+ prompt: Which strain- and condition-specific interactions explain growth and persistence in this dyad?
+ rationale: The source combines batch, continuous, density-dependent and production assays. Keep their positive
+ results without treating every partner or strain as persistent for weeks to months. Cyanobacterial growth stimulation
+ is observed, but metabolite return and byproduct absorption remain hypotheses. Light-associated inhibition is
+ supported without identifying oxygen as the exclusive cause. For Bacillus, the canonical168 production assay
+ is distinct from 3610 perturbation experiments. For E. coli, the early non-sucrose inference differs from later
+ sucrose-sensitive production; for yeast, W303Clump is not parental W303. No new causal node, direction, cultivation
+ protocol or strain optimization is added.
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ posed_by: codex
+ attaches_to:
+ - ecological_interactions#CO2 Fixation and Sucrose Production
+ - ecological_interactions#Sucrose Utilization by the Heterotrophic Partner
+ - ecological_interactions#Yeast Stimulation of Cyanobacterial Growth
+ evidence:
+ - reference: PMID:28127397
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: we hypothesize that these benefits arise from emergent cross-feeding of metabolite(s) and/or absorption
+ of byproducts
+ explanation: Source-explicit proposed mediator of cyanobacterial stimulation, not a measured transfer mechanism.
+curation_history:
+- timestamp: '2026-10-08T04:59:41Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain donor-to-W303Clump sucrose provision, not a generic yeast claim.; Retain long-term continuous
+ persistence separately from batch decline and the negative parental control.; Retain conditional reciprocal
+ growth benefit; qualify the proposed contribution of sucrose-supported yeast. Issue#1854; reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 71a9eb094..8da03ca82 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,29 @@ 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`.
+## Batch109: Strain And Assay Boundaries
+
+[Decisions](decisions/20261008-six-records-batch109.yaml),
+[provenance](cache-provenance-20261008-batch109.json),
+[validation](validation-20261008-batch109.json), and
+[self-adversarial review](adversarial-review-20261008-batch109.yaml) cover
+Sesame Fuqu, SynCom Y, Azotobacter photoproduction and the three SPC dyads.
+Sixteen of nineteen nodes and nine of twelve existing directions remain.
+Construction steps and unsupported Bacillus168 persistence are removed;
+positive flavor, biofilm, biocontrol, growth and production findings remain
+bounded to their strains, comparators and assays.
+
+Three primary main texts/captions and one primary abstract were read, together
+with SPC supplement captions S1-S12 and selected figure pixels S2/S4/S5/S8.
+Thirty-four graph/discussion quotations match fresh primary text and unchanged
+caches. Six append-only histories preserve the curation trail; four in-memory
+mutation probes reject claim inflation. All 923 caches and 454 other records
+are unchanged. The measured phenotype-scope census adds no taxa credited solely
+by the broad community-level rule. Repairs #1849-#1854 await protected-main
+merge; non-graph SPC follow-up #1855 remains open. No new topology, experimental
+protocol or Edison spend. Self-review is not independent approval or completion
+of the whole corpus review.
+
## Batch108: Process Outcomes And Molecular Responses
[Decisions](decisions/20261008-four-records-batch108.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch109.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch109.yaml
new file mode 100644
index 000000000..bcf544d34
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch109.yaml
@@ -0,0 +1,344 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5c3a89285dc4911f035a5aca26ac8d23fb0e14b8
+scope:
+- kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml
+- kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
+- kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml
+- kb/communities/Synechococcus_Bacillus_SPC.yaml
+- kb/communities/Synechococcus_Ecoli_SPC.yaml
+- kb/communities/Synechococcus_Saccharomyces_SPC.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch109.json
+findings:
+- issue: 1849
+ severity: P2
+ finding: Separate Fuqu SC3 flavor outcomes from construction order and unsupported exchange
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1850
+ severity: P2
+ finding: Bound SynCom Y predicted exchange and biocontrol mediation while retaining reciprocal biofilm growth
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1851
+ severity: P2
+ finding: Separate Azotobacter mutualistic growth from PHB mediation and potential alginate production
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1852
+ severity: P2
+ finding: Remove Bacillus168 long-term persistence inferred from other SPC partners and strains
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1853
+ severity: P2
+ finding: Distinguish early non-sucrose growth from later sucrose contribution in E. coli SPC
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1854
+ severity: P2
+ finding: Keep W303Clump persistence and reciprocal growth within their SPC assay boundaries
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1855
+ severity: P2
+ finding: Reconcile SPC summaries and growth metadata with strain-specific graph evidence
+ status: open_non_graph_follow_up
+ disposition: Coordinate summaries,ingredient wording and assay metadata without importing protocols.
+adversarial_checks:
+- Whole original targets and all changed graph/discussion diffs reviewed. All19 original nodes/12 arrows have dispositions:retain16
+ nodes/nine existing directions,remove three nodes/three arrows,rename three. No new topology or Edison spend.
+- 'Challenge overcorrection: retain measured flavor outcomes, reciprocal biofilm-associated abundance, FA tolerance/pot
+ biocontrol, omission-context mutualism/PHB, photosynthate-supported growth and conditional cyanobacterial benefits.
+ Qualification does not erase source-supported positive effects.'
+- 'Fuqu: construction rationale is not measured niche separation or metabolite exchange. SC2 did not monotonically
+ increase the flavor diversity metric; large-scale ethanol was not significantly different. Preserve SC3 comparator
+ outcomes and source-proposed bacterial-fungal synergy without adding an organism-specific mechanism or any cultivation
+ optimization.'
+- 'SynComY: reciprocal biofilm growth has species-specific qPCR support and stays MUTUALISM, whereas the FA/pot
+ endpoint is untyped. Forward additions support response,not direct transfer. Reverse additions were tested and
+ did not significantly enhance LSQ16 biofilm; this does not refute all possible exchange. Keep both existing mediation
+ arrows hypothetical. The SRA range belongs to RNA-seq,not verified genome input;source-named tools stay but unsupported
+ versions are removed. Root-colonization synergy remains unverified.'
+- 'Azotobacter: exporter dependence and failure of either partner alone under carbon/nitrogen omission support the
+ growth-context mutualism. They do not quantify PHB mediation,identify a nitrogen transfer product or establish
+ PHB assay conditions. Keep initial glutamate experiments separate. PHB is demonstrated;alginate is potential.
+ Abstract-limited review is explicit,not a claim that full text does not exist.'
+- 'Bacillus: main Figure4 plus supplementS2/S5/S9 identify3610 in growth/perturbation assays. Strain168 production
+ and supplementS4 inhibition do not establish months-long persistence. Remove the unsupported stabilization node/arrow
+ without adding a new alpha-amylase node;positive168 evidence remains as bounded context. The two remaining nodes
+ retain PARTIAL strain-specific support.'
+- 'Ecoli: early W and W delta-cscR growth is insensitive to induced sucrose export,so retain carbon support without
+ sucrose exclusivity. Other photosynthates are inferred,not chemically identified.85% background carbon-export
+ capability is not a concentration. Preserve more-than-two-week continuous persistence and conditional reciprocal
+ benefit;carbon feeding alone is not product-removal syntrophy.'
+- 'Yeast: preserve #605 corrected W303Clump identity,parentalW303 negative result,no yeast bioproduct,and batch
+ decline. The two-month constant-light persistence is distinct from diurnal experiments;source supplementS8 confirmed
+ this distinction. Uptake is an organism phenotype,not a reverse donor arrow. Metabolite return/byproduct absorption
+ remains a proposed mediator of cyanobacterial stimulation.'
+- All28 graph plus six discussion quotations match independently retrieved primary text and unchanged caches. Three
+ primary main bodies/captions and one abstract read;SPC supplement captionsS1-S12 and pixelsS2/S4/S5/S8 additionally
+ inspected. Other supplements/images,mathematical framework and raw data were not certified. Large cache headers
+ and literal quotations checked,not a whole-cache audit;literal matching remains separate from entailment.
+- Six guarded writes produce six append-only histories. Other454 records,all923 caches,non-graph raw blocks and
+ prior history/decision files are unchanged. Four phenotype-scope changes add eight taxa to the community-level
+ survey denominator but no additional solely-credited taxa. Observational census bounds update to the measured407/132
+ counts with an exact regression;connectivity rules and the share guard are unchanged.
+- Four in-memory control/mutation/restored-control probes reject transfer SUPPORT inflation,RNA-seq input misattribution,Bacillus168
+ persistence-arrow restoration and diurnal duration inflation. Mutation application and rejection were explicitly
+ checked at scientific assertions. Canonical files are unchanged and probes do not inflate the pytest count.
+- Twelve focused tests and987 combined regressions pass. Six full-record schema/strict/term/reference/snippet checks
+ and six histories validate. Network retains56 baseline warnings with zero structural defects. Deterministic rendering
+ and exact HTML parsing cover456 pages,1367 node descriptions and536 arrows;this is not screenshot QA.
+- Repair issues1849-1854 are addressed but remain open until protected-main merge;non-graph follow-up1855 remains
+ open. Existing loader1703,DOI-case1091,stub1093 and license949 are not certified. Denied/unanswered Edison scopes
+ remain untouched. Self-review is not independent approval;no artificial CI,protection bypass or premature branch
+ deletion.
+- Corpus status:350 reviewed,58 pending,52 needs_research. The whole goal is not complete. Postcommit docs-current
+ and exact-head publication require separate receipts and are not preasserted here.
+- Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Forward supplementation promoted to direct-transfer SUPPORT
+ test: test_syncom_y_positive_additions_are_not_direct_transfer
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 48
+ assertion: assert all(e["supports"] == "PARTIAL" for e in forward["evidence"])
+ restored_control: PASS
+ - mutation: RNA-seq range restored as genome-model input
+ test: test_syncom_y_model_inputs_and_versions_are_not_invented
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 69
+ assertion: assert "input_accession" not in p
+ restored_control: PASS
+ - mutation: Bacillus168 unsupported persistence arrow restored
+ test: test_bacillus168_does_not_inherit_3610_or_other_partner_persistence
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 102
+ assertion: assert not growth.get("downstream") and "interaction_type" not in growth
+ restored_control: PASS
+ - mutation: Two-month yeast persistence reassigned to diurnal assay
+ test: test_yeast_parental_control_persistence_and_product_boundaries_remain
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 127
+ assertion: assert "two-month duration is not assigned to that diurnal assay" in growth["description"]
+ restored_control: PASS
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml: f9ac5f1e3098ee43744bd8749fbba47f46eb27abace9e1a82b69d4bb64cc2c42
+ kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml: 5e1cbb5518d3e85f87662c378056e9b1dc8ff338fa7bc2a55f3c3e9a61941b02
+ kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml: a96409b502da3b96811a68db9d999ca493fd4ff455ae3e303ceb39a04538238a
+ kb/communities/Synechococcus_Bacillus_SPC.yaml: a04fd02a2219aa3518ab4e4ac9bd35503d606b3b19d5332c0df65961f939fc4c
+ kb/communities/Synechococcus_Ecoli_SPC.yaml: 529766861de184236d78198a26eba1c964d999973a1230db145330bd875c3556
+ kb/communities/Synechococcus_Saccharomyces_SPC.yaml: 9c021f5bf08a2596743a140a3b14ca90e781d294234a09257a021324e8a20ac6
+ tests/test_causal_review_batch109.py: 712d4012d107506936ed7ec95afefc92aa33bc83fdc935d5388866cffa97451e
+ scope: In-memory evidence mutations with control and restored-control; no canonical writes or inflated pytest
+ count.
+ artifact: /private/tmp/communitymech-batch109/adversarial-regression-proof.json
+ sha256: cd6824619526efdaf090890e35849bd887139ae3d58f5475a87cba713e06900b
+verification:
+ combined_regressions: 987 passed in 328.40s (0:05:28)
+ new_regression_tests: 12
+ total_recorded_gate_outputs: 55
+ primary_graph_snippet_proof:
+ graph_quotations: 28
+ new_discussion_quotations: 6
+ fresh_primary_literal_matches: 34
+ all_cached_literal_matches: 34
+ retained_nodes: 16
+ removed_nodes: 3
+ retained_arrows: 9
+ removed_arrows: 3
+ new_nodes_or_directions: 0
+ scope: All reviewed quotations match fresh primary text and unchanged caches;source entailment separately reviewed.
+ Three full primary bodies/captions,one primary abstract,SPC supplement captionsS1-S12 and selected pixelsS2/S4/S5/S8
+ read;not raw-data certification.
+ references: Six full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal
+ matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks.
+ Loader1703 not certified.
+ snippet_counts_by_record:
+ kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:
+ MATCH: 21
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml:
+ MATCH: 15
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml:
+ MATCH: 24
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Synechococcus_Bacillus_SPC.yaml:
+ MATCH: 12
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Synechococcus_Ecoli_SPC.yaml:
+ MATCH: 18
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Synechococcus_Saccharomyces_SPC.yaml:
+ MATCH: 13
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 8991
+ categories:
+ MATCH: 8854
+ RENDERING: 21
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 39
+ NOCONTENT: 76
+ caveat: Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: Sixteen nodes and nine existing directions retained;three nodes and three arrows removed. All56existing
+ warnings unchanged;zero structural defects. Non-graph SPC narratives/metadata remain1855.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml: 578f8105c6b3ed5eee6e8b6dfc762f6a781a885a4f85a3bf91971a54a5f348ec
+ tests/test_causal_review_batch109.py: 712d4012d107506936ed7ec95afefc92aa33bc83fdc935d5388866cffa97451e
+ tests/test_participating_taxa.py: 985ce17be93928b77e83365042d2129c394c4c1f0474e029f9fdd5f12ea8e844
+ tests/test_community_level_connectivity_credit.py: 3e370c6f0f5087f2c6b0b6d45f7a4a6d66c71171973535485d608a6cf2ad98af
+ reports/causal_graph_review/cache-provenance-20261008-batch109.json: d818cfaf49c796823dbd361139d124571001e8445eb523422ac092f922ff0b9e
+ kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml: f9ac5f1e3098ee43744bd8749fbba47f46eb27abace9e1a82b69d4bb64cc2c42
+ kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml: 5e1cbb5518d3e85f87662c378056e9b1dc8ff338fa7bc2a55f3c3e9a61941b02
+ kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml: a96409b502da3b96811a68db9d999ca493fd4ff455ae3e303ceb39a04538238a
+ kb/communities/Synechococcus_Bacillus_SPC.yaml: a04fd02a2219aa3518ab4e4ac9bd35503d606b3b19d5332c0df65961f939fc4c
+ kb/communities/Synechococcus_Ecoli_SPC.yaml: 529766861de184236d78198a26eba1c964d999973a1230db145330bd875c3556
+ kb/communities/Synechococcus_Saccharomyces_SPC.yaml: 9c021f5bf08a2596743a140a3b14ca90e781d294234a09257a021324e8a20ac6
+ history_sha256:
+ history/records/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus/2026-10-08T045942Z-codex-f64ce1.yaml: bfef38f62692f500414ef5d2559bedbdf047a1bb7199ec517fbc5ab36e8952f4
+ history/records/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture/2026-10-08T045943Z-codex-deec92.yaml: ecad74fa1284bafc2bfa0315d26e2e9239fe8cad2dbad6c46fe25ce2f8569123
+ history/records/Synechococcus_Azotobacter_Photoproduction_Mutualism/2026-10-08T045943Z-codex-31bb19.yaml: 6fc9dd88dd8b7c70e49fae69235deb308a18719a9cdf2dd3a360b5db9d54c1aa
+ history/records/Synechococcus_Bacillus_SPC/2026-10-08T045943Z-codex-9d0c0c.yaml: c1578773dad56df3e8bea4e9c3e7322641de1c61f8e9e3935158a4a53514b1ba
+ history/records/Synechococcus_Ecoli_SPC/2026-10-08T045944Z-codex-9a70f9.yaml: f13d4cf272949f19ffbd6b0b83c744db1224dde85a1016a9a88b9a7542eedd4c
+ history/records/Synechococcus_Saccharomyces_SPC/2026-10-08T045944Z-codex-a56048.yaml: 4c2b5e623422acab8f59287c107b5fe6d45ad751dfe9921d1a2ad2e8545c8cd3
+ unchanged_records: 454
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 833
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing-node scope/evidence repair and retention/qualification of existing directions. No new
+ topology; unrelated denied/unanswered scopes untouched.
+ post_commit_docs_current: Separate publication gate,not preasserted.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 403
+ mixed: 128
+ community_level_only: 275
+ taxa: 1544
+ credited_solely_by_the_rule: 1270
+ current:
+ records: 460
+ with_community_level: 407
+ mixed: 132
+ community_level_only: 275
+ taxa: 1552
+ credited_solely_by_the_rule: 1270
+ delta:
+ records: 0
+ with_community_level: 4
+ mixed: 4
+ community_level_only: 0
+ taxa: 8
+ credited_solely_by_the_rule: 0
+ interpretation: PHB and three heterotroph-use phenotypes gain community-level identity-only scope;SynComY outcome
+ and Sesame endpoint also gain canonical participants. Four additional mixed-scope records;no additional solely-credited
+ taxa. Observational census bounds updated to this measured scope with an exact regression;connectivity rules
+ and share guard unchanged.
+corpus:
+ records: 460
+ nodes: 1381
+ edges: 544
+ review_status_counts:
+ needs_research: 52
+ pending: 58
+ reviewed: 350
+lint_limitation: Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies
+ unchanged. Not a complete embedding runtime.
+limitations:
+- Fresh both-root baseline precedes source reads:460 records,923 caches,56 existing warnings,zero structural defects.
+ Whole six records and all19 original nodes/12 arrows reviewed;retain16 nodes/nine existing directions,remove three
+ nodes/three arrows,rename three. No new topology or Edison spend.
+- Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions
+ read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index. Exact
+ DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository
+ search is not proof of absence. No access bypass or author contact.
+- Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8
+ inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures
+ used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets were
+ not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.
+- Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading
+ used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and discussion
+ quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still say abstract_only
+ despite additional text;metadata policy949/1093 is not repaired here.
+- Sesame preserves comparator-specific flavor outcomes and source-proposed bacterial-fungal synergy,not exchange/niche
+ partitioning/reciprocal growth. Remove two assembly nodes/arrows. No cultivation,optimization,organism identity
+ or experimental design changes.
+- SynComY retains positive reciprocal biofilm-associated qPCR abundance,EPS/activity,FA tolerance and pot outcomes.
+ Positive forward supplementation is not direct transfer;negative reverse supplementation is not proof of no exchange.
+ Correct RNA-seq-as-genome-input and unsupported COBRA version;do not invent model identifiers or genome accessions.
+ Rhizosphere mediation remains explicitly unresolved.
+- Azotobacter preserves abstract-supported exporter dependence and omission-context mutualism. PHB is a community
+ endpoint;carbon/nitrogen-to-PHB mediation stays hypothetical. Dinitrogen is substrate,not a specified transfer
+ product. Initial glutamate model and potential alginate are not promoted to omission-assay or demonstrated-production
+ claims.
+- SPC records retain positive partner-specific growth and conditional mutualism without universal stability. Bacillus168
+ production evidence cannot inherit3610 trajectories or other-partner weeks/months persistence. Ecoli early growth
+ is not sucrose-exclusive and85% background export is not a concentration. W303Clump remains distinct from parentalW303
+ and no yeast bioproduct is invented. Reverse-benefit mechanism is source-proposed,not identified transfer.
+- Repair issues[1849, 1850, 1851, 1852, 1853, 1854] stay open until protected-main merge;non-graph follow-up1855
+ stays open. Fresh all-state title/body dedup matched757,714,605,310;all read plus related529. Ignored/hidden local
+ index inspected,not every matching report read;PRs/comments not exhaustively searched. No reusable taxon match
+ in ignored/hidden kb/taxa name/identifier search. Whole reviewed B12 Syn7002 neighbor read for modeling patterns,not
+ used as evidence for these targets.
+- Only graph/discussions/events change. Other454 records,923 caches,non-graph raw blocks and prior histories/decisions
+ preserved. Canonical identities reused as preferred_term+term only;no GTDB copies into graph. General growth metadata
+ and narrative claims are not recertified. No schema,validator,configuration or runtime change. Participant census
+ must be measured;any census test update must reflect actual scoped changes,not a relaxed connectivity rule. Loader1703,DOI-case1091,stub1093
+ and license949 remain separate. Self-review is not independent approval or corpus completion. Denied/unanswered
+ Edison scopes remain untouched.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch109.json b/reports/causal_graph_review/cache-provenance-20261008-batch109.json
new file mode 100644
index 000000000..b2cd1fcef
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch109.json
@@ -0,0 +1,280 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch109/azotobacter-abstract.txt": "1f74d91e93e2414da81b84ba732eda96483ad851bf6993eb0c1d34e07b5a5db2",
+ "/private/tmp/communitymech-batch109/azotobacter-crossref.json": "3b53796d05b1665660f103545d7b54d4b4a7392f984cbff7daf2f3cddc857c06",
+ "/private/tmp/communitymech-batch109/azotobacter-metadata.json": "e6147f228ef3fc2893b825ab4d73609b0b8e7bc98cf4d033bed562db2be22f5f",
+ "/private/tmp/communitymech-batch109/baseline.json": "f2f73591a7efd23eb69475ca9812e4ecd2948c21f07d8adc1a65d0150fd0cbb1",
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+ "pmid": "42121419",
+ "doi": "10.3390/foods15091476",
+ "pmcid": "PMC13163537",
+ "title": "Designing a Synthetic Microbial Community to Enhance Flavor Compound Production in Sesame Flavor-Type <i>Baijiu</i> Fermentation.",
+ "metadata": "/private/tmp/communitymech-batch109/sesame-metadata.json",
+ "metadata_sha256": "e0a07e4e9dd994756861ceccc38a44b7bfe048c0af5cffd7c663f70a226c1278",
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+ "status": "retrieved"
+ },
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+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13163537/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch109/sesame-abstract.txt",
+ "abstract_sha256": "63193c1477b96f39033c0e12fc4f8c4e77e50b10b8e314139ba0140ce3db3562",
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+ "xml_sha256": "2957eb7ceae64bf41cd591e6269e6b8cc6f9ae77ec3c649c22bfb6b92c6a1011",
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+ "primary_text_sha256": "e75319879204773a3fbe4ebaf8d536eaa315489340724218ed3d5be0ebcfa7be",
+ "license": [
+ "Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license."
+ ],
+ "crossref": "/private/tmp/communitymech-batch109/sesame-crossref.json",
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+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ }
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+ "pmid": "42125264",
+ "doi": "10.1016/j.bioflm.2026.100364",
+ "pmcid": "PMC13158395",
+ "title": "Biofilm synergy by <i>Agrobacterium deltaense</i> and <i>Bacillus velezensis</i> in co-cultures indicates bacterial interspecific cooperation.",
+ "metadata": "/private/tmp/communitymech-batch109/syncom_y-metadata.json",
+ "metadata_sha256": "f5b7c3657030705bde16d34f0ec02a8e84e6481319d62bc257070d123dcd19e6",
+ "retrievals": [
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+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42125264+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13158395/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch109/syncom_y-abstract.txt",
+ "abstract_sha256": "7b80ba54b9b7c7f2a8768864334d30d055f37055a7e71fa0eede93f956d165ea",
+ "xml": "/private/tmp/communitymech-batch109/syncom_y-primary.xml",
+ "xml_sha256": "ec096a2f25d858ffa65f90f3349ca75e294bd99a00e2dbd96c557be1b86e1061",
+ "primary_text": "/private/tmp/communitymech-batch109/syncom_y-primary.txt",
+ "primary_text_sha256": "d471ffaa6dece4d42abb5a7962463badd0ecafad9f71d7e68d724028e3244d52",
+ "license": [
+ "This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)."
+ ],
+ "crossref": "/private/tmp/communitymech-batch109/syncom_y-crossref.json",
+ "crossref_sha256": "9d02fef389b4358303d71bf18c9284dbb94216e4d0a148c9b3727c28ae5fe51a",
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+ },
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+ "delay-in-days": 0,
+ "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
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+ ]
+ ],
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+ "URL": "https://www.elsevier.com/legal/tdmrep-license"
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+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "http://creativecommons.org/licenses/by/4.0/"
+ }
+ ]
+ },
+ "azotobacter": {
+ "pmid": "27232890",
+ "doi": "10.1021/acssynbio.6b00107",
+ "pmcid": null,
+ "title": "A Designed A. vinelandii-S. elongatus Coculture for Chemical Photoproduction from Air, Water, Phosphate, and Trace Metals.",
+ "metadata": "/private/tmp/communitymech-batch109/azotobacter-metadata.json",
+ "metadata_sha256": "e6147f228ef3fc2893b825ab4d73609b0b8e7bc98cf4d033bed562db2be22f5f",
+ "retrievals": [
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A27232890+AND+SRC%3AMED&format=json&resultType=core",
+ "status": "retrieved"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch109/azotobacter-abstract.txt",
+ "abstract_sha256": "1f74d91e93e2414da81b84ba732eda96483ad851bf6993eb0c1d34e07b5a5db2",
+ "crossref": "/private/tmp/communitymech-batch109/azotobacter-crossref.json",
+ "crossref_sha256": "3b53796d05b1665660f103545d7b54d4b4a7392f984cbff7daf2f3cddc857c06",
+ "crossref_license": []
+ },
+ "spc": {
+ "pmid": "28127397",
+ "doi": "10.1186/s13036-017-0048-5",
+ "pmcid": "PMC5259876",
+ "title": "Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction.",
+ "metadata": "/private/tmp/communitymech-batch109/spc-metadata.json",
+ "metadata_sha256": "61eeea4c36ff0150f507297d64fcf51c38063dd5759aff66f320344224b6971b",
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+ "status": "retrieved"
+ },
+ {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5259876/fullTextXML",
+ "status": "retrieved_not_yet_read"
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch109/spc-abstract.txt",
+ "abstract_sha256": "cc90a0e77268d7e08716321263248e41fc841aa1e51a5dba7bf07b79ad7c0d08",
+ "xml": "/private/tmp/communitymech-batch109/spc-primary.xml",
+ "xml_sha256": "92443e9477ccde04a9ae88cf368c7df564535faf928b8272f2fc1cfbf2050bfe",
+ "primary_text": "/private/tmp/communitymech-batch109/spc-primary.txt",
+ "primary_text_sha256": "795505b53c13a667fc18eba00cf0edbc5899dab81c73334a18af63c8bc46866a",
+ "license": [
+ "Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated."
+ ],
+ "crossref": "/private/tmp/communitymech-batch109/spc-crossref.json",
+ "crossref_sha256": "53754ded60983f1240aa1f0a0deb2eea427212b737853ee5e344a8ee2d918763",
+ "crossref_license": [
+ {
+ "start": {
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+ 1,
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+ ]
+ ],
+ "date-time": "2017-01-23T00:00:00Z",
+ "timestamp": 1485129600000
+ },
+ "content-version": "tdm",
+ "delay-in-days": 0,
+ "URL": "http://creativecommons.org/licenses/by/4.0/"
+ },
+ {
+ "start": {
+ "date-parts": [
+ [
+ 2017,
+ 1,
+ 23
+ ]
+ ],
+ "date-time": "2017-01-23T00:00:00Z",
+ "timestamp": 1485129600000
+ },
+ "content-version": "vor",
+ "delay-in-days": 0,
+ "URL": "http://creativecommons.org/licenses/by/4.0/"
+ }
+ ]
+ }
+ },
+ "supplement_retrieval": {
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5259876/supplementaryFiles",
+ "earlier_cdn_attempt": "curl DNS failure; no document retrieved",
+ "entries": [
+ "13036_2017_48_Fig5_HTML.gif",
+ "13036_2017_48_Fig2_HTML.gif",
+ "13036_2017_48_Fig3_HTML.gif",
+ "13036_2017_48_Fig5_HTML.jpg",
+ "13036_2017_48_Fig3_HTML.jpg",
+ "13036_2017_48_Fig4_HTML.gif",
+ "13036_2017_48_Fig1_HTML.jpg",
+ "13036_2017_48_Fig2_HTML.jpg",
+ "13036_2017_48_Fig4_HTML.jpg",
+ "13036_2017_48_Fig1_HTML.gif",
+ "13036_2017_48_MOESM1_ESM.docx"
+ ],
+ "status": "retrieved_not_yet_read"
+ },
+ "actual_read_scope": [
+ "Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index. Exact DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository search is not proof of absence. No access bypass or author contact.",
+ "Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8 inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets were not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.",
+ "Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and discussion quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still say abstract_only despite additional text;metadata policy949/1093 is not repaired here."
+ ]
+ },
+ "limitations": [
+ "Fresh both-root baseline precedes source reads:460 records,923 caches,56 existing warnings,zero structural defects. Whole six records and all19 original nodes/12 arrows reviewed;retain16 nodes/nine existing directions,remove three nodes/three arrows,rename three. No new topology or Edison spend.",
+ "Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index. Exact DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository search is not proof of absence. No access bypass or author contact.",
+ "Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8 inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets were not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.",
+ "Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and discussion quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still say abstract_only despite additional text;metadata policy949/1093 is not repaired here.",
+ "Sesame preserves comparator-specific flavor outcomes and source-proposed bacterial-fungal synergy,not exchange/niche partitioning/reciprocal growth. Remove two assembly nodes/arrows. No cultivation,optimization,organism identity or experimental design changes.",
+ "SynComY retains positive reciprocal biofilm-associated qPCR abundance,EPS/activity,FA tolerance and pot outcomes. Positive forward supplementation is not direct transfer;negative reverse supplementation is not proof of no exchange. Correct RNA-seq-as-genome-input and unsupported COBRA version;do not invent model identifiers or genome accessions. Rhizosphere mediation remains explicitly unresolved.",
+ "Azotobacter preserves abstract-supported exporter dependence and omission-context mutualism. PHB is a community endpoint;carbon/nitrogen-to-PHB mediation stays hypothetical. Dinitrogen is substrate,not a specified transfer product. Initial glutamate model and potential alginate are not promoted to omission-assay or demonstrated-production claims.",
+ "SPC records retain positive partner-specific growth and conditional mutualism without universal stability. Bacillus168 production evidence cannot inherit3610 trajectories or other-partner weeks/months persistence. Ecoli early growth is not sucrose-exclusive and85% background export is not a concentration. W303Clump remains distinct from parentalW303 and no yeast bioproduct is invented. Reverse-benefit mechanism is source-proposed,not identified transfer.",
+ "Repair issues[1849, 1850, 1851, 1852, 1853, 1854] stay open until protected-main merge;non-graph follow-up1855 stays open. Fresh all-state title/body dedup matched757,714,605,310;all read plus related529. Ignored/hidden local index inspected,not every matching report read;PRs/comments not exhaustively searched. No reusable taxon match in ignored/hidden kb/taxa name/identifier search. Whole reviewed B12 Syn7002 neighbor read for modeling patterns,not used as evidence for these targets.",
+ "Only graph/discussions/events change. Other454 records,923 caches,non-graph raw blocks and prior histories/decisions preserved. Canonical identities reused as preferred_term+term only;no GTDB copies into graph. General growth metadata and narrative claims are not recertified. No schema,validator,configuration or runtime change. Participant census must be measured;any census test update must reflect actual scoped changes,not a relaxed connectivity rule. Loader1703,DOI-case1091,stub1093 and license949 remain separate. Self-review is not independent approval or corpus completion. Denied/unanswered Edison scopes remain untouched."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml b/reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
new file mode 100644
index 000000000..f24873a50
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
@@ -0,0 +1,1045 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5c3a89285dc4911f035a5aca26ac8d23fb0e14b8
+baseline_commit: 5c3a89285dc4911f035a5aca26ac8d23fb0e14b8
+base_tree: 31d1cdf9d46733907a0efd6a06f7a4f9bc210609
+pre_source_baseline_sha256: f2f73591a7efd23eb69475ca9812e4ecd2948c21f07d8adc1a65d0150fd0cbb1
+issues:
+- 1849
+- 1850
+- 1851
+- 1852
+- 1853
+- 1854
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1855
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 1097
+ matching_issues:
+ - 757
+ - 714
+ - 605
+ - 310
+ ignored_hidden_local_search: true
+source_access:
+ retrieval_manifest:
+ sesame:
+ pmid: '42121419'
+ doi: 10.3390/foods15091476
+ pmcid: PMC13163537
+ title: Designing a Synthetic Microbial Community to Enhance Flavor Compound Production in Sesame Flavor-Type
+ <i>Baijiu</i> Fermentation.
+ metadata: /private/tmp/communitymech-batch109/sesame-metadata.json
+ metadata_sha256: e0a07e4e9dd994756861ceccc38a44b7bfe048c0af5cffd7c663f70a226c1278
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42121419+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13163537/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch109/sesame-abstract.txt
+ abstract_sha256: 63193c1477b96f39033c0e12fc4f8c4e77e50b10b8e314139ba0140ce3db3562
+ xml: /private/tmp/communitymech-batch109/sesame-primary.xml
+ xml_sha256: 2957eb7ceae64bf41cd591e6269e6b8cc6f9ae77ec3c649c22bfb6b92c6a1011
+ primary_text: /private/tmp/communitymech-batch109/sesame-primary.txt
+ primary_text_sha256: e75319879204773a3fbe4ebaf8d536eaa315489340724218ed3d5be0ebcfa7be
+ license:
+ - Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and
+ conditions of the Creative Commons Attribution (CC BY) license.
+ crossref: /private/tmp/communitymech-batch109/sesame-crossref.json
+ crossref_sha256: 762d2f2646311862e4690b1a51b29f03438c95e4449ee001ee9bf61f3f945c9c
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2026
+ - 4
+ - 23
+ date-time: '2026-04-23T00:00:00Z'
+ timestamp: 1776902400000
+ content-version: vor
+ delay-in-days: 0
+ URL: https://creativecommons.org/licenses/by/4.0/
+ syncom_y:
+ pmid: '42125264'
+ doi: 10.1016/j.bioflm.2026.100364
+ pmcid: PMC13158395
+ title: Biofilm synergy by <i>Agrobacterium deltaense</i> and <i>Bacillus velezensis</i>
+ in co-cultures indicates bacterial interspecific cooperation.
+ metadata: /private/tmp/communitymech-batch109/syncom_y-metadata.json
+ metadata_sha256: f5b7c3657030705bde16d34f0ec02a8e84e6481319d62bc257070d123dcd19e6
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42125264+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13158395/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch109/syncom_y-abstract.txt
+ abstract_sha256: 7b80ba54b9b7c7f2a8768864334d30d055f37055a7e71fa0eede93f956d165ea
+ xml: /private/tmp/communitymech-batch109/syncom_y-primary.xml
+ xml_sha256: ec096a2f25d858ffa65f90f3349ca75e294bd99a00e2dbd96c557be1b86e1061
+ primary_text: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ primary_text_sha256: d471ffaa6dece4d42abb5a7962463badd0ecafad9f71d7e68d724028e3244d52
+ license:
+ - This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
+ crossref: /private/tmp/communitymech-batch109/syncom_y-crossref.json
+ crossref_sha256: 9d02fef389b4358303d71bf18c9284dbb94216e4d0a148c9b3727c28ae5fe51a
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2026
+ - 6
+ - 1
+ date-time: '2026-06-01T00:00:00Z'
+ timestamp: 1780272000000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://www.elsevier.com/tdm/userlicense/1.0/
+ - start:
+ date-parts:
+ - - 2026
+ - 6
+ - 1
+ date-time: '2026-06-01T00:00:00Z'
+ timestamp: 1780272000000
+ content-version: tdm
+ delay-in-days: 0
+ URL: https://www.elsevier.com/legal/tdmrep-license
+ - start:
+ date-parts:
+ - - 2026
+ - 5
+ - 1
+ date-time: '2026-05-01T00:00:00Z'
+ timestamp: 1777593600000
+ content-version: vor
+ delay-in-days: 0
+ URL: http://creativecommons.org/licenses/by/4.0/
+ azotobacter:
+ pmid: '27232890'
+ doi: 10.1021/acssynbio.6b00107
+ pmcid: null
+ title: A Designed A. vinelandii-S. elongatus Coculture for Chemical Photoproduction from Air, Water, Phosphate,
+ and Trace Metals.
+ metadata: /private/tmp/communitymech-batch109/azotobacter-metadata.json
+ metadata_sha256: e6147f228ef3fc2893b825ab4d73609b0b8e7bc98cf4d033bed562db2be22f5f
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A27232890+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ abstract: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ abstract_sha256: 1f74d91e93e2414da81b84ba732eda96483ad851bf6993eb0c1d34e07b5a5db2
+ crossref: /private/tmp/communitymech-batch109/azotobacter-crossref.json
+ crossref_sha256: 3b53796d05b1665660f103545d7b54d4b4a7392f984cbff7daf2f3cddc857c06
+ crossref_license: []
+ spc:
+ pmid: '28127397'
+ doi: 10.1186/s13036-017-0048-5
+ pmcid: PMC5259876
+ title: Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction.
+ metadata: /private/tmp/communitymech-batch109/spc-metadata.json
+ metadata_sha256: 61eeea4c36ff0150f507297d64fcf51c38063dd5759aff66f320344224b6971b
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A28127397+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5259876/fullTextXML
+ status: retrieved_not_yet_read
+ abstract: /private/tmp/communitymech-batch109/spc-abstract.txt
+ abstract_sha256: cc90a0e77268d7e08716321263248e41fc841aa1e51a5dba7bf07b79ad7c0d08
+ xml: /private/tmp/communitymech-batch109/spc-primary.xml
+ xml_sha256: 92443e9477ccde04a9ae88cf368c7df564535faf928b8272f2fc1cfbf2050bfe
+ primary_text: /private/tmp/communitymech-batch109/spc-primary.txt
+ primary_text_sha256: 795505b53c13a667fc18eba00cf0edbc5899dab81c73334a18af63c8bc46866a
+ license:
+ - Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International
+ License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
+ reproduction in any medium, provided you give appropriate credit to the original author(s) and the source,
+ provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons
+ Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data
+ made available in this article, unless otherwise stated.
+ crossref: /private/tmp/communitymech-batch109/spc-crossref.json
+ crossref_sha256: 53754ded60983f1240aa1f0a0deb2eea427212b737853ee5e344a8ee2d918763
+ crossref_license:
+ - start:
+ date-parts:
+ - - 2017
+ - 1
+ - 23
+ date-time: '2017-01-23T00:00:00Z'
+ timestamp: 1485129600000
+ content-version: tdm
+ delay-in-days: 0
+ URL: http://creativecommons.org/licenses/by/4.0/
+ - start:
+ date-parts:
+ - - 2017
+ - 1
+ - 23
+ date-time: '2017-01-23T00:00:00Z'
+ timestamp: 1485129600000
+ content-version: vor
+ delay-in-days: 0
+ URL: http://creativecommons.org/licenses/by/4.0/
+ supplement_retrieval:
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5259876/supplementaryFiles
+ earlier_cdn_attempt: curl DNS failure; no document retrieved
+ entries:
+ - 13036_2017_48_Fig5_HTML.gif
+ - 13036_2017_48_Fig2_HTML.gif
+ - 13036_2017_48_Fig3_HTML.gif
+ - 13036_2017_48_Fig5_HTML.jpg
+ - 13036_2017_48_Fig3_HTML.jpg
+ - 13036_2017_48_Fig4_HTML.gif
+ - 13036_2017_48_Fig1_HTML.jpg
+ - 13036_2017_48_Fig2_HTML.jpg
+ - 13036_2017_48_Fig4_HTML.jpg
+ - 13036_2017_48_Fig1_HTML.gif
+ - 13036_2017_48_MOESM1_ESM.docx
+ status: retrieved_not_yet_read
+ actual_read_scope:
+ - Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions
+ read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index.
+ Exact DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository
+ search is not proof of absence. No access bypass or author contact.
+ - Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8
+ inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures
+ used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets
+ were not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.
+ - Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading
+ used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and
+ discussion quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still
+ say abstract_only despite additional text;metadata policy949/1093 is not repaired here.
+primary_artifacts:
+ /private/tmp/communitymech-batch109/azotobacter-abstract.txt: 1f74d91e93e2414da81b84ba732eda96483ad851bf6993eb0c1d34e07b5a5db2
+ /private/tmp/communitymech-batch109/azotobacter-crossref.json: 3b53796d05b1665660f103545d7b54d4b4a7392f984cbff7daf2f3cddc857c06
+ /private/tmp/communitymech-batch109/azotobacter-metadata.json: e6147f228ef3fc2893b825ab4d73609b0b8e7bc98cf4d033bed562db2be22f5f
+ /private/tmp/communitymech-batch109/baseline.json: f2f73591a7efd23eb69475ca9812e4ecd2948c21f07d8adc1a65d0150fd0cbb1
+ /private/tmp/communitymech-batch109/dedup-local-current.txt: e3f39be8186691160682268cbc24390174e8650d8c27d3532ab12d968b4e6fc2
+ /private/tmp/communitymech-batch109/figure-s2.png: a19d5ae964ca102b46098b7140a723f25277a520a0ba751450f07edf01eeecaf
+ /private/tmp/communitymech-batch109/figure-s4.png: 2da981452dd7ad38dfe6119cfd0932f69cf59eedc477c9667ee87d4c694b25da
+ /private/tmp/communitymech-batch109/image5.png: 17d84fbf7dfc257dd796aff1cde70cdaaff18ff14065b4e69dcde2dd946c5713
+ /private/tmp/communitymech-batch109/image8.png: 289cc01dbb450b9bd7139d9c504bd4704cbc26eddc65aaa042c436f05aaebf99
+ /private/tmp/communitymech-batch109/issue-dedup-current.json: d1ae25209baebc035af081b16a96e5c487aa54cd1ada1a7a9b494ffc0aa2b801
+ /private/tmp/communitymech-batch109/primary-manifest.json: 9785601cae34f5c127b77b329387e70fd169d9546ebc3f2e21836d7f1059eb70
+ /private/tmp/communitymech-batch109/sesame-crossref.json: 762d2f2646311862e4690b1a51b29f03438c95e4449ee001ee9bf61f3f945c9c
+ /private/tmp/communitymech-batch109/sesame-metadata.json: e0a07e4e9dd994756861ceccc38a44b7bfe048c0af5cffd7c663f70a226c1278
+ /private/tmp/communitymech-batch109/sesame-primary.txt: e75319879204773a3fbe4ebaf8d536eaa315489340724218ed3d5be0ebcfa7be
+ /private/tmp/communitymech-batch109/spc-crossref.json: 53754ded60983f1240aa1f0a0deb2eea427212b737853ee5e344a8ee2d918763
+ /private/tmp/communitymech-batch109/spc-metadata.json: 61eeea4c36ff0150f507297d64fcf51c38063dd5759aff66f320344224b6971b
+ /private/tmp/communitymech-batch109/spc-primary.txt: 795505b53c13a667fc18eba00cf0edbc5899dab81c73334a18af63c8bc46866a
+ /private/tmp/communitymech-batch109/spc-supplement.docx: 738a87447cd1f5deedd78c2ee04c576f5b006c55a21ca1512d99b83746ae3315
+ /private/tmp/communitymech-batch109/spc-supplement.txt: 781751179b4b8ec033776475340ab37f80640c43656bff411a18727e6aa9b69a
+ /private/tmp/communitymech-batch109/supplement-retrieval.json: 5830f544a454b0825f40b30fcee8f864ea0a09db2e08343dcc785de06a8e7b19
+ /private/tmp/communitymech-batch109/syncom_y-crossref.json: 9d02fef389b4358303d71bf18c9284dbb94216e4d0a148c9b3727c28ae5fe51a
+ /private/tmp/communitymech-batch109/syncom_y-metadata.json: f5b7c3657030705bde16d34f0ec02a8e84e6481319d62bc257070d123dcd19e6
+ /private/tmp/communitymech-batch109/syncom_y-primary.txt: d471ffaa6dece4d42abb5a7962463badd0ecafad9f71d7e68d724028e3244d52
+ references_cache/PMID_27232890.md: df367aae549d70ab4ee568ac1c9f37ca4dc91a2788fa1e2e9c75966feb703ae1
+ references_cache/PMID_28127397.md: 95b3091f936508c7bda6ee82e4cac58b0115cdedc2ef63e21c8d25a5d965e928
+ references_cache/PMID_42121419.md: d5344cdaa1b90a16debe927dbb95c20227b4ba4b8ce99f50762f98f2fb5f5f8f
+ references_cache/PMID_42125264.md: bb30c18b0ab14cd4dfb024bc860b9d26c304fe732804ca22f7f5ce4d947b32fc
+reviewed_counts:
+ retained_nodes: 16
+ removed_nodes: 3
+ retained_arrows: 9
+ removed_arrows: 3
+ renamed_nodes: 3
+ graph_quotations: 28
+ discussion_quotations: 6
+primary_graph_snippet_count: 28
+snippet_checks:
+- record: SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus
+ node: Flavor-compound outcomes of SC3 versus comparator starters
+ evidence_index: 0
+ reference: PMID:42121419
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/sesame-primary.txt
+ cache_artifact: references_cache/PMID_42121419.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus
+ node: Flavor-compound outcomes of SC3 versus comparator starters
+ evidence_index: 1
+ reference: PMID:42121419
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/sesame-primary.txt
+ cache_artifact: references_cache/PMID_42121419.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus
+ node: Flavor-compound outcomes of SC3 versus comparator starters
+ evidence_index: 2
+ reference: PMID:42121419
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/sesame-primary.txt
+ cache_artifact: references_cache/PMID_42121419.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: Synergistic biofilm and EPS formation in co-culture
+ evidence_index: 0
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: Synergistic biofilm and EPS formation in co-culture
+ evidence_index: 1
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: SynCom Y Fusaric Acid and Wilt Resistance
+ evidence_index: 0
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: SynCom Y Fusaric Acid and Wilt Resistance
+ evidence_index: 1
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
+ evidence_index: 0
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
+ evidence_index: 1
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
+ evidence_index: 0
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
+ evidence_index: 1
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Azotobacter_Photoproduction_Mutualism
+ node: Photosynthetic Sucrose Transfer To Azotobacter
+ evidence_index: 0
+ reference: PMID:27232890
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ cache_artifact: references_cache/PMID_27232890.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Azotobacter_Photoproduction_Mutualism
+ node: Photosynthetic Sucrose Transfer To Azotobacter
+ evidence_index: 1
+ reference: PMID:27232890
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ cache_artifact: references_cache/PMID_27232890.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Azotobacter_Photoproduction_Mutualism
+ node: Diazotrophic Nitrogen Support
+ evidence_index: 0
+ reference: PMID:27232890
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ cache_artifact: references_cache/PMID_27232890.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Azotobacter_Photoproduction_Mutualism
+ node: Diazotrophic Nitrogen Support
+ evidence_index: 1
+ reference: PMID:27232890
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ cache_artifact: references_cache/PMID_27232890.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Azotobacter_Photoproduction_Mutualism
+ node: Light-Driven PHB Production
+ evidence_index: 0
+ reference: PMID:27232890
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ cache_artifact: references_cache/PMID_27232890.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Bacillus_SPC
+ node: CO2 Fixation and Sucrose Production
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Bacillus_SPC
+ node: Sucrose Uptake and Heterotrophic Growth
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Bacillus_SPC
+ node: Sucrose Uptake and Heterotrophic Growth
+ evidence_index: 1
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Ecoli_SPC
+ node: Photosynthetic carbon supply to E. coli
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Ecoli_SPC
+ node: Photosynthetic carbon supply to E. coli
+ evidence_index: 1
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Ecoli_SPC
+ node: E. coli growth on cyanobacterial photosynthate
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Ecoli_SPC
+ node: E. coli Stimulation of Cyanobacterial Growth
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Ecoli_SPC
+ node: E. coli Stimulation of Cyanobacterial Growth
+ evidence_index: 1
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Saccharomyces_SPC
+ node: CO2 Fixation and Sucrose Production
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Saccharomyces_SPC
+ node: Sucrose Utilization by the Heterotrophic Partner
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Saccharomyces_SPC
+ node: Yeast Stimulation of Cyanobacterial Growth
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Saccharomyces_SPC
+ node: Yeast Stimulation of Cyanobacterial Growth
+ evidence_index: 1
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+discussion_snippet_checks:
+- record: SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus
+ node: fuqu-comparator-outcomes-versus-exchange
+ evidence_index: 0
+ reference: PMID:42121419
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/sesame-primary.txt
+ cache_artifact: references_cache/PMID_42121419.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture
+ node: syncom-y-growth-versus-transfer-and-biocontrol
+ evidence_index: 0
+ reference: PMID:42125264
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/syncom_y-primary.txt
+ cache_artifact: references_cache/PMID_42125264.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Azotobacter_Photoproduction_Mutualism
+ node: azotobacter-growth-context-and-phb-mediation
+ evidence_index: 0
+ reference: PMID:27232890
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/azotobacter-abstract.txt
+ cache_artifact: references_cache/PMID_27232890.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Bacillus_SPC
+ node: spc-bacillus-assay-and-mediator-boundaries
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Ecoli_SPC
+ node: spc-ecoli-assay-and-mediator-boundaries
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+- record: Synechococcus_Saccharomyces_SPC
+ node: spc-yeast-assay-and-mediator-boundaries
+ evidence_index: 0
+ reference: PMID:28127397
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch109/spc-primary.txt
+ cache_artifact: references_cache/PMID_28127397.md
+ scope: Normalized literal match to independently retrieved primary text and unchanged cache; entailment reviewed
+ separately.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing-node scope/evidence repair and retention/qualification of existing directions. No new topology;
+ unrelated denied/unanswered scopes untouched.
+limitations:
+- Fresh both-root baseline precedes source reads:460 records,923 caches,56 existing warnings,zero structural defects.
+ Whole six records and all19 original nodes/12 arrows reviewed;retain16 nodes/nine existing directions,remove three
+ nodes/three arrows,rename three. No new topology or Edison spend.
+- Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions
+ read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index. Exact
+ DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository
+ search is not proof of absence. No access bypass or author contact.
+- Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8
+ inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures
+ used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets were
+ not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.
+- Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading
+ used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and discussion
+ quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still say abstract_only
+ despite additional text;metadata policy949/1093 is not repaired here.
+- Sesame preserves comparator-specific flavor outcomes and source-proposed bacterial-fungal synergy,not exchange/niche
+ partitioning/reciprocal growth. Remove two assembly nodes/arrows. No cultivation,optimization,organism identity
+ or experimental design changes.
+- SynComY retains positive reciprocal biofilm-associated qPCR abundance,EPS/activity,FA tolerance and pot outcomes.
+ Positive forward supplementation is not direct transfer;negative reverse supplementation is not proof of no exchange.
+ Correct RNA-seq-as-genome-input and unsupported COBRA version;do not invent model identifiers or genome accessions.
+ Rhizosphere mediation remains explicitly unresolved.
+- Azotobacter preserves abstract-supported exporter dependence and omission-context mutualism. PHB is a community
+ endpoint;carbon/nitrogen-to-PHB mediation stays hypothetical. Dinitrogen is substrate,not a specified transfer
+ product. Initial glutamate model and potential alginate are not promoted to omission-assay or demonstrated-production
+ claims.
+- SPC records retain positive partner-specific growth and conditional mutualism without universal stability. Bacillus168
+ production evidence cannot inherit3610 trajectories or other-partner weeks/months persistence. Ecoli early growth
+ is not sucrose-exclusive and85% background export is not a concentration. W303Clump remains distinct from parentalW303
+ and no yeast bioproduct is invented. Reverse-benefit mechanism is source-proposed,not identified transfer.
+- Repair issues[1849, 1850, 1851, 1852, 1853, 1854] stay open until protected-main merge;non-graph follow-up1855
+ stays open. Fresh all-state title/body dedup matched757,714,605,310;all read plus related529. Ignored/hidden local
+ index inspected,not every matching report read;PRs/comments not exhaustively searched. No reusable taxon match
+ in ignored/hidden kb/taxa name/identifier search. Whole reviewed B12 Syn7002 neighbor read for modeling patterns,not
+ used as evidence for these targets.
+- Only graph/discussions/events change. Other454 records,923 caches,non-graph raw blocks and prior histories/decisions
+ preserved. Canonical identities reused as preferred_term+term only;no GTDB copies into graph. General growth metadata
+ and narrative claims are not recertified. No schema,validator,configuration or runtime change. Participant census
+ must be measured;any census test update must reflect actual scoped changes,not a relaxed connectivity rule. Loader1703,DOI-case1091,stub1093
+ and license949 remain separate. Self-review is not independent approval or corpus completion. Denied/unanswered
+ Edison scopes remain untouched.
+records:
+- path: kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml
+ id: CommunityMech:000283
+ original_sha256: 7632231bd07c18ef98b01774b24727e9614735db23897194855dae5a791b8b3b
+ record_sha256: f9ac5f1e3098ee43744bd8749fbba47f46eb27abace9e1a82b69d4bb64cc2c42
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ scope: Whole record and all existing nodes/directions; graph repair, not whole-record certification.
+ summary: Retain comparator-specific chemical outcomes; remove construction nodes, unsupported interaction types
+ and two design-order arrows.
+ node_decisions:
+ - node: Flavor-compound outcomes of SC3 versus comparator starters
+ rationale: Retain comparator-specific chemical outcomes; remove construction nodes, unsupported interaction
+ types and two design-order arrows.
+ removed_node_decisions:
+ - node: Fuqu Starch Ethanol and Flavor Base Guild
+ rationale: Construction rationale and prior general functional roles, not a measured causal interaction in SC3.
+ - node: Lactic-Acid Bacteria Flavor-Precursor Guild
+ rationale: Construction rationale and prior general functional roles, not a measured causal interaction in SC3.
+ renamed_nodes:
+ Emergent flavor-compound co-production by the assembled SynCom: Flavor-compound outcomes of SC3 versus comparator
+ starters
+ edges_before:
+ - source: Fuqu Starch Ethanol and Flavor Base Guild
+ target: Emergent flavor-compound co-production by the assembled SynCom
+ description: The Fuqu base guild supplies starch, ethanol, and flavor-production functions used as the SC1 foundation
+ for the higher-performing SC3 SynCom.
+ - source: Lactic-Acid Bacteria Flavor-Precursor Guild
+ target: Emergent flavor-compound co-production by the assembled SynCom
+ description: The lactic-acid bacterial subguild expands the SC2 consortium with precursor-forming taxa that
+ feed flavor-compound formation.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Fuqu Starch Ethanol and Flavor Base Guild
+ target: Emergent flavor-compound co-production by the assembled SynCom
+ description: The Fuqu base guild supplies starch, ethanol, and flavor-production functions used as the SC1 foundation
+ for the higher-performing SC3 SynCom.
+ rationale: Assembly order does not establish a biological direction.
+ - source: Lactic-Acid Bacteria Flavor-Precursor Guild
+ target: Emergent flavor-compound co-production by the assembled SynCom
+ description: The lactic-acid bacterial subguild expands the SC2 consortium with precursor-forming taxa that
+ feed flavor-compound formation.
+ rationale: Assembly order does not establish a biological direction.
+ references:
+ - PMID:42121419
+ issues:
+ - 1849
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus/2026-10-08T045942Z-codex-f64ce1.yaml
+- path: kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml
+ id: CommunityMech:000272
+ original_sha256: caf56231ec4c91150f7679b19fe3de49c892091f7cfa5514b7fe3173945ec418
+ record_sha256: 5e1cbb5518d3e85f87662c378056e9b1dc8ff338fa7bc2a55f3c3e9a61941b02
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ scope: Whole record and all existing nodes/directions; graph repair, not whole-record certification.
+ summary: Retain assay-specific reciprocal biofilm growth and qualify its proposed downstream mediation.; Retain
+ measured FA tolerance and pot biocontrol as community outcomes, not a second mutualism.; Separate positive supplementation
+ from transfer and correct modeling input/version provenance.; Retain predicted return with the reported negative
+ supplementation endpoint and corrected provenance.
+ node_decisions:
+ - node: Synergistic biofilm and EPS formation in co-culture
+ rationale: Retain assay-specific reciprocal biofilm growth and qualify its proposed downstream mediation.
+ - node: SynCom Y Fusaric Acid and Wilt Resistance
+ rationale: Retain measured FA tolerance and pot biocontrol as community outcomes, not a second mutualism.
+ - node: Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
+ rationale: Separate positive supplementation from transfer and correct modeling input/version provenance.
+ - node: Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16
+ rationale: Retain predicted return with the reported negative supplementation endpoint and corrected provenance.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id001
+ source: Synergistic biofilm and EPS formation in co-culture
+ target: SynCom Y Fusaric Acid and Wilt Resistance
+ description: 'The EPS-rich dual-species biofilm tolerated more fusaric acid than either monoculture and links
+ the Agrobacterium-Bacillus biofilm synergy to pot-level watermelon Fusarium wilt suppression.
+
+ '
+ - &id003
+ source: Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
+ target: Synergistic biofilm and EPS formation in co-culture
+ description: 'Experimentally validated L-ornithine and guanine additions connect the predicted LSQ16-to-WB donation
+ route to enhanced B. velezensis biofilm formation in the measured co-culture synergy.
+
+ '
+ edges_after:
+ - &id002
+ source: Synergistic biofilm and EPS formation in co-culture
+ target: SynCom Y Fusaric Acid and Wilt Resistance
+ description: 'HYPOTHESIZED/PARTIAL: enhanced EPS-rich biofilm formation could contribute to fusaric-acid tolerance
+ and the positive pot-level biocontrol outcome. Separate in-vitro and pot comparisons do not isolate biofilm
+ mediation or establish that the in-vitro partnership occurs in the rhizosphere.'
+ - &id004
+ source: Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB
+ target: Synergistic biofilm and EPS formation in co-culture
+ description: 'HYPOTHESIZED/PARTIAL: predicted LSQ16 provision of L-ornithine and guanine could contribute to
+ WB biofilm enhancement, consistent with the positive additions and metabolite profiles. These results do not
+ establish transfer, its necessity, or its quantitative contribution to the two-strain biofilm/EPS response.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: 'HYPOTHESIZED/PARTIAL: enhanced EPS-rich biofilm formation could contribute to fusaric-acid tolerance
+ and the positive pot-level biocontrol outcome. Separate in-vitro and pot comparisons do not isolate biofilm
+ mediation or establish that the in-vitro partnership occurs in the rhizosphere.'
+ - before: *id003
+ after: *id004
+ rationale: 'HYPOTHESIZED/PARTIAL: predicted LSQ16 provision of L-ornithine and guanine could contribute to WB
+ biofilm enhancement, consistent with the positive additions and metabolite profiles. These results do not
+ establish transfer, its necessity, or its quantitative contribution to the two-strain biofilm/EPS response.'
+ removed_edge_decisions: []
+ references:
+ - PMID:42125264
+ issues:
+ - 1850
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture/2026-10-08T045943Z-codex-deec92.yaml
+- path: kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml
+ id: CommunityMech:000207
+ original_sha256: 66201890ed3f32317d605338443cdc09ded895b09c58b435184f9e24f8e3f784
+ record_sha256: a96409b502da3b96811a68db9d999ca493fd4ff455ae3e303ceb39a04538238a
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ scope: Whole record and all existing nodes/directions; graph repair, not whole-record certification.
+ summary: Retain exporter-dependent carbon support without transport-rate or PHB-tracing claims.; Retain omission-context
+ mutualism; qualify nitrogen-to-PHB mediation and substrate role.; Retain PHB production as a community endpoint
+ and distinguish potential alginate production.
+ node_decisions:
+ - node: Photosynthetic Sucrose Transfer To Azotobacter
+ rationale: Retain exporter-dependent carbon support without transport-rate or PHB-tracing claims.
+ - node: Diazotrophic Nitrogen Support
+ rationale: Retain omission-context mutualism; qualify nitrogen-to-PHB mediation and substrate role.
+ - node: Light-Driven PHB Production
+ rationale: Retain PHB production as a community endpoint and distinguish potential alginate production.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id005
+ source: Photosynthetic Sucrose Transfer To Azotobacter
+ target: Light-Driven PHB Production
+ description: 'Sucrose exported by engineered S. elongatus supplies the fixed carbon used by A. vinelandii in
+ the light-driven coculture that produced PHB.
+
+ '
+ - &id007
+ source: Diazotrophic Nitrogen Support
+ target: Light-Driven PHB Production
+ description: 'Diazotrophic nitrogen fixation by A. vinelandii enables coculture growth without added fixed nitrogen
+ in the same mutualism that produced PHB.
+
+ '
+ edges_after:
+ - &id006
+ source: Photosynthetic Sucrose Transfer To Azotobacter
+ target: Light-Driven PHB Production
+ description: 'HYPOTHESIZED/PARTIAL: cyanobacterial carbon supply supports the productive coculture and is proposed
+ to provide carbon for PHB. The abstract establishes exporter-dependent growth and PHB production, not direct
+ carbon tracing into PHB or isolated control of its yield.'
+ - &id008
+ source: Diazotrophic Nitrogen Support
+ target: Light-Driven PHB Production
+ description: 'HYPOTHESIZED/PARTIAL: diazotrophic support could enable growth of the PHB-producing coculture
+ under fixed-nitrogen omission. The abstract does not isolate nitrogen supply as the mediator of a PHB-production
+ change or establish the exact PHB assay conditions.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: 'HYPOTHESIZED/PARTIAL: cyanobacterial carbon supply supports the productive coculture and is proposed
+ to provide carbon for PHB. The abstract establishes exporter-dependent growth and PHB production, not direct
+ carbon tracing into PHB or isolated control of its yield.'
+ - before: *id007
+ after: *id008
+ rationale: 'HYPOTHESIZED/PARTIAL: diazotrophic support could enable growth of the PHB-producing coculture under
+ fixed-nitrogen omission. The abstract does not isolate nitrogen supply as the mediator of a PHB-production
+ change or establish the exact PHB assay conditions.'
+ removed_edge_decisions: []
+ references:
+ - PMID:27232890
+ issues:
+ - 1851
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Synechococcus_Azotobacter_Photoproduction_Mutualism/2026-10-08T045943Z-codex-31bb19.yaml
+- path: kb/communities/Synechococcus_Bacillus_SPC.yaml
+ id: CommunityMech:000065
+ original_sha256: 1152d4e81a2fa94dbff165e41d5be8d982c7384816671ded67a66083b3794ff7
+ record_sha256: a04fd02a2219aa3518ab4e4ac9bd35503d606b3b19d5332c0df65961f939fc4c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ scope: Whole record and all existing nodes/directions; graph repair, not whole-record certification.
+ summary: Retain cyanobacterial carbon support with explicit 168-versus-3610 scope.; Retain bounded Bacillus growth
+ support and the positive168 assay; remove unestablished long-term stability.
+ node_decisions:
+ - node: CO2 Fixation and Sucrose Production
+ rationale: Retain cyanobacterial carbon support with explicit 168-versus-3610 scope.
+ - node: Sucrose Uptake and Heterotrophic Growth
+ rationale: Retain bounded Bacillus growth support and the positive168 assay; remove unestablished long-term
+ stability.
+ removed_node_decisions:
+ - node: Sucrose-Dependent Long-Term Consortium Stabilization
+ rationale: Weeks-to-months continuous persistence was shown for E. coli and yeast, not this Bacillus168 dyad;
+ 3610 perturbation experiments cannot certify 168 persistence.
+ renamed_nodes: {}
+ edges_before:
+ - &id009
+ source: CO2 Fixation and Sucrose Production
+ target: Sucrose Uptake and Heterotrophic Growth
+ description: Secreted cyanobacterial photosynthate is taken up as the sucrose carbon source that lets the heterotrophic
+ partner grow in the light-driven coculture.
+ - source: Sucrose Uptake and Heterotrophic Growth
+ target: Sucrose-Dependent Long-Term Consortium Stabilization
+ description: Heterotrophic sucrose utilization is the positive carbon-flow process that counterbalances destabilizing
+ non-sucrose byproducts and lets both members persist for weeks to months.
+ edges_after:
+ - &id010
+ source: CO2 Fixation and Sucrose Production
+ target: Sucrose Uptake and Heterotrophic Growth
+ description: 'PARTIAL: cyanobacterial sucrose export is the proposed carbon supply for the existing heterotrophic-growth
+ node. Sucrose-dependent Bacillus growth and the 168-specific production assay support this route, but exact
+ growth kinetics must remain strain-specific.'
+ retained_edge_decisions:
+ - before: *id009
+ after: *id010
+ rationale: 'PARTIAL: cyanobacterial sucrose export is the proposed carbon supply for the existing heterotrophic-growth
+ node. Sucrose-dependent Bacillus growth and the 168-specific production assay support this route, but exact
+ growth kinetics must remain strain-specific.'
+ removed_edge_decisions:
+ - source: Sucrose Uptake and Heterotrophic Growth
+ target: Sucrose-Dependent Long-Term Consortium Stabilization
+ description: Heterotrophic sucrose utilization is the positive carbon-flow process that counterbalances destabilizing
+ non-sucrose byproducts and lets both members persist for weeks to months.
+ rationale: Strain168 long-term persistence is not supported by other-partner continuous cultures or3610 perturbation
+ assays.
+ references:
+ - PMID:28127397
+ issues:
+ - 1852
+ - 1855
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Synechococcus_Bacillus_SPC/2026-10-08T045943Z-codex-9d0c0c.yaml
+- path: kb/communities/Synechococcus_Ecoli_SPC.yaml
+ id: CommunityMech:000066
+ original_sha256: 5f7859ba7ca36adb228aa2f48fa1f0d69501df96f2d06c302b38c132ed5efda4
+ record_sha256: 529766861de184236d78198a26eba1c964d999973a1230db145330bd875c3556
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ scope: Whole record and all existing nodes/directions; graph repair, not whole-record certification.
+ summary: Retain carbon supply while distinguishing early non-sucrose dependence and removing the invalid concentration.;
+ Retain strain-specific growth/persistence, not sucrose-exclusive growth or syntrophy.; Retain conditional reciprocal
+ growth benefit; mediator of cyanobacterial stimulation is unresolved.
+ node_decisions:
+ - node: Photosynthetic carbon supply to E. coli
+ rationale: Retain carbon supply while distinguishing early non-sucrose dependence and removing the invalid concentration.
+ - node: E. coli growth on cyanobacterial photosynthate
+ rationale: Retain strain-specific growth/persistence, not sucrose-exclusive growth or syntrophy.
+ - node: E. coli Stimulation of Cyanobacterial Growth
+ rationale: Retain conditional reciprocal growth benefit; mediator of cyanobacterial stimulation is unresolved.
+ removed_node_decisions: []
+ renamed_nodes:
+ CO2 Fixation and Sucrose Production: Photosynthetic carbon supply to E. coli
+ Sucrose Uptake and Heterotrophic Growth: E. coli growth on cyanobacterial photosynthate
+ edges_before:
+ - &id011
+ source: CO2 Fixation and Sucrose Production
+ target: Sucrose Uptake and Heterotrophic Growth
+ description: Secreted sucrose supports E. coli growth
+ - &id013
+ source: Sucrose Uptake and Heterotrophic Growth
+ target: E. coli Stimulation of Cyanobacterial Growth
+ description: E. coli W delta-cscR growth on Synechococcus-derived photosynthate establishes the reciprocal dyad
+ in which the heterotroph increases cyanobacterial growth relative to axenic controls.
+ edges_after:
+ - &id012
+ source: Photosynthetic carbon supply to E. coli
+ target: E. coli growth on cyanobacterial photosynthate
+ description: 'Cyanobacterial photosynthate supports E. coli growth. PARTIAL for sucrose-specific mediation:
+ early growth was insensitive to export induction, so that phase cannot be attributed solely to sucrose; later
+ productive cocultures show a sucrose contribution.'
+ - &id014
+ source: E. coli growth on cyanobacterial photosynthate
+ target: E. coli Stimulation of Cyanobacterial Growth
+ description: 'HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed
+ cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate
+ sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend
+ on culture context.'
+ retained_edge_decisions:
+ - before: *id011
+ after: *id012
+ rationale: 'Cyanobacterial photosynthate supports E. coli growth. PARTIAL for sucrose-specific mediation: early
+ growth was insensitive to export induction, so that phase cannot be attributed solely to sucrose; later productive
+ cocultures show a sucrose contribution.'
+ - before: *id013
+ after: *id014
+ rationale: 'HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed
+ cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate
+ sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend
+ on culture context.'
+ removed_edge_decisions: []
+ references:
+ - PMID:28127397
+ issues:
+ - 1853
+ - 1855
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Synechococcus_Ecoli_SPC/2026-10-08T045944Z-codex-9a70f9.yaml
+- path: kb/communities/Synechococcus_Saccharomyces_SPC.yaml
+ id: CommunityMech:000067
+ original_sha256: c3232bec75e071dab221f453dd282e3e1122c11b6b892b7bcf7181170f20c6fe
+ record_sha256: 9c021f5bf08a2596743a140a3b14ca90e781d294234a09257a021324e8a20ac6
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml
+ scope: Whole record and all existing nodes/directions; graph repair, not whole-record certification.
+ summary: Retain donor-to-W303Clump sucrose provision, not a generic yeast claim.; Retain long-term continuous
+ persistence separately from batch decline and the negative parental control.; Retain conditional reciprocal
+ growth benefit; qualify the proposed contribution of sucrose-supported yeast.
+ node_decisions:
+ - node: CO2 Fixation and Sucrose Production
+ rationale: Retain donor-to-W303Clump sucrose provision, not a generic yeast claim.
+ - node: Sucrose Utilization by the Heterotrophic Partner
+ rationale: Retain long-term continuous persistence separately from batch decline and the negative parental control.
+ - node: Yeast Stimulation of Cyanobacterial Growth
+ rationale: Retain conditional reciprocal growth benefit; qualify the proposed contribution of sucrose-supported
+ yeast.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id015
+ source: CO2 Fixation and Sucrose Production
+ target: Sucrose Utilization by the Heterotrophic Partner
+ description: The sucrose exported by engineered S. elongatus is the fixed carbon source that supports the evolved
+ Saccharomyces cerevisiae W303Clump partner in continuous coculture.
+ - &id017
+ source: Sucrose Utilization by the Heterotrophic Partner
+ target: Yeast Stimulation of Cyanobacterial Growth
+ description: 'Sucrose utilization sustains W303Clump in the light-driven dyad, and the presence of each tested
+ heterotroph, including the yeast partner, reciprocally increased S. elongatus growth.
+
+ '
+ edges_after:
+ - &id016
+ source: CO2 Fixation and Sucrose Production
+ target: Sucrose Utilization by the Heterotrophic Partner
+ description: The sucrose exported by engineered S. elongatus is the fixed carbon source that supports the evolved
+ Saccharomyces cerevisiae W303Clump partner in continuous coculture.
+ - &id018
+ source: Sucrose Utilization by the Heterotrophic Partner
+ target: Yeast Stimulation of Cyanobacterial Growth
+ description: 'HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed
+ cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate
+ sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend
+ on culture context.'
+ retained_edge_decisions:
+ - before: *id015
+ after: *id016
+ rationale: The sucrose exported by engineered S. elongatus is the fixed carbon source that supports the evolved
+ Saccharomyces cerevisiae W303Clump partner in continuous coculture.
+ - before: *id017
+ after: *id018
+ rationale: 'HYPOTHESIZED/PARTIAL: photosynthate-supported heterotroph activity could contribute to the observed
+ cyanobacterial growth benefit through metabolite return or byproduct absorption. The study does not isolate
+ sucrose uptake as its cause or identify a necessary exchanged compound; positive and negative effects depend
+ on culture context.'
+ removed_edge_decisions: []
+ references:
+ - PMID:28127397
+ issues:
+ - 1854
+ - 1855
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Synechococcus_Saccharomyces_SPC/2026-10-08T045944Z-codex-a56048.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index b017168ce..e79ad8db8 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -396,14 +396,14 @@ kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml CommunityMech:00
kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml CommunityMech:000285 f76054afccd798d444ad3e51a74e13afbed91762384966fb998b842dc54dfeb2 3 0 63.3 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml reviewed
kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml CommunityMech:000302 a1fe9ffb3e47c18fa4d8ac5abb97a451dc8bffd7940b3b741d682729bb47bfb7 3 1 80.0 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml needs_research
kb/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml CommunityMech:000292 88b173ca8cef1393eedf415783725e0befc985adcf2cc3b2564fb7465df3d279 3 0 65.0 reports/causal_graph_review/decisions/20261008-four-records-batch108.yaml reviewed
-kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml CommunityMech:000283 7632231bd07c18ef98b01774b24727e9614735db23897194855dae5a791b8b3b 3 2 100.0 pending
-kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml CommunityMech:000272 caf56231ec4c91150f7679b19fe3de49c892091f7cfa5514b7fe3173945ec418 4 2 100.0 pending
-kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml CommunityMech:000207 66201890ed3f32317d605338443cdc09ded895b09c58b435184f9e24f8e3f784 3 2 100.0 pending
-kb/communities/Synechococcus_Bacillus_SPC.yaml CommunityMech:000065 1152d4e81a2fa94dbff165e41d5be8d982c7384816671ded67a66083b3794ff7 3 2 100.0 pending
-kb/communities/Synechococcus_Ecoli_SPC.yaml CommunityMech:000066 5f7859ba7ca36adb228aa2f48fa1f0d69501df96f2d06c302b38c132ed5efda4 3 2 100.0 pending
+kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml CommunityMech:000283 f9ac5f1e3098ee43744bd8749fbba47f46eb27abace9e1a82b69d4bb64cc2c42 1 0 55.0 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
+kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml CommunityMech:000272 5e1cbb5518d3e85f87662c378056e9b1dc8ff338fa7bc2a55f3c3e9a61941b02 4 2 97.5 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
+kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml CommunityMech:000207 a96409b502da3b96811a68db9d999ca493fd4ff455ae3e303ceb39a04538238a 3 2 96.7 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
+kb/communities/Synechococcus_Bacillus_SPC.yaml CommunityMech:000065 a04fd02a2219aa3518ab4e4ac9bd35503d606b3b19d5332c0df65961f939fc4c 2 1 80.0 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
+kb/communities/Synechococcus_Ecoli_SPC.yaml CommunityMech:000066 529766861de184236d78198a26eba1c964d999973a1230db145330bd875c3556 3 2 96.7 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
kb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml CommunityMech:000198 5990528941355c726bbeca0d65db9327c4455a131cd32d14c5e39a9f50dce4b1 3 2 100.0 pending
kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml CommunityMech:000167 f923cbc0711714b969a4d0c5769186050048b7af3521a1dc2c7bc6d39e040bdb 4 2 100.0 pending
-kb/communities/Synechococcus_Saccharomyces_SPC.yaml CommunityMech:000067 c3232bec75e071dab221f453dd282e3e1122c11b6b892b7bcf7181170f20c6fe 3 2 100.0 pending
+kb/communities/Synechococcus_Saccharomyces_SPC.yaml CommunityMech:000067 9c021f5bf08a2596743a140a3b14ca90e781d294234a09257a021324e8a20ac6 3 2 96.7 reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml reviewed
kb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml CommunityMech:000211 bde403de6edb430affdf758c26fca337040374a2b9ae74aa7623acfb55b22c59 3 2 100.0 pending
kb/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml CommunityMech:000363 0d0dd8d3ab938241d8e9f44d4aa1a9847058883cb5167c79aba7c5c5148392fa 2 1 85.0 pending
kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml CommunityMech:000149 7824f8a6761528794f6d43efede940228e490a140dc57174a7c8ded5e6d7a208 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 868d77a29..b16fd751e 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -2,14 +2,14 @@
"scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
- "nodes": 1384,
- "edges": 547,
+ "nodes": 1381,
+ "edges": 544,
"records_without_nodes": 10,
- "records_without_edges": 184,
+ "records_without_edges": 185,
"review_status_counts": {
"needs_research": 52,
- "pending": 64,
- "reviewed": 344
+ "pending": 58,
+ "reviewed": 350
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch109.json b/reports/causal_graph_review/validation-20261008-batch109.json
new file mode 100644
index 000000000..848a6033f
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch109.json
@@ -0,0 +1,1363 @@
+{
+ "base_commit": "5c3a89285dc4911f035a5aca26ac8d23fb0e14b8",
+ "scope": [
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch109.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/focused.log",
+ "log_sha256": "5aff46aa3e35ddb1da4ef16403e98cee6e297ac179b11542d51f3a3d260b8b09",
+ "output_tail": "............ [100%]\n12 passed in 40.58s\n"
+ },
+ {
+ "check": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch109/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-strict.tsv",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-strict.log",
+ "log_sha256": "09b883e7d263eaf6ad502a2226b1ec06e0f630a72bad670a3ae71f8a0ea31460",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch109/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-batch109/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-strict.tsv\n"
+ },
+ {
+ "check": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-references.log",
+ "log_sha256": "50c245f8b1a94e4b9cd138b4f7afd3aeba2dacc8787086edb6fa8f55a46e3007",
+ "output_tail": "Validating kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.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/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.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": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-snippets.log",
+ "log_sha256": "cbb2cdedf7d2ed5756aac506b60071c409906c876d5eb3586f860c596629a58e",
+ "output_tail": "# 21 evidence snippets scanned across 1 files\n MATCH 21\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": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-rank.log",
+ "log_sha256": "e4f6f033e28eb9e6e39b9872035d66fd2954be45a632babafb5a359073b0dc69",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000283\",\n \"name\": \"Sesame-flavor Baijiu Fuqu SynCom (13-genus)\",\n \"score\": 55.0,\n \"taxonomy\": 13,\n \"connected_taxa\": 13,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 1,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus/2026-10-08T045942Z-codex-f64ce1.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch109/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-strict.tsv",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-strict.log",
+ "log_sha256": "1f88a2c51b285fd23e456ef0e7f433451347a725de00c8cfda531c9ff6f0ae33",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch109/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-batch109/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-references.log",
+ "log_sha256": "fdb894951678471627b1a187c5e38a25681410ca15e32aba8c6d9b53b3d36dea",
+ "output_tail": "Validating kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-snippets.log",
+ "log_sha256": "826e9c1ef5038bfe5995c8f56b27f9f6d8418cb9a40f124b1547f2d75876c305",
+ "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\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": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-rank.log",
+ "log_sha256": "a53fd1231f60c5765bba13568375683cef16e81923feada26fc593eadea7510c",
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+ },
+ {
+ "check": "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture/2026-10-08T045943Z-codex-deec92.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Azotobacter_Photoproduction_Mutualism-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Azotobacter_Photoproduction_Mutualism-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch109/Synechococcus_Azotobacter_Photoproduction_Mutualism-strict.tsv",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-strict.log",
+ "log_sha256": "77d442be8378f9058f8e3596939324d87f403eab252129d41e8036a2a85479ac",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch109/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-batch109/Synechococcus_Azotobacter_Photoproduction_Mutualism-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Azotobacter_Photoproduction_Mutualism-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Azotobacter_Photoproduction_Mutualism-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-references.log",
+ "log_sha256": "8b3a70ad3c65f0e9f29a5bf78bda5415feb89a50452a157804821f57fbbbd2bd",
+ "output_tail": "Validating kb/communities/Synechococcus_Azotobacter_Photoproduction_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/Synechococcus_Azotobacter_Photoproduction_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": "Synechococcus_Azotobacter_Photoproduction_Mutualism-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-snippets.log",
+ "log_sha256": "2ffa6e242265b4c1c2eb555bd8bd14abb6cc63ed4d5a8a818da9b515db44daff",
+ "output_tail": "# 24 evidence snippets scanned across 1 files\n MATCH 24\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Synechococcus_Azotobacter_Photoproduction_Mutualism-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-rank.log",
+ "log_sha256": "96845937779b67e28b6307acdc574ee8e1dc47766b5825779c2101263bd1aafb",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000207\",\n \"name\": \"Synechococcus-Azotobacter Photoproduction Mutualism\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Azotobacter_Photoproduction_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/Synechococcus_Azotobacter_Photoproduction_Mutualism/2026-10-08T045943Z-codex-31bb19.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Azotobacter_Photoproduction_Mutualism-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Bacillus_SPC-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Bacillus_SPC-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch109/Synechococcus_Bacillus_SPC-strict.tsv",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-strict.log",
+ "log_sha256": "98466d8bee13744b7bcf2674c4e2a4146257dbc7f1d339e1e413bdbc6d547273",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch109/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-batch109/Synechococcus_Bacillus_SPC-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Bacillus_SPC-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Bacillus_SPC-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-references.log",
+ "log_sha256": "0d20454e19001b649e03c2cc15fbff37efb76a94a796d5b9525d25edee0f7b36",
+ "output_tail": "Validating kb/communities/Synechococcus_Bacillus_SPC.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/Synechococcus_Bacillus_SPC.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": "Synechococcus_Bacillus_SPC-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-snippets.log",
+ "log_sha256": "389f1d2b093a1648cf407d53853e429a283f80eed2628a1a14cf1f38649ca780",
+ "output_tail": "# 12 evidence snippets scanned across 1 files\n MATCH 12\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": "Synechococcus_Bacillus_SPC-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-rank.log",
+ "log_sha256": "4723cf42ed0710b3ce2811a480bc8c98bb89033637e6d232e4772aa3bf8b5bc0",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000065\",\n \"name\": \"Synechococcus-Bacillus Synthetic Photosynthetic Consortium\",\n \"score\": 80.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 2,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_interactions\",\n \"additional_downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Bacillus_SPC.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Bacillus_SPC-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Synechococcus_Bacillus_SPC/2026-10-08T045943Z-codex-9d0c0c.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Bacillus_SPC-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Ecoli_SPC-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Ecoli_SPC-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch109/Synechococcus_Ecoli_SPC-strict.tsv",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-strict.log",
+ "log_sha256": "480ea5965ba1bd609ac7a26489c815a457a5a083b40e28f749aef29ebcb2c6ef",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch109/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-batch109/Synechococcus_Ecoli_SPC-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Ecoli_SPC-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Ecoli_SPC-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-references.log",
+ "log_sha256": "a51c278b7ba91016cfcd705ddea413ff5072b7cc15ebf4b551cfd9bb10fc9318",
+ "output_tail": "Validating kb/communities/Synechococcus_Ecoli_SPC.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/Synechococcus_Ecoli_SPC.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": "Synechococcus_Ecoli_SPC-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-snippets.log",
+ "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+ "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\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": "Synechococcus_Ecoli_SPC-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-rank.log",
+ "log_sha256": "3cdd55773bd8d07add741e401f694cb66c130d2ee268af48a031dc856c9a7dd0",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000066\",\n \"name\": \"Synechococcus-E.coli Synthetic Photosynthetic Consortium\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Ecoli_SPC.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Ecoli_SPC-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Synechococcus_Ecoli_SPC/2026-10-08T045944Z-codex-9a70f9.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Ecoli_SPC-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Saccharomyces_SPC-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Synechococcus_Saccharomyces_SPC-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch109/Synechococcus_Saccharomyces_SPC-strict.tsv",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-strict.log",
+ "log_sha256": "808309e66bcc34a923faf44661a296fe08b2bf23d201e377e226703f6e9dd809",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch109/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-batch109/Synechococcus_Saccharomyces_SPC-strict.tsv\n"
+ },
+ {
+ "check": "Synechococcus_Saccharomyces_SPC-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Synechococcus_Saccharomyces_SPC-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-references.log",
+ "log_sha256": "0e1da13dfdd6563e3ad719fa06b8617fb0f4a5b5e53c387d240f811648c4b7f8",
+ "output_tail": "Validating kb/communities/Synechococcus_Saccharomyces_SPC.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/Synechococcus_Saccharomyces_SPC.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": "Synechococcus_Saccharomyces_SPC-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-snippets.log",
+ "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+ "output_tail": "# 13 evidence snippets scanned across 1 files\n MATCH 13\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": "Synechococcus_Saccharomyces_SPC-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-rank.log",
+ "log_sha256": "cf1d5eff690ec4219e17af4c9dd342f1dba380bba1d8f1cc8e956029d93918d8",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000067\",\n \"name\": \"Synechococcus-Saccharomyces Synthetic Photosynthetic Consortium\",\n \"score\": 96.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 4,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Synechococcus_Saccharomyces_SPC.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Synechococcus_Saccharomyces_SPC-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Synechococcus_Saccharomyces_SPC/2026-10-08T045944Z-codex-a56048.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/Synechococcus_Saccharomyces_SPC-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-batch109/verification/inventory.log",
+ "log_sha256": "5a273f06979defa817e3d300cf59f8afc6718b89d776f560183d838a99fdf93e",
+ "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\": 1381,\n \"edges\": 544,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 185,\n \"review_status_counts\": {\n \"needs_research\": 52,\n \"pending\": 58,\n \"reviewed\": 350\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-batch109/verification/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch109/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-batch109/verification/rank-all.log",
+ "log_sha256": "3669224d4b68a7cd7ff60470a202349374718f510bd081240ba14d207774ac34",
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Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
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/private/tmp/communitymech-causal-batch109/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch109/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch109/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch109/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-batch109/verification/render-repeat.log",
+ "log_sha256": "1f0683cda034ae1c36b5fe36fa940784833dabb9bbb34a4d5080f53e56305521",
+ "output_tail": "unitymech-causal-batch109/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch109/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch109/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch109/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch109/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch108')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/connectivity-survey.log",
+ "log_sha256": "0c0549a8511584f80ea8c6e74dbec026c4e77271a034fb5e90aefe82cead074d",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 407, \"mixed\": 132, \"community_level_only\": 275, \"taxa\": 1552, \"credited_solely_by_the_rule\": 1270}}\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_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/regressions.log",
+ "log_sha256": "1fbd1e85bf3b448b6f7620a7270230a79948b2c10ea0d57f7f6b356d46dc3408",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 21%]\n........................................................................ [ 29%]\n........................................................................ [ 36%]\n........................................................................ [ 43%]\n........................................................................ [ 51%]\n........................................................................ [ 58%]\n........................................................................ [ 65%]\n........................................................................ [ 72%]\n........................................................................ [ 80%]\n........................................................................ [ 87%]\n........................................................................ [ 94%]\n................................................... [100%]\n987 passed in 328.40s (0:05:28)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch109/verification/just-lint.log",
+ "log_sha256": "7b3203ccab495540e2c09da0ef6439a0d3574bf744cc90aa1f48475146db61a6",
+ "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\n362 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-batch109/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-batch109/verification/audit-snippets-all.log",
+ "log_sha256": "f635c795e64bc81d277fc69fc14d4833ca840c31fc27133c45a88454df02a529",
+ "output_tail": "# 8991 evidence snippets scanned across 460 files\n MATCH 8854\n RENDERING 21\n ASSEMBLED 1\n WEAK 0\n MISMATCH 39\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\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-batch109/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh both-root baseline precedes source reads:460 records,923 caches,56 existing warnings,zero structural defects. Whole six records and all19 original nodes/12 arrows reviewed;retain16 nodes/nine existing directions,remove three nodes/three arrows,rename three. No new topology or Edison spend.",
+ "Whole independently retrieved primary Sesame,SynComY and SPC abstract/main text/methods/results/discussion/captions read from EuropePMC XML;Azotobacter primary abstract read independently and checked against publisher index. Exact DOI metadata cross-checked. Azotobacter full article and supplements were not retrieved;bounded publisher/repository search is not proof of absence. No access bypass or author contact.",
+ "Public SPC supplement retrieved through EuropePMC after CDN DNS failure. CaptionsS1-S12 read and pixelsS2/S4/S5/S8 inspected. S2/S5 confirm3610 growth/stimulation scope;S4 identifies168 inhibition;S8 long-duration yeast cultures used constant light,not the separate diurnal assay. Remaining images,mathematical framework and raw datasets were not reviewed. No separate Sesame/SynComY supplements or main-figure pixels inspected.",
+ "Cache headers inspected and all graph quotations literal-checked against the three large caches;contextual reading used fresh primary text. Azotobacter cache read whole. Not a whole-cache audit. Every retained/new graph and discussion quotation matches fresh primary text and unchanged committed cache. Sesame/SynComY headers still say abstract_only despite additional text;metadata policy949/1093 is not repaired here.",
+ "Sesame preserves comparator-specific flavor outcomes and source-proposed bacterial-fungal synergy,not exchange/niche partitioning/reciprocal growth. Remove two assembly nodes/arrows. No cultivation,optimization,organism identity or experimental design changes.",
+ "SynComY retains positive reciprocal biofilm-associated qPCR abundance,EPS/activity,FA tolerance and pot outcomes. Positive forward supplementation is not direct transfer;negative reverse supplementation is not proof of no exchange. Correct RNA-seq-as-genome-input and unsupported COBRA version;do not invent model identifiers or genome accessions. Rhizosphere mediation remains explicitly unresolved.",
+ "Azotobacter preserves abstract-supported exporter dependence and omission-context mutualism. PHB is a community endpoint;carbon/nitrogen-to-PHB mediation stays hypothetical. Dinitrogen is substrate,not a specified transfer product. Initial glutamate model and potential alginate are not promoted to omission-assay or demonstrated-production claims.",
+ "SPC records retain positive partner-specific growth and conditional mutualism without universal stability. Bacillus168 production evidence cannot inherit3610 trajectories or other-partner weeks/months persistence. Ecoli early growth is not sucrose-exclusive and85% background export is not a concentration. W303Clump remains distinct from parentalW303 and no yeast bioproduct is invented. Reverse-benefit mechanism is source-proposed,not identified transfer.",
+ "Repair issues[1849, 1850, 1851, 1852, 1853, 1854] stay open until protected-main merge;non-graph follow-up1855 stays open. Fresh all-state title/body dedup matched757,714,605,310;all read plus related529. Ignored/hidden local index inspected,not every matching report read;PRs/comments not exhaustively searched. No reusable taxon match in ignored/hidden kb/taxa name/identifier search. Whole reviewed B12 Syn7002 neighbor read for modeling patterns,not used as evidence for these targets.",
+ "Only graph/discussions/events change. Other454 records,923 caches,non-graph raw blocks and prior histories/decisions preserved. Canonical identities reused as preferred_term+term only;no GTDB copies into graph. General growth metadata and narrative claims are not recertified. No schema,validator,configuration or runtime change. Participant census must be measured;any census test update must reflect actual scoped changes,not a relaxed connectivity rule. Loader1703,DOI-case1091,stub1093 and license949 remain separate. Self-review is not independent approval or corpus completion. Denied/unanswered Edison scopes remain untouched."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml": {
+ "MATCH": 21,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml": {
+ "MATCH": 15,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml": {
+ "MATCH": 24,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml": {
+ "MATCH": 12,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml": {
+ "MATCH": 18,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml": {
+ "MATCH": 13,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 454,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 76,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "Existing-node scope/evidence repair and retention/qualification of existing directions. No new topology; unrelated denied/unanswered scopes untouched."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch109/azotobacter-abstract.txt": "1f74d91e93e2414da81b84ba732eda96483ad851bf6993eb0c1d34e07b5a5db2",
+ "/private/tmp/communitymech-batch109/azotobacter-crossref.json": "3b53796d05b1665660f103545d7b54d4b4a7392f984cbff7daf2f3cddc857c06",
+ "/private/tmp/communitymech-batch109/azotobacter-metadata.json": "e6147f228ef3fc2893b825ab4d73609b0b8e7bc98cf4d033bed562db2be22f5f",
+ "/private/tmp/communitymech-batch109/baseline.json": "f2f73591a7efd23eb69475ca9812e4ecd2948c21f07d8adc1a65d0150fd0cbb1",
+ "/private/tmp/communitymech-batch109/dedup-local-current.txt": "e3f39be8186691160682268cbc24390174e8650d8c27d3532ab12d968b4e6fc2",
+ "/private/tmp/communitymech-batch109/figure-s2.png": "a19d5ae964ca102b46098b7140a723f25277a520a0ba751450f07edf01eeecaf",
+ "/private/tmp/communitymech-batch109/figure-s4.png": "2da981452dd7ad38dfe6119cfd0932f69cf59eedc477c9667ee87d4c694b25da",
+ "/private/tmp/communitymech-batch109/image5.png": "17d84fbf7dfc257dd796aff1cde70cdaaff18ff14065b4e69dcde2dd946c5713",
+ "/private/tmp/communitymech-batch109/image8.png": "289cc01dbb450b9bd7139d9c504bd4704cbc26eddc65aaa042c436f05aaebf99",
+ "/private/tmp/communitymech-batch109/issue-dedup-current.json": "d1ae25209baebc035af081b16a96e5c487aa54cd1ada1a7a9b494ffc0aa2b801",
+ "/private/tmp/communitymech-batch109/primary-manifest.json": "9785601cae34f5c127b77b329387e70fd169d9546ebc3f2e21836d7f1059eb70",
+ "/private/tmp/communitymech-batch109/sesame-crossref.json": "762d2f2646311862e4690b1a51b29f03438c95e4449ee001ee9bf61f3f945c9c",
+ "/private/tmp/communitymech-batch109/sesame-metadata.json": "e0a07e4e9dd994756861ceccc38a44b7bfe048c0af5cffd7c663f70a226c1278",
+ "/private/tmp/communitymech-batch109/sesame-primary.txt": "e75319879204773a3fbe4ebaf8d536eaa315489340724218ed3d5be0ebcfa7be",
+ "/private/tmp/communitymech-batch109/spc-crossref.json": "53754ded60983f1240aa1f0a0deb2eea427212b737853ee5e344a8ee2d918763",
+ "/private/tmp/communitymech-batch109/spc-metadata.json": "61eeea4c36ff0150f507297d64fcf51c38063dd5759aff66f320344224b6971b",
+ "/private/tmp/communitymech-batch109/spc-primary.txt": "795505b53c13a667fc18eba00cf0edbc5899dab81c73334a18af63c8bc46866a",
+ "/private/tmp/communitymech-batch109/spc-supplement.docx": "738a87447cd1f5deedd78c2ee04c576f5b006c55a21ca1512d99b83746ae3315",
+ "/private/tmp/communitymech-batch109/spc-supplement.txt": "781751179b4b8ec033776475340ab37f80640c43656bff411a18727e6aa9b69a",
+ "/private/tmp/communitymech-batch109/supplement-retrieval.json": "5830f544a454b0825f40b30fcee8f864ea0a09db2e08343dcc785de06a8e7b19",
+ "/private/tmp/communitymech-batch109/syncom_y-crossref.json": "9d02fef389b4358303d71bf18c9284dbb94216e4d0a148c9b3727c28ae5fe51a",
+ "/private/tmp/communitymech-batch109/syncom_y-metadata.json": "f5b7c3657030705bde16d34f0ec02a8e84e6481319d62bc257070d123dcd19e6",
+ "/private/tmp/communitymech-batch109/syncom_y-primary.txt": "d471ffaa6dece4d42abb5a7962463badd0ecafad9f71d7e68d724028e3244d52",
+ "references_cache/PMID_27232890.md": "df367aae549d70ab4ee568ac1c9f37ca4dc91a2788fa1e2e9c75966feb703ae1",
+ "references_cache/PMID_28127397.md": "95b3091f936508c7bda6ee82e4cac58b0115cdedc2ef63e21c8d25a5d965e928",
+ "references_cache/PMID_42121419.md": "d5344cdaa1b90a16debe927dbb95c20227b4ba4b8ce99f50762f98f2fb5f5f8f",
+ "references_cache/PMID_42125264.md": "bb30c18b0ab14cd4dfb024bc860b9d26c304fe732804ca22f7f5ce4d947b32fc"
+ },
+ "immutable_prior_history_and_decision_files": 833,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 28,
+ "new_discussion_quotations": 6,
+ "fresh_primary_literal_matches": 34,
+ "all_cached_literal_matches": 34,
+ "retained_nodes": 16,
+ "removed_nodes": 3,
+ "retained_arrows": 9,
+ "removed_arrows": 3,
+ "new_nodes_or_directions": 0,
+ "scope": "All reviewed quotations match fresh primary text and unchanged caches;source entailment separately reviewed. Three full primary bodies/captions,one primary abstract,SPC supplement captionsS1-S12 and selected pixelsS2/S4/S5/S8 read;not raw-data certification."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "Sixteen nodes and nine existing directions retained;three nodes and three arrows removed. All56existing warnings unchanged;zero structural defects. Non-graph SPC narratives/metadata remain1855."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1367,
+ "arrows": 536
+ },
+ "render_scope": "Deterministic rendering and exact HTML-description parser,not screenshots;postcommit docs-current separately required.",
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 403,
+ "mixed": 128,
+ "community_level_only": 275,
+ "taxa": 1544,
+ "credited_solely_by_the_rule": 1270
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 407,
+ "mixed": 132,
+ "community_level_only": 275,
+ "taxa": 1552,
+ "credited_solely_by_the_rule": 1270
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 4,
+ "mixed": 4,
+ "community_level_only": 0,
+ "taxa": 8,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "PHB and three heterotroph-use phenotypes gain community-level identity-only scope;SynComY outcome and Sesame endpoint also gain canonical participants. Four additional mixed-scope records;no additional solely-credited taxa. Observational census bounds updated to this measured scope with an exact regression;connectivity rules and share guard unchanged."
+ },
+ "lint_limitation": "Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.",
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies unchanged. Not a complete embedding runtime."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8991,
+ "categories": {
+ "MATCH": 8854,
+ "RENDERING": 21,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 39,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1381,
+ "edges": 544,
+ "records_without_nodes": 10,
+ "records_without_edges": 185,
+ "review_status_counts": {
+ "needs_research": 52,
+ "pending": 58,
+ "reviewed": 350
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml": "578f8105c6b3ed5eee6e8b6dfc762f6a781a885a4f85a3bf91971a54a5f348ec",
+ "tests/test_causal_review_batch109.py": "712d4012d107506936ed7ec95afefc92aa33bc83fdc935d5388866cffa97451e",
+ "tests/test_participating_taxa.py": "985ce17be93928b77e83365042d2129c394c4c1f0474e029f9fdd5f12ea8e844",
+ "tests/test_community_level_connectivity_credit.py": "3e370c6f0f5087f2c6b0b6d45f7a4a6d66c71171973535485d608a6cf2ad98af",
+ "reports/causal_graph_review/cache-provenance-20261008-batch109.json": "d818cfaf49c796823dbd361139d124571001e8445eb523422ac092f922ff0b9e",
+ "kb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml": "f9ac5f1e3098ee43744bd8749fbba47f46eb27abace9e1a82b69d4bb64cc2c42",
+ "kb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml": "5e1cbb5518d3e85f87662c378056e9b1dc8ff338fa7bc2a55f3c3e9a61941b02",
+ "kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml": "a96409b502da3b96811a68db9d999ca493fd4ff455ae3e303ceb39a04538238a",
+ "kb/communities/Synechococcus_Bacillus_SPC.yaml": "a04fd02a2219aa3518ab4e4ac9bd35503d606b3b19d5332c0df65961f939fc4c",
+ "kb/communities/Synechococcus_Ecoli_SPC.yaml": "529766861de184236d78198a26eba1c964d999973a1230db145330bd875c3556",
+ "kb/communities/Synechococcus_Saccharomyces_SPC.yaml": "9c021f5bf08a2596743a140a3b14ca90e781d294234a09257a021324e8a20ac6"
+ },
+ "pre_research_baseline": {
+ "base_commit": "5c3a89285dc4911f035a5aca26ac8d23fb0e14b8",
+ "base_tree": "31d1cdf9d46733907a0efd6a06f7a4f9bc210609",
+ "research_worktree": "/private/tmp/communitymech-causal-batch108",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch109/baseline-rank.log",
+ "sha256": "7aafa585816fbd2d213c0a79e8c446f1012b0b872b5e92e0fc17b35df112c944"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch109/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-batch109/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch109/baseline-downstream.log",
+ "sha256": "cfeb644d771f9bd0092efd7d5e9cf144d00188f574585e6d19fb538c25085d44"
+ }
+ ],
+ "baseline_sha256": "f2f73591a7efd23eb69475ca9812e4ecd2948c21f07d8adc1a65d0150fd0cbb1"
+ },
+ "reference_validator_caveat": "Six full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.",
+ "status": "verified_existing_graph_repairs_with_source_access_limits",
+ "total_recorded_gate_outputs": 55
+}
diff --git a/tests/test_causal_review_batch109.py b/tests/test_causal_review_batch109.py
new file mode 100644
index 000000000..227442f37
--- /dev/null
+++ b/tests/test_causal_review_batch109.py
@@ -0,0 +1,189 @@
+"""Preserve positive outcomes without transferring evidence across assays or strains."""
+
+import hashlib
+import runpy
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-six-records-batch109.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_fuqu_comparators_are_not_construction_causality_or_mutualism():
+ _, rows, docs = records()
+ nodes = docs[0]["ecological_interactions"]
+ assert len(nodes) == 1
+ outcome = nodes[0]
+ assert "interaction_type" not in outcome and not outcome.get("downstream")
+ assert "0.45, 0.40 and 0.64" in outcome["description"]
+ assert "ethanol did not differ significantly" in outcome["description"]
+ assert len(outcome["participating_taxa"]) == 13
+ assert len(rows[0]["removed_node_decisions"]) == len(rows[0]["removed_edge_decisions"]) == 2
+
+
+def test_syncom_y_preserves_reciprocal_biofilm_growth_not_just_total_biomass():
+ _, _, docs = records()
+ biofilm, outcome, _, _ = docs[1]["ecological_interactions"]
+ assert biofilm["interaction_type"] == "MUTUALISM"
+ assert "cell-equivalent abundance of both strains" in biofilm["description"]
+ assert "WB abundance did not increase in the planktonic fraction" in biofilm["description"]
+ assert "growth of both strains" in biofilm["evidence"][1]["snippet"]
+ assert "interaction_type" not in outcome and "biological_processes" not in outcome
+ assert "18.33%" in outcome["description"] and "79.13%" in outcome["description"]
+ assert biofilm["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+
+
+def test_syncom_y_positive_additions_are_not_direct_transfer():
+ _, _, docs = records()
+ forward = docs[1]["ecological_interactions"][2]
+ assert "not direct donor-to-recipient transfer" in forward["description"]
+ assert "Malate and guanosine were also included" in forward["description"]
+ assert all(e["supports"] == "PARTIAL" for e in forward["evidence"])
+ assert forward["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+
+
+def test_syncom_y_reverse_additions_were_negative_not_untested():
+ _, _, docs = records()
+ reverse = docs[1]["ecological_interactions"][3]
+ assert "did not significantly enhance" in reverse["description"]
+ assert "does not prove that exchange is absent" in reverse["description"]
+ result = reverse["evidence"][1]
+ assert result["evidence_source"] == "IN_VITRO" and result["supports"] == "PARTIAL"
+ assert "did not result in a significant enhancement" in result["snippet"]
+
+
+def test_syncom_y_model_inputs_and_versions_are_not_invented():
+ _, _, docs = records()
+ predictions = docs[1]["ecological_interactions"][2:]
+ for n in predictions:
+ e = next(e for e in n["evidence"] if e["evidence_source"] == "COMPUTATIONAL")
+ p = e["computational_provenance"]
+ assert e["supports"] == "PARTIAL" and p["prediction_type"] == "FLUX_BALANCE_ANALYSIS"
+ assert "input_accession" not in p
+ assert all("tool_version" not in tool for tool in p["tools"])
+ assert [t["tool_name"] for t in p["tools"]] == [
+ "CarveMe",
+ "COBRA Toolbox",
+ "Flux Balance Analysis (FBA)",
+ ]
+ assert "RNA-seq, not verified genome inputs" in p["parameters"]
+
+
+def test_azotobacter_growth_mutualism_is_distinct_from_phb_endpoint():
+ _, _, docs = records()
+ carbon, nitrogen, outcome = docs[2]["ecological_interactions"]
+ assert carbon["interaction_type"] == "CROSS_FEEDING"
+ assert nitrogen["interaction_type"] == "MUTUALISM"
+ assert "neither member grows alone" in nitrogen["description"]
+ assert (
+ "not a claimed donor-to-recipient transfer product" in nitrogen["metabolites"][0]["notes"]
+ )
+ assert "interaction_type" not in outcome and "biological_processes" not in outcome
+ assert outcome["scope"] == "COMMUNITY_LEVEL" and len(outcome["evidence"]) == 1
+ assert "potential product, not demonstrated production" in outcome["description"]
+ assert all(
+ n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ for n in [carbon, nitrogen]
+ )
+
+
+def test_bacillus168_does_not_inherit_3610_or_other_partner_persistence():
+ _, rows, docs = records()
+ carbon, growth = docs[3]["ecological_interactions"]
+ assert carbon["target_taxon"]["preferred_term"] == "Bacillus subtilis 168"
+ assert "3610" in carbon["description"] and "PARTIAL" in growth["description"]
+ assert not growth.get("downstream") and "interaction_type" not in growth
+ assert "does not establish weeks-to-months persistence" in growth["description"]
+ assert "B. subtilis 168 produces alpha-amylase" in growth["evidence"][1]["snippet"]
+ assert (
+ rows[3]["removed_node_decisions"][0]["node"]
+ == "Sucrose-Dependent Long-Term Consortium Stabilization"
+ )
+
+
+def test_ecoli_early_growth_is_not_sucrose_exclusive_or_a_concentration():
+ _, _, docs = records()
+ carbon, growth, reverse = docs[4]["ecological_interactions"]
+ assert "concentration" not in carbon["metabolites"][0]
+ assert "independently of induced sucrose export" in carbon["description"]
+ assert "more than two weeks" in growth["evidence"][0]["snippet"]
+ assert "interaction_type" not in growth
+ assert reverse["interaction_type"] == "MUTUALISM"
+ assert growth["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+
+
+def test_yeast_parental_control_persistence_and_product_boundaries_remain():
+ _, _, docs = records()
+ carbon, growth, reverse = docs[5]["ecological_interactions"]
+ assert carbon["target_taxon"]["preferred_term"] == "Saccharomyces cerevisiae W303Clump"
+ assert "more than two months" in growth["description"]
+ assert "two-month duration is not assigned to that diurnal assay" in growth["description"]
+ assert "Parental W303 did not grow" in growth["description"]
+ assert "does not demonstrate a bioproduct" in growth["description"]
+ assert "interaction_type" not in growth and reverse["interaction_type"] == "MUTUALISM"
+ assert "HYPOTHESIZED/PARTIAL" in growth["downstream"][0]["description"]
+
+
+def test_all_original_nodes_and_edges_have_dispositions_without_extensions():
+ ledger, rows, docs = records()
+ assert ledger["reviewed_counts"] == {
+ "retained_nodes": 16,
+ "removed_nodes": 3,
+ "retained_arrows": 9,
+ "removed_arrows": 3,
+ "renamed_nodes": 3,
+ "graph_quotations": 28,
+ "discussion_quotations": 6,
+ }
+ assert sum(len(r["edges_before"]) for r in rows) == 12
+ assert sum(len(d["ecological_interactions"]) for d in docs) == 16
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert ledger["unresolved_non_graph_issues"] == [1855]
+ assert ledger["issues"] == [1849, 1850, 1851, 1852, 1853, 1854]
+
+
+def test_hashes_histories_and_canonical_identity_only_scope_are_explicit():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ for row, doc in zip(rows, docs, strict=True):
+ assert row["status"] == "reviewed"
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert set(row["allowed_changed_fields"]) == {
+ "ecological_interactions",
+ "discussions",
+ "curation_history",
+ }
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).exists()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ canonical = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for n in doc["ecological_interactions"]:
+ assert all(e["target"] in names for e in n.get("downstream", []))
+ assert all(
+ t in canonical and set(t) == {"preferred_term", "term"}
+ for t in n.get("participating_taxa", [])
+ )
+
+
+def test_measured_scope_change_adds_no_solely_credited_taxa():
+ survey = runpy.run_path(str(ROOT / "tests/test_community_level_connectivity_credit.py"))[
+ "_survey"
+ ]()
+ assert survey == {
+ "records": 460,
+ "with_community_level": 407,
+ "mixed": 132,
+ "community_level_only": 275,
+ "taxa": 1552,
+ "credited_solely_by_the_rule": 1270,
+ }
diff --git a/tests/test_community_level_connectivity_credit.py b/tests/test_community_level_connectivity_credit.py
index 02463490e..261287157 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -106,7 +106,8 @@ def test_most_records_carry_a_community_level_interaction(survey):
# Census: 399 -> 402; exactly named participants, no extra solely-credited taxa.
# #1786 re-scopes Atacama's six-member subset as a community profile (402 -> 403).
# #1799 separates the Shewanella current endpoint from reverse cross-feeding (403 -> 404).
- assert 130 <= survey["with_community_level"] <= 404, survey
+ # #1851-#1854 separate four phenotype endpoints (403 -> 407); no new solely-credited taxa.
+ assert 130 <= survey["with_community_level"] <= 407, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
@@ -122,7 +123,8 @@ def test_the_mixed_records_are_where_the_coarseness_bites(survey):
coarse — there is no pairwise edge it could be masking.
"""
# #1772-#1774 change the mixed-record census from 125 to 128.
- assert 35 <= survey["mixed"] <= 128, survey
+ # #1851-#1854 add four mixed-scope records; batch109 pins the exact measured census.
+ assert 35 <= survey["mixed"] <= 132, survey
assert survey["mixed"] + survey["community_level_only"] == survey["with_community_level"]
diff --git a/tests/test_datamodel.py b/tests/test_datamodel.py
index 89e306e50..2cdaa15b8 100644
--- a/tests/test_datamodel.py
+++ b/tests/test_datamodel.py
@@ -41,21 +41,28 @@ def test_load_synechococcus_ecoli():
# Check first interaction
interaction1 = community["ecological_interactions"][0]
- assert interaction1["name"] == "CO2 Fixation and Sucrose Production"
+ assert interaction1["name"] == "Photosynthetic carbon supply to E. coli"
assert interaction1["interaction_type"] == "CROSS_FEEDING"
+ assert interaction1["scope"] == "PAIRWISE"
+ assert interaction1["source_taxon"]["term"]["id"] == "NCBITaxon:32046"
+ assert interaction1["target_taxon"]["term"]["id"] == "NCBITaxon:562"
assert len(interaction1["metabolites"]) == 1
assert interaction1["metabolites"][0]["term"]["id"] == "CHEBI:17992" # sucrose
# Verify downstream edges
assert len(interaction1["downstream"]) == 1
- assert interaction1["downstream"][0]["target"] == "Sucrose Uptake and Heterotrophic Growth"
-
- # Verify evidence
- assert len(interaction1["evidence"]) == 1
- evidence = interaction1["evidence"][0]
- assert evidence["reference"] == "PMID:28127397"
- assert evidence["supports"] == "SUPPORT"
- assert evidence["evidence_source"] == "IN_VITRO"
+ target = interaction1["downstream"][0]["target"]
+ assert target == "E. coli growth on cyanobacterial photosynthate"
+ assert sum(n["name"] == target for n in community["ecological_interactions"]) == 1
+ assert "PARTIAL for sucrose-specific mediation" in interaction1["downstream"][0]["description"]
+
+ # Export capacity does not establish sucrose as the sole early-growth substrate.
+ assert len(interaction1["evidence"]) == 2
+ assert [e["supports"] for e in interaction1["evidence"]] == ["SUPPORT", "PARTIAL"]
+ for evidence in interaction1["evidence"]:
+ assert evidence["reference"] == "PMID:28127397"
+ assert evidence["evidence_source"] == "IN_VITRO"
+ assert "other metabolites" in interaction1["evidence"][1]["snippet"]
# Verify environmental factors (3)
assert len(community["environmental_factors"]) == 3
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index b6f17b353..23966d9b9 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -419,8 +419,13 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml",
"SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml",
"SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
+ "SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml",
+ "Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml",
+ "Synechococcus_Bacillus_SPC.yaml",
+ "Synechococcus_Ecoli_SPC.yaml",
"Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",
"Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml",
+ "Synechococcus_Saccharomyces_SPC.yaml",
"Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml",
"Syntrophobacter_Methanobacterium_Syntrophy.yaml",
"Syntrophobacter_Methanospirillum_Syntrophy.yaml",