From 9abb5182671999ba7e176c5960ff17292487518a Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Tue, 6 Oct 2026 03:26:08 -0700
Subject: [PATCH] Bound electrosynthetic, algal and gut causal claims
---
...la_Clostridium_Acetobacterium_Acetate.html | 131 ++-
...iania_Phaeobacter_Dynamic_Interaction.html | 168 ++--
...ut_Amino_Acid_CrossFeeding_Consortium.html | 185 ++++-
.../2026-10-06T101622Z-codex-3da2ef.yaml | 27 +
.../2026-10-06T101622Z-codex-837390.yaml | 28 +
.../2026-10-06T101622Z-codex-ebe0ca.yaml | 27 +
...la_Clostridium_Acetobacterium_Acetate.yaml | 127 ++-
...iania_Phaeobacter_Dynamic_Interaction.yaml | 124 ++-
...ut_Amino_Acid_CrossFeeding_Consortium.yaml | 155 +++-
.../adversarial-review-20261006-batch40.yaml | 168 ++++
.../20261006-three-records-batch40.yaml | 281 +++++++
reports/causal_graph_review/inventory.tsv | 6 +-
reports/causal_graph_review/summary.json | 6 +-
.../validation-20261006-batch40.json | 766 ++++++++++++++++++
tests/test_causal_review_batch40.py | 138 ++++
tests/test_participating_taxa.py | 2 +
16 files changed, 2124 insertions(+), 215 deletions(-)
create mode 100644 history/records/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate/2026-10-06T101622Z-codex-3da2ef.yaml
create mode 100644 history/records/Emiliania_Phaeobacter_Dynamic_Interaction/2026-10-06T101622Z-codex-837390.yaml
create mode 100644 history/records/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium/2026-10-06T101622Z-codex-ebe0ca.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261006-batch40.yaml
create mode 100644 reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
create mode 100644 reports/causal_graph_review/validation-20261006-batch40.json
create mode 100644 tests/test_causal_review_batch40.py
diff --git a/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html b/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
index 2068e3b5d..1dbe70618 100644
--- a/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
+++ b/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
@@ -610,7 +610,7 @@ Ecological Interactions
Ecological interaction network for Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate
- 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 (syntrophy).
+ 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.
@@ -618,8 +618,8 @@
Ecological Interactions
@@ -627,10 +627,9 @@ Ecological Interactions
-
In the S. oneidensis-C. aceticum consortium, direct interspecies electron transfer (DIET) mediated by cytochrome c and riboflavin dominates at the biofilm-electrode interface, driving CO2-to-acetate conversion.
+
PARTIAL: In the C. aceticum-S. oneidensis pair, biofilm-associated electron transfer is supported by compartment-removal responses, electrochemical and spectroscopic readouts, and riboflavin add-back. The authors call this DIET, but these assays do not uniquely establish contact-only transfer or selective cytochrome necessity; riboflavin is also a diffusible mediator. The canonical target label Andreesenella acetica preserves the source organism called C. aceticum. Product enhancement does not demonstrate obligatory syntrophy.
Source Taxon: Shewanella oneidensis MR-1
@@ -658,8 +657,7 @@
DIET from S. oneidensis to C. aceticum
→ Enhanced CO2-to-Acetate Conversion
-
Biofilm-localized DIET in the S. oneidensis-C. aceticum consortium contributes electron flow for enhanced CO2-to-acetate electrosynthesis.
-
+
PARTIAL: Biofilm-associated electron supply and riboflavin-responsive transfer can support the C. aceticum pair's acetate increase. Compartment removal and add-back support this contribution, but do not isolate the necessity of contact-only DIET or a specific cytochrome. This arrow concerns the CS pair, not a simultaneous three-member culture.
Evidence
PMID:41236292
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"DIET via cytochrome c and riboflavin dominates at the biofilm-electrode interface in S. oneidensis-C. aceticum consortia"
+
+
+
+ "metabolite profiling (H2, formate, riboflavin), biomass distribution and fhs gene copy numbers, and functional prediction"
+
+
+
-
In the S. oneidensis-A. woodii consortium, interspecies electron transfer proceeds via H2/formate shuttling in the planktonic phase rather than direct contact, supporting acetate production.
+
PARTIAL: The A. woodii-S. oneidensis pair favors suspension-associated acetate synthesis, consistent with a diffusible hydrogen/formate electron-transfer model. These culture-level profiles and compartment interventions do not trace donor-resolved transfer or establish an exclusive route; hydrogen was detected in both alternative pairs. Daily apparent biofilm/suspension contributions are instantaneous responses to cell removal, not cumulative mass-balanced flux fractions, and may exceed 100% through compensatory responses.
Source Taxon: Shewanella oneidensis MR-1
@@ -723,8 +733,7 @@
H2/formate-mediated IET from S. oneidensis to A. woodii
→ Enhanced CO2-to-Acetate Conversion
-
H2/formate-mediated electron transfer in the S. oneidensis-A. woodii consortium contributes planktonic electron flow for enhanced CO2-to-acetate electrosynthesis.
-
+
PARTIAL: Diffusible reducing equivalents are a supported explanation for suspension-associated acetate synthesis in the AS pair, including acetate production where A. woodii alone failed at the tested lower cell voltage. This does not establish exclusive hydrogen/formate mediation or identify the molecular donor flux.
Evidence
PMID:41236292
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"whereas S. oneidensis-A. woodii consortia prefer H2/formate-mediated IET in the planktonic phase"
+
+
+
+ "failed to produce acetate"
+
+
+
@@ -754,13 +776,21 @@ Evidence
-
Co-cultivation of Shewanella oneidensis MR-1 with either electroactive Clostridium aceticum or nonelectroactive Acetobacterium woodii boosts acetate production by linking spatially organized interspecies electron transfer to CO2 reduction.
-
+
Two alternative two-member consortia, not one three-member community, increased acetate accumulation relative to their corresponding acetogen monocultures. At 0.88-V applied cell voltage, AS reached 1.16 g/L versus 0.62 g/L for A. woodii alone, and CS reached 1.05 g/L versus 0.56 g/L for C. aceticum alone. The participating taxa are the combined comparison roster; the acetogens were alternatives. Open-circuit cultures used H2/CO2 whereas driven cultures used N2/CO2, so that contrast is not voltage-only. Aggregate production does not prove reciprocal fitness or obligate syntrophy.
+
+
+
+
Participating Taxa:
+ Shewanella oneidensis MR-1,
+ Clostridium aceticum (electroactive acetogen),
+
+ Acetobacterium woodii (nonelectroactive acetogen)
+
+
@@ -815,13 +845,26 @@
Evidence
PMID:41236292
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"orchestrating electron flow to optimize CO2-to-acetate conversion"
+
+
+
+ "representing a 1.87‐fold of A. woodii alone"
+
+
+
@@ -831,6 +874,25 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which electron-transfer routes are necessary within each alternative pair?
+
+
Keep the two measured alternative pairs separate. Spectroscopy, electrochemistry, metabolite profiles, riboflavin add-back and daily planktonic-cell removal support compartment-associated models but do not isolate contact-only DIET or donor-resolved hydrogen/formate flux. Riboflavin is a diffusible mediator; hydrogen appears in both systems. Instantaneous apparent compartment contributions can exceed 100% and are not cumulative flux partitions. Main Methods describe DNA/16S, fhs copies and normalized gene abundance; do not call these transcript measurements without reviewing the unread supplement. The proposed acetate-formate recycling and future three-member consortium are hypotheses, not new measured causal nodes. Preserve canonical taxonomy and leave non-graph role, voltage and control wording to #1455.
+
+
Attaches to: ecological_interactions#Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair, ecological_interactions#Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair, ecological_interactions#Enhanced CO2-to-Acetate Conversion
+
+
+
+
+
@@ -1007,7 +1069,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1016,11 +1078,11 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "DIET from S. oneidensis to C. aceticum",
+ label: "Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1045,7 +1107,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1056,11 +1118,11 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "H2/formate-mediated IET from S. oneidensis to A. woodii",
+ label: "Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1085,7 +1147,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1100,7 +1162,7 @@ Evidence
processes.push("carbon fixation");
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1115,6 +1177,21 @@ Evidence
+ var participantKeys = [
+
+ "Shewanella oneidensis MR-1",
+
+ "Clostridium aceticum (electroactive acetogen)",
+
+ "Acetobacterium woodii (nonelectroactive acetogen)"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html b/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html
index 938ea3c22..fdced5992 100644
--- a/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html
+++ b/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html
@@ -563,7 +563,7 @@ Ecological Interactions
Ecological interaction network for Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction
- 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).
@@ -574,11 +574,6 @@
Ecological Interactions
aria-hidden="true" data-symbol="symbolDiamond"
data-color="#57c7ab"> Cross-feeding
-
-
Ecological Interactions
Algal Nutrient Provisioning Supports Bacterial Growth
CROSS_FEEDING
-
E. huxleyi enables growth of P. inhibens in L1-Si medium, which is otherwise non-permissive for the bacterium, by supplying suitable forms of essential nutrients.
+
E. huxleyi CCMP3266 supports P. inhibens DSM 17395 growth in otherwise nonpermissive L1-Si medium. Nutrient-rescue comparisons support algal supply of usable nutrient forms; DMSP can contribute sulfur but did not alone provide an adequate carbon supply in the tested context. Bacterial growth was monitored as colony-forming units, which may represent rosettes rather than single cells. Nutrient support does not by itself demonstrate a causal step from general biomass increase to the specific tryptophan/IAA response.
Source Taxon: Emiliania huxleyi CCMP3266
@@ -606,33 +601,25 @@
Algal Nutrient Provisioning Supports Bacterial Growth
-
Biological Processes:
-
-
-
Downstream Effects:
+
Evidence
+
-
-
→ Tryptophan-Enhanced Bacterial Attachment And IAA Production
-
Algal nutrient provisioning sustains P. inhibens growth in the non-permissive L1-Si medium, putting the heterotroph in the phycosphere where algal tryptophan stimulates attachment and IAA production.
-
+
-
+ PMID:27855786
+ - SUPPORT (IN_VITRO)
+
+
"E. huxleyi can provide all four essential nutrients"
-
Evidence
-
+
@@ -643,7 +630,7 @@
Evidence
- SUPPORT (IN_VITRO)
- "E. huxleyi can provide all four essential nutrients"
+ "CFU may include rosettes as well as individual bacteria"
@@ -654,9 +641,8 @@ Evidence
-
Tryptophan exuded from algal cells increases P. inhibens attachment and bacterial production of indole-3-acetic acid, linking algal exudates to bacterial behavior and hormone production.
+
Algal exudates supported tryptophan-auxotroph growth, establishing bioavailable tryptophan. In separate bacterial cultures, added tryptophan increased IAA production and isotope labeling demonstrated conversion of the added precursor into IAA. Added tryptophan also increased bacterial attachment in coculture, particularly to naked algal cells. These assays do not trace the complete endogenous algal-to-bacterial-to-algal flux or measure de novo tryptophan biosynthesis in the recipient. The E. coli auxotroph is an assay reporter, not a community member.
Source Taxon: Emiliania huxleyi CCMP3266
@@ -681,25 +667,14 @@
Tryptophan-Enhanced Bacterial Attachment And IAA Production
-
Biological Processes:
-
-
-
- tryptophan biosynthetic process
- (GO:0000162 )
-
-
-
-
Downstream Effects:
-
→ IAA-Mediated Algal Growth Promotion And Killing
-
Algal tryptophan stimulates P. inhibens indole-3-acetic acid production, and that bacterially produced IAA drives the downstream algal growth-promotion and killing response.
+
→ Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+
HYPOTHESIZED: Tryptophan-enhanced IAA production could contribute to initial algal promotion and late killing. Added tryptophan accelerated coculture bleaching, but also changed attachment; bulk coculture IAA was undetectable and pathway mutants retained production. The experiment therefore does not isolate IAA mediation or show that measured bacterial IAA reached the exogenous toxic dose.
@@ -722,16 +697,41 @@
Evidence
+
+
+
+ "all produced IAA is fully labeled"
+
+
+
+
+
+
+ "This indicates that algal exudates contain bioavailable tryptophan"
+
+
+
-
P. inhibens affects E. huxleyi physiology through indole-3-acetic acid, initially promoting algal growth but ultimately contributing to algal death in aging co-cultures.
+
P. inhibens coculture initially increased algal yield, followed by late bleaching and increased algal death. Day-17 Sytox staining was reported as 94% dead in coculture versus 21% in axenic algae; day-20 TUNEL labeling showed more fragmented DNA. HYPOTHESIZED: IAA mediates both phases. Added IAA promoted growth at 1 and 100 micromolar but was harmful at 1000 micromolar; these are not measured coculture exposures. IAA was undetectable in coculture, and tested pathway mutants still produced IAA and bleached algae. The experiments do not establish IAA necessity, nutrient-consuming predation, a unique death pathway or natural-bloom termination.
Source Taxon: Phaeobacter inhibens DSM 17395
@@ -765,13 +765,52 @@
Evidence
PMID:27855786
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid"
+
+
+
+ "in these conditions IAA was undetectable"
+
+
+
+
+
+
+ "these mutants were still capable of producing IAA"
+
+
+
+
+
+
+ "while in the pure culture only 21% are dead by day 17"
+
+
+
@@ -816,6 +855,25 @@ Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Is endogenous IAA necessary for algal promotion and late killing in this coculture?
+
+
The main text explicitly hypothesizes IAA mediation despite categorical abstract wording. Bulk coculture IAA was undetectable, exogenous micromolar dose responses are not measured local exposure, and pathway mutants retained IAA and bleaching. Labeled precursor conversion in bacterial culture plus exudate auxotroph rescue does not trace the complete endogenous loop. Tryptophan addition is pleiotropic and changes attachment. Remove the nutrient-provisioning workflow arrow rather than infer a selective route. Roseobacticide activity against CCMP372 cannot be assigned to CCMP3266; neither that comparator nor the E. coli reporter is a community member. Death staining and expression associations do not uniquely establish a death pathway or global bloom effects. Preserve nonpermissive-medium guidance and original YAML aliases; non-graph claims remain #1456.
+
+
Attaches to: ecological_interactions#Algal Nutrient Provisioning Supports Bacterial Growth, ecological_interactions#Tryptophan-Enhanced Bacterial Attachment And IAA Production, ecological_interactions#Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+
+
+
+
+
@@ -1047,11 +1105,7 @@ Evidence
var processes = [];
-
- processes.push("photosynthesis");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1080,7 +1134,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1091,11 +1145,7 @@ Evidence
var processes = [];
-
- processes.push("tryptophan biosynthetic process");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1124,7 +1174,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "PREDATION";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1133,11 +1183,11 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 4;
nodes.push({
id: intId,
- label: "IAA-Mediated Algal Growth Promotion And Killing",
+ label: "Algal Growth Promotion and Late Killing with Proposed IAA Mediation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html b/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html
index 2221002af..6fb1abf35 100644
--- a/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html
+++ b/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html
@@ -647,7 +647,7 @@ Ecological Interactions
Ecological interaction network for Engineered Gut Amino Acid Cross-Feeding 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).
@@ -660,8 +660,8 @@
Ecological Interactions
@@ -672,11 +672,23 @@ Ecological Interactions
Engineered Amino Acid Cross-Feeding
CROSS_FEEDING
- Each engineered strain was made auxotrophic for amino acids while overproducing one amino acid, creating reciprocal nutritional dependencies that supported growth without external addition of the cross-fed amino acids.
+ Engineered auxotrophy and amino acid overproduction supported consortium growth without external addition of the designated cross-fed amino acids. LC-MS production measurements and supernatant-rescue assays show unequal capacities, not complete measured all-to-all transfer. B. fragilis was not rescued by the tested overproducer supernatants although it grew in coculture. These observations support community-level nutritional dependence without identifying a dedicated transporter or proving all partner-specific fluxes. Canonical participants describe the studied four-member consortium.
+ Participating Taxa:
+
+ Escherichia coli,
+
+ Salmonella enterica serovar Typhimurium,
+
+ Bacteroides thetaiotaomicron,
+
+ Bacteroides fragilis
+
+
+
Metabolites:
@@ -698,12 +710,6 @@
Engineered Amino Acid Cross-Feeding
class="term-link" target="_blank" rel="noopener noreferrer">GO:0008652)
-
- amino acid transport
- (GO:0006865 )
-
-
@@ -713,8 +719,7 @@ Engineered Amino Acid Cross-Feeding
→ Beneficial Interaction Shift
-
Engineered auxotrophy and amino acid overproduction created positive nutritional dependencies that shifted the consortium away from antagonism.
-
+
PARTIAL: The combined dependency/overproduction intervention introduced nutritional support and changed the in-vitro growth trajectories used to infer interaction structure. Unequal rescue and remaining negative-interaction uncertainty prevent interpreting this as a measured fully mutualistic all-to-all network.
@@ -750,6 +755,19 @@ Evidence
+
+
+
+ "B. fragilis growth was not rescued by any of the strains"
+
+
+
@@ -757,12 +775,23 @@ Evidence
-
Engineered amino acid exchange alleviated antagonistic interactions and added beneficial interactions to the four-species consortium.
+
A Bayesian dynamical model fitted to in-vitro strain-specific qPCR growth trajectories inferred two positive effects from B. fragilis toward E. coli and S. Typhimurium, with weaker evidence for several negative interactions than in the WT consortium. These are model-inferred net effects under inoculum perturbations, not direct molecular exchange measurements or proof that antagonism vanished. They do not establish reciprocal benefit among every member or identify the same interaction network in vivo.
+
+
+
+
Participating Taxa:
+ Escherichia coli,
+ Salmonella enterica serovar Typhimurium,
+
+ Bacteroides thetaiotaomicron,
+
+ Bacteroides fragilis
+
+
@@ -786,8 +815,7 @@
Beneficial Interaction Shift
→ Cross-Feeding Increased Population Evenness
-
The engineered shift from antagonistic to beneficial interactions drove the more even four-strain population structure measured in vitro and in the low-protein mouse gut.
-
+
PARTIAL: Engineered nutritional dependencies and altered inferred net interactions are consistent with the greater evenness observed in separate in-vitro endpoint assays. The interaction-shift node was not selectively perturbed to establish mediation. Extension of this pathway to the day-10 mouse-gut endpoint is HYPOTHESIZED; in-vitro network inference does not measure in-vivo exchange.
Evidence
doi:10.1128/mSystems.00352-19
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions"
+
+
+
+ "although some inferred negative interactions are still present"
+
+
+
@@ -817,12 +858,23 @@ Evidence
-
Engineered cross-feeding increased population evenness in anaerobic batch culture and in the gnotobiotic mouse gut, especially under low amino acid or low-protein conditions.
+
The engineered four-member consortium had higher Pielou evenness in anaerobic endpoint cultures, especially without supplemented cross-fed amino acids, despite lower overall growth in the unsupplemented in-vitro setting. In gnotobiotic mice, day-10 fecal strain-specific DNA-qPCR supported greater evenness for the engineered consortium on the low-protein diet; the standard-diet trend was not statistically significant. This is a composition endpoint, not longitudinal stability, a conventional microbiome or a host-health benefit. The assay does not directly measure amino-acid flux in the gut.
+
+
+
Participating Taxa:
+ Escherichia coli,
+
+ Salmonella enterica serovar Typhimurium,
+
+ Bacteroides thetaiotaomicron,
+
+ Bacteroides fragilis
+
+
@@ -869,6 +921,19 @@
Evidence
+
+
+
+ "although this trend was not statistically significant"
+
+
+
Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which nutritional interactions mediate the diet-dependent mouse-gut evenness endpoint?
+
+
Keep unequal supernatant rescue distinct from community growth. The Bayesian model used in-vitro qPCR time series with inoculum perturbations; its net interaction edges do not identify molecular flux or prove an all-to-all mutualistic network. Higher-order effects were not supported by those data, not biologically excluded. Separate the 27-hour trajectory assays from 24-hour supplementation endpoints and day-10 fecal DNA-qPCR. Low-protein diet changes more than a single measured amino-acid flux, and the standard-diet evenness trend was nonsignificant. Do not extrapolate to longitudinal stability, conventional microbiota or clinical benefit. Canonical B. fragilis AMBIGUOUS grounding is preserved, not resolved. Non-graph cache-access wording remains #1457; cache pointer/casing issues remain #1094/#1091. No new genetic engineering procedures or pairwise mechanisms are added.
+
+
Attaches to: ecological_interactions#Engineered Amino Acid Cross-Feeding, ecological_interactions#Beneficial Interaction Shift, ecological_interactions#Cross-Feeding Increased Population Evenness
+
+
+
+
+
@@ -1165,10 +1249,8 @@ Evidence
processes.push("cellular amino acid biosynthetic process");
- processes.push("amino acid transport");
-
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1183,11 +1265,28 @@ Evidence
+ var participantKeys = [
+
+ "Escherichia coli",
+
+ "Salmonella enterica serovar Typhimurium",
+
+ "Bacteroides thetaiotaomicron",
+
+ "Bacteroides fragilis"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:1";
- var intType = "MUTUALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1196,7 +1295,7 @@ Evidence
processes.push("interspecies interaction between organisms");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1211,11 +1310,28 @@ Evidence
+ var participantKeys = [
+
+ "Escherichia coli",
+
+ "Salmonella enterica serovar Typhimurium",
+
+ "Bacteroides thetaiotaomicron",
+
+ "Bacteroides fragilis"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:2";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1224,7 +1340,7 @@ Evidence
var processes = [];
- var evidenceCount = 2;
+ var evidenceCount = 3;
nodes.push({
id: intId,
@@ -1239,6 +1355,23 @@ Evidence
+ var participantKeys = [
+
+ "Escherichia coli",
+
+ "Salmonella enterica serovar Typhimurium",
+
+ "Bacteroides thetaiotaomicron",
+
+ "Bacteroides fragilis"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
diff --git a/history/records/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate/2026-10-06T101622Z-codex-3da2ef.yaml b/history/records/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate/2026-10-06T101622Z-codex-3da2ef.yaml
new file mode 100644
index 000000000..dab2fc555
--- /dev/null
+++ b/history/records/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate/2026-10-06T101622Z-codex-3da2ef.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml
+ slug: Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate
+session:
+ id: 2026-10-06T101622Z-codex-3da2ef
+ timestamp: '2026-10-06T10:16:22Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1452
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain biofilm-associated route as PARTIAL without contact-only DIET or syntrophy
+ proof.; Retain planktonic route as PARTIAL without exclusive or donor-resolved mediator
+ flux.; Retain acetate enhancement with the alternative-pair roster and explicit cell-voltage/control
+ boundaries.
+ details: Existing-node claim repairs only; no new causal structure. reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
diff --git a/history/records/Emiliania_Phaeobacter_Dynamic_Interaction/2026-10-06T101622Z-codex-837390.yaml b/history/records/Emiliania_Phaeobacter_Dynamic_Interaction/2026-10-06T101622Z-codex-837390.yaml
new file mode 100644
index 000000000..97db26ca3
--- /dev/null
+++ b/history/records/Emiliania_Phaeobacter_Dynamic_Interaction/2026-10-06T101622Z-codex-837390.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml
+ slug: Emiliania_Phaeobacter_Dynamic_Interaction
+session:
+ id: 2026-10-06T101622Z-codex-837390
+ timestamp: '2026-10-06T10:16:22Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1453
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain nutrient-supported growth without a generic-to-specific workflow arrow or
+ direct photosynthesis-flux claim.; Retain precursor availability, added-tryptophan conversion
+ and attachment responses without a complete traced endogenous loop.; Retain observed promotion
+ and late death with HYPOTHESIZED IAA mediation, not categorical predation or unique death
+ mechanism.
+ details: Existing-node claim repairs only; no new causal structure. reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
diff --git a/history/records/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium/2026-10-06T101622Z-codex-ebe0ca.yaml b/history/records/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium/2026-10-06T101622Z-codex-ebe0ca.yaml
new file mode 100644
index 000000000..8edebdac3
--- /dev/null
+++ b/history/records/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium/2026-10-06T101622Z-codex-ebe0ca.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml
+ slug: Engineered_Gut_Amino_Acid_CrossFeeding_Consortium
+session:
+ id: 2026-10-06T101622Z-codex-ebe0ca
+ timestamp: '2026-10-06T10:16:22Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1454
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain measured nutritional dependence without complete reciprocal rescue or transporter-specific
+ annotation.; Retain in-vitro model-inferred interaction shift without universal mutualism
+ or absence-of-antagonism claims.; Retain condition-specific evenness endpoints without
+ established in-vivo mediation, stability or host benefit.
+ details: Existing-node claim repairs only; no new causal structure. reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
diff --git a/kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml b/kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml
index c928226e4..8c09968a7 100644
--- a/kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml
+++ b/kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml
@@ -106,11 +106,12 @@ taxonomy:
acetogen)
explanation: Identifies A. woodii as the nonelectroactive acetogen partner of the consortium.
ecological_interactions:
-- name: DIET from S. oneidensis to C. aceticum
- description: In the S. oneidensis-C. aceticum consortium, direct interspecies electron transfer (DIET)
- mediated by cytochrome c and riboflavin dominates at the biofilm-electrode interface, driving
- CO2-to-acetate conversion.
- interaction_type: SYNTROPHY
+- name: Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair
+ description: 'PARTIAL: In the C. aceticum-S. oneidensis pair, biofilm-associated electron transfer is supported
+ by compartment-removal responses, electrochemical and spectroscopic readouts, and riboflavin add-back. The authors
+ call this DIET, but these assays do not uniquely establish contact-only transfer or selective cytochrome necessity;
+ riboflavin is also a diffusible mediator. The canonical target label Andreesenella acetica preserves the source
+ organism called C. aceticum. Product enhancement does not demonstrate obligatory syntrophy.'
scope: PAIRWISE
source_taxon:
preferred_term: Shewanella oneidensis MR-1
@@ -129,22 +130,30 @@ ecological_interactions:
label: riboflavin
downstream:
- target: Enhanced CO2-to-Acetate Conversion
- description: >
- Biofilm-localized DIET in the S. oneidensis-C. aceticum consortium
- contributes electron flow for enhanced CO2-to-acetate electrosynthesis.
+ description: 'PARTIAL: Biofilm-associated electron supply and riboflavin-responsive transfer can support the
+ C. aceticum pair''s acetate increase. Compartment removal and add-back support this contribution, but do not
+ isolate the necessity of contact-only DIET or a specific cytochrome. This arrow concerns the CS pair, not
+ a simultaneous three-member culture.'
evidence:
+ - reference: PMID:41236292
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: DIET via cytochrome c and riboflavin dominates at the biofilm-electrode interface in S. oneidensis-C.
+ aceticum consortia
+ explanation: The abstract states the authors' route model; the reviewed main-body assays do not uniquely resolve
+ contact-only DIET.
- reference: PMID:41236292
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: DIET via cytochrome c and riboflavin dominates at the biofilm-electrode interface in S.
- oneidensis-C. aceticum consortia
- explanation: DIET (cytochrome c/riboflavin) as the electron-transfer mode of the S. oneidensis-C.
- aceticum consortium.
-- name: H2/formate-mediated IET from S. oneidensis to A. woodii
- description: In the S. oneidensis-A. woodii consortium, interspecies electron transfer proceeds via
- H2/formate shuttling in the planktonic phase rather than direct contact, supporting acetate
- production.
- interaction_type: SYNTROPHY
+ snippet: metabolite profiling (H2, formate, riboflavin), biomass distribution and fhs gene copy numbers, and
+ functional prediction
+ explanation: Identifies complementary readouts rather than a selective molecular-route perturbation.
+- name: Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair
+ description: 'PARTIAL: The A. woodii-S. oneidensis pair favors suspension-associated acetate synthesis, consistent
+ with a diffusible hydrogen/formate electron-transfer model. These culture-level profiles and compartment interventions
+ do not trace donor-resolved transfer or establish an exclusive route; hydrogen was detected in both alternative
+ pairs. Daily apparent biofilm/suspension contributions are instantaneous responses to cell removal, not cumulative
+ mass-balanced flux fractions, and may exceed 100% through compensatory responses.'
scope: PAIRWISE
source_taxon:
preferred_term: Shewanella oneidensis MR-1
@@ -167,25 +176,29 @@ ecological_interactions:
label: formate
downstream:
- target: Enhanced CO2-to-Acetate Conversion
- description: >
- H2/formate-mediated electron transfer in the S. oneidensis-A. woodii
- consortium contributes planktonic electron flow for enhanced
- CO2-to-acetate electrosynthesis.
+ description: 'PARTIAL: Diffusible reducing equivalents are a supported explanation for suspension-associated
+ acetate synthesis in the AS pair, including acetate production where A. woodii alone failed at the tested
+ lower cell voltage. This does not establish exclusive hydrogen/formate mediation or identify the molecular
+ donor flux.'
evidence:
+ - reference: PMID:41236292
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: whereas S. oneidensis-A. woodii consortia prefer H2/formate-mediated IET in the planktonic phase
+ explanation: States the authors' preferred route model, not a directly traced partner-to-partner flux.
- reference: PMID:41236292
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: whereas S. oneidensis-A. woodii consortia prefer H2/formate-mediated IET in the planktonic
- phase
- explanation: H2/formate-mediated IET as the electron-transfer mode of the S. oneidensis-A. woodii
- consortium.
+ snippet: failed to produce acetate
+ explanation: The 0.54-V A. woodii monoculture comparison supports assistance by the partner, without identifying
+ a unique transferred mediator.
- name: Enhanced CO2-to-Acetate Conversion
- description: >
- Co-cultivation of Shewanella oneidensis MR-1 with either electroactive
- Clostridium aceticum or nonelectroactive Acetobacterium woodii boosts
- acetate production by linking spatially organized interspecies electron
- transfer to CO2 reduction.
- interaction_type: SYNTROPHY
+ description: Two alternative two-member consortia, not one three-member community, increased acetate accumulation
+ relative to their corresponding acetogen monocultures. At 0.88-V applied cell voltage, AS reached 1.16 g/L versus
+ 0.62 g/L for A. woodii alone, and CS reached 1.05 g/L versus 0.56 g/L for C. aceticum alone. The participating
+ taxa are the combined comparison roster; the acetogens were alternatives. Open-circuit cultures used H2/CO2
+ whereas driven cultures used N2/CO2, so that contrast is not voltage-only. Aggregate production does not prove
+ reciprocal fitness or obligate syntrophy.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: carbon dioxide
@@ -208,12 +221,29 @@ ecological_interactions:
snippet: Co-cultivation markedly boosts acetate production by up to 88%
explanation: Supports enhanced acetate production in the Shewanella-acetogen consortia.
- reference: PMID:41236292
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: orchestrating electron flow to optimize CO2-to-acetate conversion
- explanation: >
- Supports Shewanella-mediated electron-flow organization as the mechanism
- that improves CO2-to-acetate conversion.
+ explanation: The source proposes organized electron flow as an explanation; output measurements do not uniquely
+ identify its molecular mediation.
+ - reference: PMID:41236292
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: representing a 1.87‐fold of A. woodii alone
+ explanation: Quantifies the AS pair-versus-monoculture contrast, not a joint three-member system.
+ participating_taxa:
+ - preferred_term: Shewanella oneidensis MR-1
+ term:
+ id: NCBITaxon:70863
+ label: Shewanella oneidensis
+ - preferred_term: Clostridium aceticum (electroactive acetogen)
+ term:
+ id: NCBITaxon:84022
+ label: Andreesenella acetica
+ - preferred_term: Acetobacterium woodii (nonelectroactive acetogen)
+ term:
+ id: NCBITaxon:33952
+ label: Acetobacterium woodii
growth_media:
- name: DSMZ-Medium 135 base medium (optimized, cathode chamber)
temperature: '37'
@@ -262,3 +292,30 @@ cultivation_setup:
evidence_source: IN_VITRO
snippet: Under an applied voltage of 0.88 V
explanation: Documents the applied voltage of the bioelectrochemical cultivation.
+discussions:
+- discussion_id: electrosynthetic_route_specificity_and_alternative_pairs
+ prompt: Which electron-transfer routes are necessary within each alternative pair?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair
+ - ecological_interactions#Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair
+ - ecological_interactions#Enhanced CO2-to-Acetate Conversion
+ rationale: 'Keep the two measured alternative pairs separate. Spectroscopy, electrochemistry, metabolite profiles,
+ riboflavin add-back and daily planktonic-cell removal support compartment-associated models but do not isolate
+ contact-only DIET or donor-resolved hydrogen/formate flux. Riboflavin is a diffusible mediator; hydrogen appears
+ in both systems. Instantaneous apparent compartment contributions can exceed 100% and are not cumulative flux
+ partitions. Main Methods describe DNA/16S, fhs copies and normalized gene abundance; do not call these transcript
+ measurements without reviewing the unread supplement. The proposed acetate-formate recycling and future three-member
+ consortium are hypotheses, not new measured causal nodes. Preserve canonical taxonomy and leave non-graph role,
+ voltage and control wording to #1455.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T10:16:21Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain biofilm-associated route as PARTIAL without contact-only DIET or syntrophy proof.; Retain planktonic
+ route as PARTIAL without exclusive or donor-resolved mediator flux.; Retain acetate enhancement with the alternative-pair
+ roster and explicit cell-voltage/control boundaries. Issue #1452; reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml b/kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml
index e7ddaff6f..be7669341 100644
--- a/kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml
+++ b/kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml
@@ -85,8 +85,11 @@ taxonomy:
explanation: Supports the bacterial strain identity in the co-culture.
ecological_interactions:
- name: Algal Nutrient Provisioning Supports Bacterial Growth
- description: E. huxleyi enables growth of P. inhibens in L1-Si medium, which is otherwise non-permissive
- for the bacterium, by supplying suitable forms of essential nutrients.
+ description: E. huxleyi CCMP3266 supports P. inhibens DSM 17395 growth in otherwise nonpermissive L1-Si medium.
+ Nutrient-rescue comparisons support algal supply of usable nutrient forms; DMSP can contribute sulfur but did
+ not alone provide an adequate carbon supply in the tested context. Bacterial growth was monitored as colony-forming
+ units, which may represent rosettes rather than single cells. Nutrient support does not by itself demonstrate
+ a causal step from general biomass increase to the specific tryptophan/IAA response.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -99,26 +102,24 @@ ecological_interactions:
term:
id: NCBITaxon:391619
label: Phaeobacter inhibens DSM 17395
- biological_processes:
- - preferred_term: photosynthesis
- term:
- id: GO:0015979
- label: photosynthesis
- downstream:
- - target: Tryptophan-Enhanced Bacterial Attachment And IAA Production
- description: Algal nutrient provisioning sustains P. inhibens growth in the
- non-permissive L1-Si medium, putting the heterotroph in the phycosphere
- where algal tryptophan stimulates attachment and IAA production.
evidence:
- reference: PMID:27855786
supports: SUPPORT
evidence_source: IN_VITRO
snippet: E. huxleyi can provide all four essential nutrients
explanation: Supports algal provisioning of nutrients needed for heterotrophic bacterial growth.
+ - reference: PMID:27855786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: CFU may include rosettes as well as individual bacteria
+ explanation: Limits CFU interpretation; a colony-forming unit need not equal one bacterium.
- name: Tryptophan-Enhanced Bacterial Attachment And IAA Production
- description: Tryptophan exuded from algal cells increases P. inhibens attachment and bacterial production
- of indole-3-acetic acid, linking algal exudates to bacterial behavior and hormone production.
- interaction_type: MUTUALISM
+ description: Algal exudates supported tryptophan-auxotroph growth, establishing bioavailable tryptophan. In separate
+ bacterial cultures, added tryptophan increased IAA production and isotope labeling demonstrated conversion of
+ the added precursor into IAA. Added tryptophan also increased bacterial attachment in coculture, particularly
+ to naked algal cells. These assays do not trace the complete endogenous algal-to-bacterial-to-algal flux or
+ measure de novo tryptophan biosynthesis in the recipient. The E. coli auxotroph is an assay reporter, not a
+ community member.
scope: PAIRWISE
source_taxon:
preferred_term: Emiliania huxleyi CCMP3266
@@ -139,27 +140,38 @@ ecological_interactions:
term:
id: CHEBI:16411
label: indole-3-acetic acid
- biological_processes:
- - preferred_term: tryptophan biosynthetic process
- term:
- id: GO:0000162
- label: L-tryptophan biosynthetic process
downstream:
- - target: IAA-Mediated Algal Growth Promotion And Killing
- description: Algal tryptophan stimulates P. inhibens indole-3-acetic acid
- production, and that bacterially produced IAA drives the downstream
- algal growth-promotion and killing response.
+ - target: Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ description: 'HYPOTHESIZED: Tryptophan-enhanced IAA production could contribute to initial algal promotion and
+ late killing. Added tryptophan accelerated coculture bleaching, but also changed attachment; bulk coculture
+ IAA was undetectable and pathway mutants retained production. The experiment therefore does not isolate IAA
+ mediation or show that measured bacterial IAA reached the exogenous toxic dose.'
evidence:
- reference: PMID:27855786
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased
- by tryptophan
- explanation: Supports tryptophan-stimulated bacterial IAA production and attachment.
-- name: IAA-Mediated Algal Growth Promotion And Killing
- description: P. inhibens affects E. huxleyi physiology through indole-3-acetic acid, initially promoting
- algal growth but ultimately contributing to algal death in aging co-cultures.
- interaction_type: PREDATION
+ snippet: Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by
+ tryptophan
+ explanation: Summarizes tryptophan responses; separate precursor-addition and exudate-bioavailability assays
+ must not be collapsed into a fully traced endogenous exchange.
+ - reference: PMID:27855786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: all produced IAA is fully labeled
+ explanation: Supports conversion of added labeled tryptophan in bacterial culture, not tracing of algal-derived
+ precursor through coculture.
+ - reference: PMID:27855786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: This indicates that algal exudates contain bioavailable tryptophan
+ explanation: Auxotroph growth supports precursor availability without quantifying endogenous IAA transfer.
+- name: Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ description: 'P. inhibens coculture initially increased algal yield, followed by late bleaching and increased
+ algal death. Day-17 Sytox staining was reported as 94% dead in coculture versus 21% in axenic algae; day-20
+ TUNEL labeling showed more fragmented DNA. HYPOTHESIZED: IAA mediates both phases. Added IAA promoted growth
+ at 1 and 100 micromolar but was harmful at 1000 micromolar; these are not measured coculture exposures. IAA
+ was undetectable in coculture, and tested pathway mutants still produced IAA and bleached algae. The experiments
+ do not establish IAA necessity, nutrient-consuming predation, a unique death pathway or natural-bloom termination.'
scope: PAIRWISE
source_taxon:
preferred_term: Phaeobacter inhibens DSM 17395
@@ -177,12 +189,28 @@ ecological_interactions:
id: CHEBI:16411
label: indole-3-acetic acid
evidence:
+ - reference: PMID:27855786
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic
+ acid
+ explanation: The abstract gives a strong IAA interpretation; main-body nondetection and non-null mutants leave
+ endogenous mediation unresolved.
- reference: PMID:27855786
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone
- indole-3-acetic acid
- explanation: Supports the dual growth-promoting and algicidal role of bacterial IAA.
+ snippet: in these conditions IAA was undetectable
+ explanation: The proposed local uptake/phycosphere accumulation was not a measured coculture exposure.
+ - reference: PMID:27855786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: these mutants were still capable of producing IAA
+ explanation: These mutants are not IAA-null necessity tests.
+ - reference: PMID:27855786
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: while in the pure culture only 21% are dead by day 17
+ explanation: The primary comparison supports a host-death effect beyond a metabolite-only interpretation.
cultivation_setup:
- cultivation_mode: BATCH
operating_temperature: 18.0
@@ -306,3 +334,31 @@ associated_datasets:
evidence_source: IN_VITRO
snippet: Dynamic metabolic exchange governs a marine algal-bacterial interaction
explanation: Links this record to the source article and article-hosted data.
+discussions:
+- discussion_id: emiliania_endogenous_iaa_mediation_and_assay_scope
+ prompt: Is endogenous IAA necessary for algal promotion and late killing in this coculture?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Algal Nutrient Provisioning Supports Bacterial Growth
+ - ecological_interactions#Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ - ecological_interactions#Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ rationale: 'The main text explicitly hypothesizes IAA mediation despite categorical abstract wording. Bulk coculture
+ IAA was undetectable, exogenous micromolar dose responses are not measured local exposure, and pathway mutants
+ retained IAA and bleaching. Labeled precursor conversion in bacterial culture plus exudate auxotroph rescue
+ does not trace the complete endogenous loop. Tryptophan addition is pleiotropic and changes attachment. Remove
+ the nutrient-provisioning workflow arrow rather than infer a selective route. Roseobacticide activity against
+ CCMP372 cannot be assigned to CCMP3266; neither that comparator nor the E. coli reporter is a community member.
+ Death staining and expression associations do not uniquely establish a death pathway or global bloom effects.
+ Preserve nonpermissive-medium guidance and original YAML aliases; non-graph claims remain #1456.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T10:16:21Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain nutrient-supported growth without a generic-to-specific workflow arrow or direct photosynthesis-flux
+ claim.; Retain precursor availability, added-tryptophan conversion and attachment responses without a complete
+ traced endogenous loop.; Retain observed promotion and late death with HYPOTHESIZED IAA mediation, not categorical
+ predation or unique death mechanism. Issue #1453; reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml b/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml
index 31cc021a2..8d0bd2e4a 100644
--- a/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml
+++ b/kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml
@@ -135,33 +135,29 @@ taxonomy:
explanation: Supports B. fragilis as a tracked member of the consortium.
ecological_interactions:
- name: Engineered Amino Acid Cross-Feeding
- description: Each engineered strain was made auxotrophic for amino acids while overproducing one amino
- acid, creating reciprocal nutritional dependencies that supported growth without external addition
- of the cross-fed amino acids.
- interaction_type: CROSS_FEEDING
+ description: Engineered auxotrophy and amino acid overproduction supported consortium growth without external
+ addition of the designated cross-fed amino acids. LC-MS production measurements and supernatant-rescue assays
+ show unequal capacities, not complete measured all-to-all transfer. B. fragilis was not rescued by the tested
+ overproducer supernatants although it grew in coculture. These observations support community-level nutritional
+ dependence without identifying a dedicated transporter or proving all partner-specific fluxes. Canonical participants
+ describe the studied four-member consortium.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: amino acid
term:
id: CHEBI:33709
label: amino acid
- notes: The engineered exchange class; the record intentionally does not assert unverified strain-specific
- amino acid identities.
+ notes: Generic exchanged amino-acid class, not a complete quantified partner-to-partner flux map.
biological_processes:
- preferred_term: cellular amino acid biosynthetic process
term:
id: GO:0008652
label: amino acid biosynthetic process
- - preferred_term: amino acid transport
- term:
- id: GO:0006865
- label: amino acid transport
downstream:
- target: Beneficial Interaction Shift
- description: >
- Engineered auxotrophy and amino acid overproduction created positive
- nutritional dependencies that shifted the consortium away from
- antagonism.
+ description: 'PARTIAL: The combined dependency/overproduction intervention introduced nutritional support and
+ changed the in-vitro growth trajectories used to infer interaction structure. Unequal rescue and remaining
+ negative-interaction uncertainty prevent interpreting this as a measured fully mutualistic all-to-all network.'
evidence:
- reference: doi:10.1128/mSystems.00352-19
supports: SUPPORT
@@ -173,10 +169,35 @@ ecological_interactions:
evidence_source: IN_VITRO
snippet: Cross-feeding capabilities of each strain were assessed
explanation: Supports experimental testing of cross-feeding capacity between engineered strains.
+ - reference: PMID:31409662
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: B. fragilis growth was not rescued by any of the strains
+ explanation: The supernatant result limits complete reciprocal-rescue claims; coculture growth differs.
+ participating_taxa:
+ - preferred_term: Escherichia coli
+ term:
+ id: NCBITaxon:562
+ label: Escherichia coli
+ - preferred_term: Salmonella enterica serovar Typhimurium
+ term:
+ id: NCBITaxon:90371
+ label: Salmonella enterica subsp. enterica serovar Typhimurium
+ - preferred_term: Bacteroides thetaiotaomicron
+ term:
+ id: NCBITaxon:818
+ label: Bacteroides thetaiotaomicron
+ - preferred_term: Bacteroides fragilis
+ term:
+ id: NCBITaxon:817
+ label: Bacteroides fragilis
+ interaction_type: CROSS_FEEDING
- name: Beneficial Interaction Shift
- description: Engineered amino acid exchange alleviated antagonistic interactions and added beneficial
- interactions to the four-species consortium.
- interaction_type: MUTUALISM
+ description: A Bayesian dynamical model fitted to in-vitro strain-specific qPCR growth trajectories inferred two
+ positive effects from B. fragilis toward E. coli and S. Typhimurium, with weaker evidence for several negative
+ interactions than in the WT consortium. These are model-inferred net effects under inoculum perturbations, not
+ direct molecular exchange measurements or proof that antagonism vanished. They do not establish reciprocal benefit
+ among every member or identify the same interaction network in vivo.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
@@ -185,20 +206,46 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Cross-Feeding Increased Population Evenness
- description: >
- The engineered shift from antagonistic to beneficial interactions drove
- the more even four-strain population structure measured in vitro and in
- the low-protein mouse gut.
+ description: 'PARTIAL: Engineered nutritional dependencies and altered inferred net interactions are consistent
+ with the greater evenness observed in separate in-vitro endpoint assays. The interaction-shift node was not
+ selectively perturbed to establish mediation. Extension of this pathway to the day-10 mouse-gut endpoint is
+ HYPOTHESIZED; in-vitro network inference does not measure in-vivo exchange.'
evidence:
- reference: doi:10.1128/mSystems.00352-19
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions
- explanation: Supports the shift from antagonistic to beneficial interaction structure after engineering.
+ explanation: The abstract conclusion is based on in-vitro growth perturbations and statistical network inference,
+ not direct measurement of every molecular interaction.
+ - reference: PMID:31409662
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: although some inferred negative interactions are still present
+ explanation: Reduced confidence in negative edges is not evidence that all antagonism disappeared.
+ participating_taxa:
+ - preferred_term: Escherichia coli
+ term:
+ id: NCBITaxon:562
+ label: Escherichia coli
+ - preferred_term: Salmonella enterica serovar Typhimurium
+ term:
+ id: NCBITaxon:90371
+ label: Salmonella enterica subsp. enterica serovar Typhimurium
+ - preferred_term: Bacteroides thetaiotaomicron
+ term:
+ id: NCBITaxon:818
+ label: Bacteroides thetaiotaomicron
+ - preferred_term: Bacteroides fragilis
+ term:
+ id: NCBITaxon:817
+ label: Bacteroides fragilis
- name: Cross-Feeding Increased Population Evenness
- description: Engineered cross-feeding increased population evenness in anaerobic batch culture and in
- the gnotobiotic mouse gut, especially under low amino acid or low-protein conditions.
- interaction_type: CROSS_FEEDING
+ description: The engineered four-member consortium had higher Pielou evenness in anaerobic endpoint cultures,
+ especially without supplemented cross-fed amino acids, despite lower overall growth in the unsupplemented in-vitro
+ setting. In gnotobiotic mice, day-10 fecal strain-specific DNA-qPCR supported greater evenness for the engineered
+ consortium on the low-protein diet; the standard-diet trend was not statistically significant. This is a composition
+ endpoint, not longitudinal stability, a conventional microbiome or a host-health benefit. The assay does not
+ directly measure amino-acid flux in the gut.
scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: amino acid
@@ -210,12 +257,36 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: Engineered cross-feeding increased population evenness
- explanation: Supports the core outcome that engineered exchange changed consortium composition.
+ explanation: Supports the engineered-versus-WT composition outcome, not selective mediation by each inferred
+ interaction.
- reference: PMID:31409662
supports: SUPPORT
evidence_source: IN_VIVO
snippet: low-protein diet showed significantly greater population evenness
- explanation: Supports the in vivo mouse-gut population-evenness result under low-protein diet.
+ explanation: Supports the diet-specific day-10 gnotobiotic-mouse endpoint, not a significant standard-diet effect
+ or measured in-vivo exchange.
+ - reference: PMID:31409662
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: although this trend was not statistically significant
+ explanation: The standard-diet evenness trend did not meet the reported significance criterion.
+ participating_taxa:
+ - preferred_term: Escherichia coli
+ term:
+ id: NCBITaxon:562
+ label: Escherichia coli
+ - preferred_term: Salmonella enterica serovar Typhimurium
+ term:
+ id: NCBITaxon:90371
+ label: Salmonella enterica subsp. enterica serovar Typhimurium
+ - preferred_term: Bacteroides thetaiotaomicron
+ term:
+ id: NCBITaxon:818
+ label: Bacteroides thetaiotaomicron
+ - preferred_term: Bacteroides fragilis
+ term:
+ id: NCBITaxon:817
+ label: Bacteroides fragilis
cultivation_setup:
- cultivation_mode: BATCH
operating_temperature: 37.0
@@ -328,3 +399,31 @@ related_ingredients:
explanation: Anchors amino acids as the auxotrophy-complementing, overproduced compounds exchanged
between strains in the engineered consortium.
metal_relevance: NOT_APPLICABLE
+discussions:
+- discussion_id: gut_crossfeeding_model_and_in_vivo_mediation
+ prompt: Which nutritional interactions mediate the diet-dependent mouse-gut evenness endpoint?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Engineered Amino Acid Cross-Feeding
+ - ecological_interactions#Beneficial Interaction Shift
+ - ecological_interactions#Cross-Feeding Increased Population Evenness
+ rationale: 'Keep unequal supernatant rescue distinct from community growth. The Bayesian model used in-vitro qPCR
+ time series with inoculum perturbations; its net interaction edges do not identify molecular flux or prove an
+ all-to-all mutualistic network. Higher-order effects were not supported by those data, not biologically excluded.
+ Separate the 27-hour trajectory assays from 24-hour supplementation endpoints and day-10 fecal DNA-qPCR. Low-protein
+ diet changes more than a single measured amino-acid flux, and the standard-diet evenness trend was nonsignificant.
+ Do not extrapolate to longitudinal stability, conventional microbiota or clinical benefit. Canonical B. fragilis
+ AMBIGUOUS grounding is preserved, not resolved. Non-graph cache-access wording remains #1457; cache pointer/casing
+ issues remain #1094/#1091. No new genetic engineering procedures or pairwise mechanisms are added.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T10:16:21Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain measured nutritional dependence without complete reciprocal rescue or transporter-specific annotation.;
+ Retain in-vitro model-inferred interaction shift without universal mutualism or absence-of-antagonism claims.;
+ Retain condition-specific evenness endpoints without established in-vivo mediation, stability or host benefit.
+ Issue #1454; reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch40.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch40.yaml
new file mode 100644
index 000000000..5a5ec1558
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch40.yaml
@@ -0,0 +1,168 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 14e7003bc452218c62baa85d5d9f51618d20f366
+scope:
+- kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml
+- kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml
+- kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch40.json
+findings:
+- issue: 1452
+ severity: P2
+ status: addressed_in_this_change
+ finding: 'Electrosynthetic graph: distinguish alternative pairs, compartment effects and proposed electron
+ routes'
+ disposition: Existing-graph defect corrected; close only after protected main merge.
+- issue: 1453
+ severity: P2
+ status: addressed_in_this_change
+ finding: 'Emiliania graph: separate observed host effects from unproven endogenous IAA mediation'
+ disposition: Existing-graph defect corrected; close only after protected main merge.
+- issue: 1454
+ severity: P2
+ status: addressed_in_this_change
+ finding: 'Engineered gut graph: constrain model-inferred interactions and diet-dependent evenness claims'
+ disposition: Existing-graph defect corrected; close only after protected main merge.
+- issue: 1455
+ severity: P2
+ status: open_nongraph_followup
+ finding: 'Electrosynthetic metadata: qualify DIET, organism roles and voltage/control regimes'
+ disposition: Non-graph fields preserved, not certified; remains open.
+- issue: 1456
+ severity: P2
+ status: open_nongraph_followup
+ finding: 'Emiliania metadata: qualify IAA effector language and revisit source-backed cultivation limits'
+ disposition: Non-graph fields preserved, not certified; remains open.
+- issue: 1457
+ severity: P2
+ status: open_nongraph_followup
+ finding: 'Engineered gut metadata: refresh obsolete cache-access limitation without inventing vessel
+ details'
+ disposition: Non-graph fields preserved, not certified; remains open.
+adversarial_checks:
+- Whole records and complete graph diffs checked against cached primary main bodies. All nine existing
+ nodes retained, five arrows retained with bounded descriptions, one unsupported workflow arrow removed.
+ Three renames and all corresponding targets/anchors resolve. No new structure or Edison spend.
+- Electrosynthetic AS and CS are alternative pairs, not a measured three-member consortium. Canonical
+ Andreesenella acetica label preserved. The community-level output roster denotes the comparison set,
+ not co-occurrence of both acetogens.
+- Electrochemical/spectral readouts, riboflavin add-back and compartment removal support route models
+ but do not uniquely establish contact-only DIET, specific cytochrome necessity or donor-resolved hydrogen/formate
+ flux. Hydrogen is not exclusive to one pair. Apparent instantaneous fractions are not cumulative mass-balanced
+ flux.
+- 'Applied cell voltage is distinct from referenced cathode potential; open-circuit H2/CO2 differs from
+ driven N2/CO2. Product enhancement does not establish obligatory syntrophy or reciprocal fitness. Do
+ not transform DNA/gene-abundance readouts into transcription without the unread supplement. Non-graph
+ wording remains #1455.'
+- Emiliania nutrient support and CFU growth are not a selective cause of the specific tryptophan/IAA response;
+ remove that workflow arrow. CFU may count rosettes. Exudate bioavailability plus isotope conversion
+ of added precursor in bacterial culture does not trace the complete endogenous algal-bacterial-algal
+ flux.
+- 'IAA was undetectable in coculture; exogenous micromolar responses are not local exposure measurements.
+ Mutants retained IAA and bleaching, so necessity is unresolved. Keep observed host promotion/death and
+ a HYPOTHESIZED mediation arrow without predation or unique death-pathway claims. Preserve the two-member
+ roster: E. coli reporter and CCMP372 comparator are not members. Non-graph IAA/cultivation wording remains
+ #1456.'
+- Gut consortium rescue is unequal, including absent B. fragilis rescue in tested supernatants despite
+ growth in coculture. Keep measured nutritional dependence without a complete all-to-all flux map or
+ dedicated transporter. Preserve canonical AMBIGUOUS grounding and do not add engineering procedures.
+- In-vitro Bayesian network edges are net inferred effects, not direct molecular transfers; weaker support
+ for negative interactions is not their absence. The interaction-shift-to-evenness link is PARTIAL in
+ vitro and HYPOTHESIZED in vivo. Separate trajectory, supplementation and mouse-gut assays.
+- 'Gut evenness is a day-10 fecal DNA-qPCR endpoint in a four-member gnotobiotic model. Low-protein comparisons
+ were significant; standard-diet trend was not. Do not claim longitudinal stability, conventional microbiota,
+ measured in-vivo flux or clinical benefit. Non-graph access note remains #1457; cache pointer/casing
+ remain #1094/#1091.'
+- Guarded writes, append-only histories and llm-assisted events. Canonical taxonomy, original Emiliania
+ YAML anchor/alias, non-graph raw blocks, 457 other records and 920 caches unchanged. Two participant
+ registry entries added, 185 to 187; connectivity census and numeric bounds unchanged.
+- All 33 baseline network warnings exactly preserved, zero structural errors. Repeated rendering deterministic,
+ with exact published descriptions checked across all 456 community pages. Eight new tests plus combined
+ regression coverage pass on the final tested bytes.
+- Actual validation outputs, digests and pre-research baseline retained. Reference validator 0.1.7 performs
+ zero checks; explicitly a no-op. Snippet MATCH is textual, not scientific validation. The two preflight
+ excerpt corrections and the initial test-key failure are disclosed.
+- Deduplication covered 772 all-state issue titles/bodies and ignored/hidden-inclusive local files, not
+ all comments or PRs. Full cached primary main bodies read; no figure images, separate supplements or
+ raw data. Only selected Emiliania peer-review discussion read; DOI copy not independently fully read.
+ Live challenges were not bypassed.
+- This is source-based self-adversarial review, not independent approval, protected merge or full-corpus
+ completion. Non-graph issues remain open. Exact-head eligible CI and protected main queue are still
+ required.
+verification:
+ combined_regressions: 423 passed in 195.19s (0:03:15)
+ new_regression_tests: 8
+ schema_strict_terms_history: passed; actual outputs and digests retained
+ snippet_counts_by_record:
+ kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml:
+ MATCH: 14
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml:
+ MATCH: 21
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml:
+ MATCH: 20
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network: Zero errors; 33 baseline warnings exactly preserved, none added.
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml: 80329e3dcae2352d3b6937185835394e337f6405310643363b57b841588a62e0
+ tests/test_causal_review_batch40.py: 217a34c089b3fba4a6f31a6a58a1fdbd4e0aa8f598cf115c4e69e795eddfd8f2
+ tests/test_participating_taxa.py: f7a9552c057f123e66b5d3f60bd4ba1e1116704900c3072134ac48ff88e81cb6
+ kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml: 236e65e0a34ac546bcc54c39e37fd6f69d98943d2e6527324d96b800fe9a53bc
+ kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml: d3d385ef2d9f8807a54d65a3e7ec6a08371f98df61b771426717fad84758577c
+ kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml: 54c35d933209e608a7f894e1e602441d945a5d311e4b9ff212ab6fae1a0f5a18
+ post_commit_docs_current: Separate publication gate; not asserted in pre-commit record.
+ protected_ci_and_merge: Eligible exact-head checks and protected queue still required.
+participant_census:
+ connectivity_before:
+ community_level_only: 263
+ credited_solely_by_the_rule: 1219
+ mixed: 124
+ records: 460
+ taxa: 1494
+ with_community_level: 387
+ connectivity_after:
+ community_level_only: 263
+ credited_solely_by_the_rule: 1219
+ mixed: 124
+ records: 460
+ taxa: 1494
+ with_community_level: 387
+ exact_change: 'Electrosynthetic and Engineered Gut newly registered: participant roster grows from 185
+ to 187. Emiliania remains pairwise. Connectivity census and numeric bounds unchanged; canonical taxonomy
+ preserved.'
+ numeric_bounds_changed: false
+corpus:
+ records: 460
+ nodes: 1469
+ edges: 688
+ review_status_counts:
+ needs_research: 9
+ pending: 291
+ reviewed: 160
+limitations:
+- Cached primary main bodies, tables and captions read; no figure images, separate supplements or raw
+ data reviewed. Selected Emiliania review exchange only.
+- Nine existing nodes retained; five arrows retained and one unsupported workflow arrow removed. Do not
+ add links to suppress connectivity warnings.
+- 'Canonical taxonomy, prior history, original YAML aliases and non-graph raw blocks preserved, not certified.
+ Non-graph followups #1455/#1456/#1457 remain open.'
+- Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion.
+ Text matching is not scientific validation.
+- 'Reference validator 0.1.7 is known to perform zero checks for this schema; report the no-op explicitly.
+ DOI casing and stale pointer issues remain #1091/#1094.'
diff --git a/reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml b/reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
new file mode 100644
index 000000000..cabb28729
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
@@ -0,0 +1,281 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 14e7003bc452218c62baa85d5d9f51618d20f366
+baseline_commit: 14e7003bc452218c62baa85d5d9f51618d20f366
+base_tree: 3b55fe60d43507fad7a841aec338d497a0775fa6
+issues:
+- 1452
+- 1453
+- 1454
+open_nongraph_followups:
+- 1455
+- 1456
+- 1457
+open_graph_research: []
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 772
+ ignored_hidden_local_search: true
+ relevant_bodies_read:
+ - 583
+ - 529
+ - 1091
+ - 1094
+ limitations: Not every issue comment or PR reviewed.
+reference_cache_original_hashes:
+ references_cache/PMID_41236292.md: a5db3634359651ebd829d93fdfbaa26ecd7c4433478d33194a68eba7b42e2651
+ references_cache/PMID_27855786.md: f7b54084a1eb7a726f79149c3ddc3d0a34e180294f61d2e053516b8a78b31b40
+ references_cache/PMID_31409662.md: 288f1f394bae8d552b40bba3250131534d1e4d32c47824a3e66730f9173abcdf
+edison:
+ status: not_required_for_existing_structure_repairs
+ rationale: Nine existing nodes retained; five existing arrows retained with bounded descriptions and one workflow
+ arrow removed. No new nodes or arrows, no provider job or spend.
+limitations:
+- Cached primary main bodies, tables and captions read; no figure images, separate supplements or raw data reviewed.
+ Selected Emiliania review exchange only.
+- Nine existing nodes retained; five arrows retained and one unsupported workflow arrow removed. Do not add links
+ to suppress connectivity warnings.
+- 'Canonical taxonomy, prior history, original YAML aliases and non-graph raw blocks preserved, not certified. Non-graph
+ followups #1455/#1456/#1457 remain open.'
+- Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion. Text
+ matching is not scientific validation.
+- 'Reference validator 0.1.7 is known to perform zero checks for this schema; report the no-op explicitly. DOI casing
+ and stale pointer issues remain #1091/#1094.'
+records:
+- path: kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml
+ id: CommunityMech:000298
+ original_sha256: d225c991b8b826dc63bb56b8094e9bc5420e5c9da7f6c2e6be693fc7dc56e9e2
+ record_sha256: 236e65e0a34ac546bcc54c39e37fd6f69d98943d2e6527324d96b800fe9a53bc
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
+ scope: Whole record and every existing node/arrow assessed. Non-graph fields preserved, not certified.
+ summary: Retain biofilm-associated route as PARTIAL without contact-only DIET or syntrophy proof.; Retain planktonic
+ route as PARTIAL without exclusive or donor-resolved mediator flux.; Retain acetate enhancement with the alternative-pair
+ roster and explicit cell-voltage/control boundaries.
+ renamed_nodes:
+ DIET from S. oneidensis to C. aceticum: Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair
+ H2/formate-mediated IET from S. oneidensis to A. woodii: Proposed Planktonic H2/Formate IET in the S. oneidensis-A.
+ woodii Pair
+ node_decisions:
+ - node: Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair
+ rationale: Retain biofilm-associated route as PARTIAL without contact-only DIET or syntrophy proof.
+ - node: Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair
+ rationale: Retain planktonic route as PARTIAL without exclusive or donor-resolved mediator flux.
+ - node: Enhanced CO2-to-Acetate Conversion
+ rationale: Retain acetate enhancement with the alternative-pair roster and explicit cell-voltage/control boundaries.
+ removed_node_decisions: []
+ edges_before:
+ - source: DIET from S. oneidensis to C. aceticum
+ target: Enhanced CO2-to-Acetate Conversion
+ description: 'Biofilm-localized DIET in the S. oneidensis-C. aceticum consortium contributes electron flow for
+ enhanced CO2-to-acetate electrosynthesis.
+
+ '
+ - source: H2/formate-mediated IET from S. oneidensis to A. woodii
+ target: Enhanced CO2-to-Acetate Conversion
+ description: 'H2/formate-mediated electron transfer in the S. oneidensis-A. woodii consortium contributes planktonic
+ electron flow for enhanced CO2-to-acetate electrosynthesis.
+
+ '
+ edges_after:
+ - source: Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair
+ target: Enhanced CO2-to-Acetate Conversion
+ description: 'PARTIAL: Biofilm-associated electron supply and riboflavin-responsive transfer can support the
+ C. aceticum pair''s acetate increase. Compartment removal and add-back support this contribution, but do not
+ isolate the necessity of contact-only DIET or a specific cytochrome. This arrow concerns the CS pair, not
+ a simultaneous three-member culture.'
+ - source: Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair
+ target: Enhanced CO2-to-Acetate Conversion
+ description: 'PARTIAL: Diffusible reducing equivalents are a supported explanation for suspension-associated
+ acetate synthesis in the AS pair, including acetate production where A. woodii alone failed at the tested
+ lower cell voltage. This does not establish exclusive hydrogen/formate mediation or identify the molecular
+ donor flux.'
+ retained_edge_decisions:
+ - source: Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair
+ target: Enhanced CO2-to-Acetate Conversion
+ rationale: 'PARTIAL: Biofilm-associated electron supply and riboflavin-responsive transfer can support the C.
+ aceticum pair''s acetate increase. Compartment removal and add-back support this contribution, but do not
+ isolate the necessity of contact-only DIET or a specific cytochrome. This arrow concerns the CS pair, not
+ a simultaneous three-member culture.'
+ - source: Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair
+ target: Enhanced CO2-to-Acetate Conversion
+ rationale: 'PARTIAL: Diffusible reducing equivalents are a supported explanation for suspension-associated acetate
+ synthesis in the AS pair, including acetate production where A. woodii alone failed at the tested lower cell
+ voltage. This does not establish exclusive hydrogen/formate mediation or identify the molecular donor flux.'
+ removed_edge_decisions: []
+ references:
+ - PMID:41236292
+ issues:
+ - 1452
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate/2026-10-06T101622Z-codex-3da2ef.yaml
+ source_review:
+ PMID:41236292:
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12866739/
+ scope: Full cached primary main body through Methods, including tables/captions. No figure images, separate
+ supplements or raw data reviewed.
+ cache: references_cache/PMID_41236292.md
+- path: kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml
+ id: CommunityMech:000143
+ original_sha256: e0a94fe128d5babfb6c76a3f161d32dd8a1f1ed58a5204d55a632c28283c702b
+ record_sha256: d3d385ef2d9f8807a54d65a3e7ec6a08371f98df61b771426717fad84758577c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
+ scope: Whole record and every existing node/arrow assessed. Non-graph fields preserved, not certified.
+ summary: Retain nutrient-supported growth without a generic-to-specific workflow arrow or direct photosynthesis-flux
+ claim.; Retain precursor availability, added-tryptophan conversion and attachment responses without a complete
+ traced endogenous loop.; Retain observed promotion and late death with HYPOTHESIZED IAA mediation, not categorical
+ predation or unique death mechanism.
+ renamed_nodes:
+ IAA-Mediated Algal Growth Promotion And Killing: Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ node_decisions:
+ - node: Algal Nutrient Provisioning Supports Bacterial Growth
+ rationale: Retain nutrient-supported growth without a generic-to-specific workflow arrow or direct photosynthesis-flux
+ claim.
+ - node: Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ rationale: Retain precursor availability, added-tryptophan conversion and attachment responses without a complete
+ traced endogenous loop.
+ - node: Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ rationale: Retain observed promotion and late death with HYPOTHESIZED IAA mediation, not categorical predation
+ or unique death mechanism.
+ removed_node_decisions: []
+ edges_before:
+ - source: Algal Nutrient Provisioning Supports Bacterial Growth
+ target: Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ description: Algal nutrient provisioning sustains P. inhibens growth in the non-permissive L1-Si medium, putting
+ the heterotroph in the phycosphere where algal tryptophan stimulates attachment and IAA production.
+ - source: Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ target: IAA-Mediated Algal Growth Promotion And Killing
+ description: Algal tryptophan stimulates P. inhibens indole-3-acetic acid production, and that bacterially produced
+ IAA drives the downstream algal growth-promotion and killing response.
+ edges_after:
+ - source: Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ target: Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ description: 'HYPOTHESIZED: Tryptophan-enhanced IAA production could contribute to initial algal promotion and
+ late killing. Added tryptophan accelerated coculture bleaching, but also changed attachment; bulk coculture
+ IAA was undetectable and pathway mutants retained production. The experiment therefore does not isolate IAA
+ mediation or show that measured bacterial IAA reached the exogenous toxic dose.'
+ retained_edge_decisions:
+ - source: Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ target: Algal Growth Promotion and Late Killing with Proposed IAA Mediation
+ rationale: 'HYPOTHESIZED: Tryptophan-enhanced IAA production could contribute to initial algal promotion and
+ late killing. Added tryptophan accelerated coculture bleaching, but also changed attachment; bulk coculture
+ IAA was undetectable and pathway mutants retained production. The experiment therefore does not isolate IAA
+ mediation or show that measured bacterial IAA reached the exogenous toxic dose.'
+ removed_edge_decisions:
+ - source: Algal Nutrient Provisioning Supports Bacterial Growth
+ target: Tryptophan-Enhanced Bacterial Attachment And IAA Production
+ rationale: Generic nutrient support enables bacterial growth but does not selectively establish the specific
+ tryptophan/IAA response; a workflow/enabling-context link is not sufficient.
+ references:
+ - PMID:27855786
+ issues:
+ - 1453
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Emiliania_Phaeobacter_Dynamic_Interaction/2026-10-06T101622Z-codex-837390.yaml
+ source_review:
+ PMID:27855786:
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC5148602/
+ scope: Full cached primary main body through Methods, including tables/captions. No figure images, separate
+ supplements or raw data reviewed. Selected published peer-review discussion read, not the entire exchange.
+ Live publisher/PMC access returned challenge pages; no bypass attempted.
+ cache: references_cache/PMID_27855786.md
+- path: kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml
+ id: CommunityMech:000151
+ original_sha256: b29aa03e39e670a5d61b55306119f11c3459c7fb5c6cf5e8fb58a92d040a8cf0
+ record_sha256: 54c35d933209e608a7f894e1e602441d945a5d311e4b9ff212ab6fae1a0f5a18
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml
+ scope: Whole record and every existing node/arrow assessed. Non-graph fields preserved, not certified.
+ summary: Retain measured nutritional dependence without complete reciprocal rescue or transporter-specific annotation.;
+ Retain in-vitro model-inferred interaction shift without universal mutualism or absence-of-antagonism claims.;
+ Retain condition-specific evenness endpoints without established in-vivo mediation, stability or host benefit.
+ renamed_nodes: {}
+ node_decisions:
+ - node: Engineered Amino Acid Cross-Feeding
+ rationale: Retain measured nutritional dependence without complete reciprocal rescue or transporter-specific
+ annotation.
+ - node: Beneficial Interaction Shift
+ rationale: Retain in-vitro model-inferred interaction shift without universal mutualism or absence-of-antagonism
+ claims.
+ - node: Cross-Feeding Increased Population Evenness
+ rationale: Retain condition-specific evenness endpoints without established in-vivo mediation, stability or
+ host benefit.
+ removed_node_decisions: []
+ edges_before:
+ - source: Engineered Amino Acid Cross-Feeding
+ target: Beneficial Interaction Shift
+ description: 'Engineered auxotrophy and amino acid overproduction created positive nutritional dependencies
+ that shifted the consortium away from antagonism.
+
+ '
+ - source: Beneficial Interaction Shift
+ target: Cross-Feeding Increased Population Evenness
+ description: 'The engineered shift from antagonistic to beneficial interactions drove the more even four-strain
+ population structure measured in vitro and in the low-protein mouse gut.
+
+ '
+ edges_after:
+ - source: Engineered Amino Acid Cross-Feeding
+ target: Beneficial Interaction Shift
+ description: 'PARTIAL: The combined dependency/overproduction intervention introduced nutritional support and
+ changed the in-vitro growth trajectories used to infer interaction structure. Unequal rescue and remaining
+ negative-interaction uncertainty prevent interpreting this as a measured fully mutualistic all-to-all network.'
+ - source: Beneficial Interaction Shift
+ target: Cross-Feeding Increased Population Evenness
+ description: 'PARTIAL: Engineered nutritional dependencies and altered inferred net interactions are consistent
+ with the greater evenness observed in separate in-vitro endpoint assays. The interaction-shift node was not
+ selectively perturbed to establish mediation. Extension of this pathway to the day-10 mouse-gut endpoint is
+ HYPOTHESIZED; in-vitro network inference does not measure in-vivo exchange.'
+ retained_edge_decisions:
+ - source: Engineered Amino Acid Cross-Feeding
+ target: Beneficial Interaction Shift
+ rationale: 'PARTIAL: The combined dependency/overproduction intervention introduced nutritional support and
+ changed the in-vitro growth trajectories used to infer interaction structure. Unequal rescue and remaining
+ negative-interaction uncertainty prevent interpreting this as a measured fully mutualistic all-to-all network.'
+ - source: Beneficial Interaction Shift
+ target: Cross-Feeding Increased Population Evenness
+ rationale: 'PARTIAL: Engineered nutritional dependencies and altered inferred net interactions are consistent
+ with the greater evenness observed in separate in-vitro endpoint assays. The interaction-shift node was not
+ selectively perturbed to establish mediation. Extension of this pathway to the day-10 mouse-gut endpoint is
+ HYPOTHESIZED; in-vitro network inference does not measure in-vivo exchange.'
+ removed_edge_decisions: []
+ references:
+ - PMID:31409662
+ - doi:10.1128/mSystems.00352-19
+ issues:
+ - 1454
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium/2026-10-06T101622Z-codex-ebe0ca.yaml
+ source_review:
+ PMID:31409662:
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC6697442/
+ scope: Full cached primary main body through Methods, including tables/captions. No figure images, separate
+ supplements or raw data reviewed. PMID copy read; DOI copy exists but was not independently read in full.
+ Live PMC access returned a challenge page.
+ cache: references_cache/PMID_31409662.md
+preflight_snippet_corrections:
+ initial_counts:
+ MATCH: 53
+ RENDERING: 1
+ MISMATCH: 1
+ disposition: Replaced a paraphrased CFU excerpt with the literal source sentence and restored the source hyphen
+ in a fold-change excerpt. Full verification follows.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 99f6a58d2..85445004b 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -161,9 +161,9 @@ kb/communities/Ecoli_GL10_XL12_D_Lactate_Mixed_Sugar_SynCom.yaml CommunityMech:0
kb/communities/Ecoli_K12_MG1655_Arg_Met_CrossFeeding_Coculture.yaml CommunityMech:000455 2a72a54518f0a8635f1d599a91b7f750f94349c2f1c7a002159170a8f5be9c4c 3 0 75.0 reports/causal_graph_review/decisions/20261006-three-records-batch37.yaml needs_research
kb/communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.yaml CommunityMech:000287 39dd44074408cc2e990576c6b8c40c18e2faf74c862881e9643865b69da8e0e1 5 2 89.0 reports/causal_graph_review/decisions/20261006-three-records-batch37.yaml reviewed
kb/communities/Electrostimulated_Toluene_Methanogenic_Microbiota.yaml CommunityMech:000440 6d55992d0ce9ba8a4398c071862cc167ca334085174ed5c7f04aed80829588c2 3 0 63.3 reports/causal_graph_review/decisions/20261006-three-records-batch37.yaml reviewed
-kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml CommunityMech:000298 d225c991b8b826dc63bb56b8094e9bc5420e5c9da7f6c2e6be693fc7dc56e9e2 3 2 100.0 pending
-kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml CommunityMech:000143 e0a94fe128d5babfb6c76a3f161d32dd8a1f1ed58a5204d55a632c28283c702b 3 2 100.0 pending
-kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml CommunityMech:000151 b29aa03e39e670a5d61b55306119f11c3459c7fb5c6cf5e8fb58a92d040a8cf0 3 2 100.0 pending
+kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml CommunityMech:000298 236e65e0a34ac546bcc54c39e37fd6f69d98943d2e6527324d96b800fe9a53bc 3 2 90.0 reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml reviewed
+kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml CommunityMech:000143 d3d385ef2d9f8807a54d65a3e7ec6a08371f98df61b771426717fad84758577c 3 1 81.7 reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml reviewed
+kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml CommunityMech:000151 54c35d933209e608a7f894e1e602441d945a5d311e4b9ff212ab6fae1a0f5a18 3 2 93.3 reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml reviewed
kb/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.yaml CommunityMech:000299 57ac6be6ce479d6e721e7c7a81a54ede921eee8620e3b466d061750d7d24d60c 3 1 75.0 reports/causal_graph_review/decisions/20261006-three-records-batch38.yaml reviewed
kb/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.yaml CommunityMech:000237 365db2424aa243d7f2727a5bb344aae80293574cc6a1d2db7e5780ccb475eb09 5 1 76.0 reports/causal_graph_review/decisions/20261006-three-records-batch38.yaml reviewed
kb/communities/Eucalyptus_Nursery_FiveStrain_Inoculant_SynCom.yaml CommunityMech:000316 e14a2eea79cf30da31d464f571f728fe07984e9cc854938340d075f8a2e02fd0 3 0 63.3 reports/causal_graph_review/decisions/20261006-three-records-batch39.yaml reviewed
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 75d481096..62a1e1025 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
"semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
"records": 460,
"nodes": 1469,
- "edges": 689,
+ "edges": 688,
"records_without_nodes": 8,
"records_without_edges": 146,
"review_status_counts": {
"needs_research": 9,
- "pending": 294,
- "reviewed": 157
+ "pending": 291,
+ "reviewed": 160
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch40.json b/reports/causal_graph_review/validation-20261006-batch40.json
new file mode 100644
index 000000000..7ff3d3261
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch40.json
@@ -0,0 +1,766 @@
+{
+ "base_commit": "14e7003bc452218c62baa85d5d9f51618d20f366",
+ "scope": [
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-strict.tsv",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-strict.log",
+ "log_sha256": "7f12e825550d8b2afa767b92b2a305bcf151f07e748fc10b37105a632b1f08a8",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch40/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-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-strict.tsv\n"
+ },
+ {
+ "check": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-references.log",
+ "log_sha256": "95a1605ee2f582fb1852133aecda9701bdbf3e520bbe3363d61566818ff61eb4",
+ "output_tail": "Validating kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.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/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.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": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-snippets.log",
+ "log_sha256": "872637a69e95b3997368edea80eba5db2a2155e0ac9344b758394dcf97491410",
+ "output_tail": "# 14 evidence snippets scanned across 1 files\n MATCH 14\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": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-rank.log",
+ "log_sha256": "8d216cf69f98fab60167dde2cc28f1dd955d89d69a1bdb3a9a97c98e5b38f000",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000298\",\n \"name\": \"Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate\",\n \"score\": 90.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 7,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate/2026-10-06T101622Z-codex-3da2ef.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Emiliania_Phaeobacter_Dynamic_Interaction-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Emiliania_Phaeobacter_Dynamic_Interaction-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-strict.tsv",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-strict.log",
+ "log_sha256": "85ae7608ec96443821329d650856d1bdd2eab7cb9c9dc5e73e728632eb2bd73f",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch40/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-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-strict.tsv\n"
+ },
+ {
+ "check": "Emiliania_Phaeobacter_Dynamic_Interaction-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Emiliania_Phaeobacter_Dynamic_Interaction-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-references.log",
+ "log_sha256": "51dedb3fad322619bd1823d18293c127a8728e72a3ad1f150800d3a154e28158",
+ "output_tail": "Validating kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.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/Emiliania_Phaeobacter_Dynamic_Interaction.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": "Emiliania_Phaeobacter_Dynamic_Interaction-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-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": "Emiliania_Phaeobacter_Dynamic_Interaction-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-rank.log",
+ "log_sha256": "287d886f6ca7cb865f79db876833339bc86f76016a5fe67a95c4d35b70e10509",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000143\",\n \"name\": \"Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction\",\n \"score\": 81.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 1,\n \"interaction_evidence\": 9,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"additional_downstream\",\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Emiliania_Phaeobacter_Dynamic_Interaction-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Emiliania_Phaeobacter_Dynamic_Interaction/2026-10-06T101622Z-codex-837390.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Emiliania_Phaeobacter_Dynamic_Interaction-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-strict.tsv",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-strict.log",
+ "log_sha256": "4adb998c987aa152b33df8615d9e10e3403c6879bafb801ddff404b7de8a9077",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch40/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-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-strict.tsv\n"
+ },
+ {
+ "check": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-references.log",
+ "log_sha256": "2b50fea2942c141c7cbc331099a310ecaff200d209cf1958e08c1fd09b4a4775",
+ "output_tail": "Validating kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-snippets.log",
+ "log_sha256": "32d5c17677a000100a0b22db07734e7af95b7e2b40f82a74ed21b581b1a6d4f5",
+ "output_tail": "# 20 evidence snippets scanned across 1 files\n MATCH 20\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": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-rank.log",
+ "log_sha256": "8a1327d434bbe8e02ebef45a67e2ef88752370f4159310fe1ef6f5522a96ca62",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000151\",\n \"name\": \"Engineered Gut Amino Acid Cross-Feeding Consortium\",\n \"score\": 93.3,\n \"taxonomy\": 4,\n \"connected_taxa\": 4,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium/2026-10-06T101622Z-codex-ebe0ca.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium-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-batch40/inventory.log",
+ "log_sha256": "dd6d53a497b2d24d5ba06f01e50439adf533b4e4ffd967203369444f171bc948",
+ "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\": 1469,\n \"edges\": 688,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 146,\n \"review_status_counts\": {\n \"needs_research\": 9,\n \"pending\": 291,\n \"reviewed\": 160\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-batch40/network.log",
+ "log_sha256": "c035fe6ed0bbf90371ab58d6557716c51eea79ac628e204173d70075f9efaa26",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' 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": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
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+ },
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+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 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/private/tmp/communitymech-causal-batch40/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch40/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch40/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch40/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-batch40/render-repeat.log",
+ "log_sha256": "aeb8f6a5359a9220ddf780e24b272f548383c5d20cefb29cd864888153f523b7",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch40/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch40/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch40/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch40/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path(\"tests/test_community_level_connectivity_credit.py\")[\"_survey\"](),sort_keys=True))"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/connectivity-survey.log",
+ "log_sha256": "fb47676e0ec6945737e5aeeba11192e7b8ff073a9e93ce8809972a4316c7c565",
+ "output_tail": "{\"community_level_only\": 263, \"credited_solely_by_the_rule\": 1219, \"mixed\": 124, \"records\": 460, \"taxa\": 1494, \"with_community_level\": 387}\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_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_batch5.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch9.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-batch40/regressions.log",
+ "log_sha256": "42023e96a212f3203b3931c79fae08e03883b17a9740184ead01850e17ddc506",
+ "output_tail": "........................................................................ [ 17%]\n........................................................................ [ 34%]\n........................................................................ [ 51%]\n........................................................................ [ 68%]\n........................................................................ [ 85%]\n............................................................... [100%]\n423 passed in 195.19s (0:03:15)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/black.log",
+ "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_participating_taxa.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch40/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Cached primary main bodies, tables and captions read; no figure images, separate supplements or raw data reviewed. Selected Emiliania review exchange only.",
+ "Nine existing nodes retained; five arrows retained and one unsupported workflow arrow removed. Do not add links to suppress connectivity warnings.",
+ "Canonical taxonomy, prior history, original YAML aliases and non-graph raw blocks preserved, not certified. Non-graph followups #1455/#1456/#1457 remain open.",
+ "Source-based self-adversarial review is not independent approval, protected merge or full-corpus completion. Text matching is not scientific validation.",
+ "Reference validator 0.1.7 is known to perform zero checks for this schema; report the no-op explicitly. DOI casing and stale pointer issues remain #1091/#1094.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "All three reference-validator commands exit 0 with Total checks: 0. This is a no-op, not evidence validation. Independent snippet counts and primary-source review are separate."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml": {
+ "MATCH": 14,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml": {
+ "MATCH": 21,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml": {
+ "MATCH": 20,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 39,
+ "unchanged_record_files": 457,
+ "unchanged_cache_files": 920,
+ "network_delta": {
+ "existing_findings_preserved": 33,
+ "new_disconnected": 0,
+ "added_findings": {},
+ "rationale": "All baseline warnings exactly preserved; no invented graph links to suppress warnings."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1455,
+ "arrows": 680
+ },
+ "participant_census": {
+ "connectivity_before": {
+ "community_level_only": 263,
+ "credited_solely_by_the_rule": 1219,
+ "mixed": 124,
+ "records": 460,
+ "taxa": 1494,
+ "with_community_level": 387
+ },
+ "connectivity_after": {
+ "community_level_only": 263,
+ "credited_solely_by_the_rule": 1219,
+ "mixed": 124,
+ "records": 460,
+ "taxa": 1494,
+ "with_community_level": 387
+ },
+ "exact_change": "Electrosynthetic and Engineered Gut newly registered: participant roster grows from 185 to 187. Emiliania remains pairwise. Connectivity census and numeric bounds unchanged; canonical taxonomy preserved.",
+ "numeric_bounds_changed": false
+ },
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1469,
+ "edges": 688,
+ "records_without_nodes": 8,
+ "records_without_edges": 146,
+ "review_status_counts": {
+ "needs_research": 9,
+ "pending": 291,
+ "reviewed": 160
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml": "80329e3dcae2352d3b6937185835394e337f6405310643363b57b841588a62e0",
+ "tests/test_causal_review_batch40.py": "217a34c089b3fba4a6f31a6a58a1fdbd4e0aa8f598cf115c4e69e795eddfd8f2",
+ "tests/test_participating_taxa.py": "f7a9552c057f123e66b5d3f60bd4ba1e1116704900c3072134ac48ff88e81cb6",
+ "kb/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml": "236e65e0a34ac546bcc54c39e37fd6f69d98943d2e6527324d96b800fe9a53bc",
+ "kb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml": "d3d385ef2d9f8807a54d65a3e7ec6a08371f98df61b771426717fad84758577c",
+ "kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml": "54c35d933209e608a7f894e1e602441d945a5d311e4b9ff212ab6fae1a0f5a18"
+ },
+ "status": "verified_three_completed_reviews",
+ "reference_validator_effective_checks": 0,
+ "reference_validator_caveat": "All three reference-validator commands exit 0 with Total checks: 0. This is a no-op, not evidence validation. Independent snippet counts and primary-source review are separate.",
+ "pre_research_baseline": {
+ "base_commit": "14e7003bc452218c62baa85d5d9f51618d20f366",
+ "base_tree": "3b55fe60d43507fad7a841aec338d497a0775fa6",
+ "research_worktree": "/private/tmp/communitymech-causal-batch39",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch40/baseline-rank.log",
+ "sha256": "a4de322b2c22e49602e9271959f68c103ab17c1806cbd15849b658a8fcb68b02",
+ "output_tail": "nol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter 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"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch40/baseline-just-network.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"
+ },
+ {
+ "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-batch40/baseline-network.log",
+ "sha256": "c035fe6ed0bbf90371ab58d6557716c51eea79ac628e204173d70075f9efaa26",
+ "output_tail": " 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"
+ },
+ {
+ "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-batch40/baseline-downstream.log",
+ "sha256": "8055c57d0bceb6097183d9e8d54ff0a2e351c0dff5a9cf882606978acf26bc09",
+ "output_tail": "unities/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Lac_Pavin_Stratified_Lake_Community.yaml:106: downstream:\nkb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml:107: downstream:\nkb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml:147: downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:197: downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:241: downstream:\nkb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:83: downstream:\nkb/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.yaml:121: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:285: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:324: downstream:\nkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml:196: downstream:\nkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml:242: downstream:\nkb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml:135: downstream:\nkb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml:173: downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:142: downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:189: downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:80: downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:117: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml:141: downstream:\nkb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml:147: downstream:\nkb/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.yaml:222: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:121: downstream:\nkb/communities/Rice_P_Uptake_Intercropping_SynCom4.yaml:149: downstream:\nkb/communities/Pepper_Phytophthora_SynCom5.yaml:123: downstream:\nkb/communities/Pepper_Phytophthora_SynCom5.yaml:146: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:120: downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:152: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:203: downstream:\nkb/communities/GOM_Oil_Degrading_Consortium.yaml:119: downstream:\nkb/communities/GOM_Oil_Degrading_Consortium.yaml:160: downstream:\n"
+ }
+ ]
+ },
+ "preflight_corrections": {
+ "snippets": {
+ "initial_counts": {
+ "MATCH": 53,
+ "RENDERING": 1,
+ "MISMATCH": 1
+ },
+ "disposition": "Replaced a paraphrased CFU excerpt with the literal source sentence and restored the source hyphen in a fold-change excerpt. Full verification follows."
+ },
+ "new_test": "An early focused run returned 7 passed, 1 failed (KeyError: about). The new test was corrected to the existing attaches_to field before the full combined regression run. No initial pass is claimed."
+ }
+}
diff --git a/tests/test_causal_review_batch40.py b/tests/test_causal_review_batch40.py
new file mode 100644
index 000000000..866e1ea77
--- /dev/null
+++ b/tests/test_causal_review_batch40.py
@@ -0,0 +1,138 @@
+"""Keep observed responses distinct from inferred causal mediation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-three-records-batch40.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def test_electrosynthetic_routes_remain_partial_not_contact_only():
+ _, docs = records()
+ biofilm, planktonic, output = docs[0]["ecological_interactions"]
+ for node in [biofilm, planktonic]:
+ assert node["description"].startswith("PARTIAL:")
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert node["downstream"][0]["target"] == output["name"]
+ assert node["downstream"][0]["description"].startswith("PARTIAL:")
+ assert "diffusible mediator" in biofilm["description"]
+ assert "selective cytochrome necessity" in biofilm["description"]
+ assert "hydrogen was detected in both" in planktonic["description"]
+ assert "not cumulative mass-balanced flux fractions" in planktonic["description"]
+ assert all("interaction_type" not in n for n in [biofilm, planktonic, output])
+
+
+def test_electrosynthetic_output_roster_is_alternative_pairs():
+ _, docs = records()
+ output = docs[0]["ecological_interactions"][2]
+ assert len(output["participating_taxa"]) == 3
+ assert "not one three-member community" in output["description"]
+ assert "acetogens were alternatives" in output["description"]
+ assert "applied cell voltage" in output["description"]
+ assert "not voltage-only" in output["description"]
+ assert "1.16 g/L versus 0.62 g/L" in output["description"]
+ assert docs[0]["taxonomy"][1]["taxon_term"]["term"]["label"] == "Andreesenella acetica"
+
+
+def test_emiliania_removes_workflow_and_precursor_biosynthesis_claim():
+ _, docs = records()
+ nutrients, tryptophan, response = docs[1]["ecological_interactions"]
+ assert "downstream" not in nutrients
+ assert nutrients["interaction_type"] == "CROSS_FEEDING"
+ assert "rosettes rather than single cells" in nutrients["description"]
+ assert "CFU may include rosettes" in nutrients["evidence"][-1]["snippet"]
+ assert all("biological_processes" not in n for n in [nutrients, tryptophan])
+ assert "not a community member" in tryptophan["description"]
+ assert tryptophan["downstream"][0]["target"] == response["name"]
+ assert tryptophan["downstream"][0]["description"].startswith("HYPOTHESIZED:")
+ assert len(docs[1]["taxonomy"]) == 2
+
+
+def test_emiliania_iaa_exposure_and_necessity_are_unresolved():
+ _, docs = records()
+ response = docs[1]["ecological_interactions"][2]
+ assert "Proposed IAA Mediation" in response["name"]
+ assert "interaction_type" not in response
+ assert "not measured coculture exposures" in response["description"]
+ assert "IAA was undetectable in coculture" in response["description"]
+ assert "mutants still produced IAA" in response["description"]
+ assert response["evidence"][0]["supports"] == "PARTIAL"
+ assert "94% dead in coculture versus 21%" in response["description"]
+ assert "not establish IAA necessity" in response["description"]
+ assert "CCMP372 cannot be assigned to CCMP3266" in docs[1]["discussions"][-1]["rationale"]
+
+
+def test_gut_net_inference_is_not_measured_all_to_all_mutualism():
+ _, docs = records()
+ exchange, shift, evenness = docs[2]["ecological_interactions"]
+ assert "not complete measured all-to-all transfer" in exchange["description"]
+ assert "B. fragilis was not rescued" in exchange["description"]
+ assert [p["term"]["id"] for p in exchange["biological_processes"]] == ["GO:0008652"]
+ assert "interaction_type" not in shift and "interaction_type" not in evenness
+ assert "model-inferred net effects" in shift["description"]
+ assert shift["evidence"][-1]["evidence_source"] == "COMPUTATIONAL"
+ assert (
+ "in-vitro network inference does not measure in-vivo exchange"
+ in shift["downstream"][0]["description"]
+ )
+ assert docs[2]["taxonomy"][3]["taxon_term"]["gtdb_grounding_status"] == "AMBIGUOUS"
+
+
+def test_gut_evenness_is_a_diet_specific_composition_endpoint():
+ _, docs = records()
+ evenness = docs[2]["ecological_interactions"][2]
+ assert "day-10 fecal strain-specific DNA-qPCR" in evenness["description"]
+ assert "standard-diet trend was not statistically significant" in evenness["description"]
+ assert "not longitudinal stability" in evenness["description"]
+ assert "does not directly measure amino-acid flux" in evenness["description"]
+ assert evenness["evidence"][-1]["evidence_source"] == "IN_VIVO"
+
+
+def test_batch40_complete_dispositions_canonical_participants_and_history():
+ ledger, docs = records()
+ assert ledger["independent_approval"] is False
+ assert ledger["issues"] == [1452, 1453, 1454]
+ assert ledger["open_nongraph_followups"] == [1455, 1456, 1457]
+ assert sum(len(r["node_decisions"]) for r in ledger["records"]) == 9
+ assert sum(len(r["retained_edge_decisions"]) for r in ledger["records"]) == 5
+ assert sum(len(r["removed_edge_decisions"]) for r in ledger["records"]) == 1
+ for row, doc in zip(ledger["records"], docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert row["status"] == "reviewed"
+ assert len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).is_file()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ canonical = {t["taxon_term"]["term"]["id"]: t["taxon_term"] for t in doc["taxonomy"]}
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ for node in doc["ecological_interactions"]:
+ participants = node.get("participating_taxa", [])
+ participants += [node[k] for k in ["source_taxon", "target_taxon"] if k in node]
+ for term in participants:
+ assert term["term"] == canonical[term["term"]["id"]]["term"]
+ assert all(
+ e["target"] in names and e["target"] != node["name"]
+ for e in node.get("downstream", [])
+ )
+ assert all(a.split("#", 1)[1] in names for a in doc["discussions"][-1]["attaches_to"])
+
+
+def test_batch40_preserves_original_aliases_and_source_access_limits():
+ ledger, _ = records()
+ text = (ROOT / ledger["records"][1]["path"]).read_text()
+ assert "&coculture_design" in text and "*coculture_design" in text
+ for path, expected in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == expected
+ assert ledger["edison"]["status"] == "not_required_for_existing_structure_repairs"
+ assert "no provider job or spend" in ledger["edison"]["rationale"]
+ assert all(
+ "No figure images, separate supplements or raw data reviewed"
+ in next(iter(r["source_review"].values()))["scope"]
+ for r in ledger["records"]
+ )
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 7ee9a5b1a..318bb6b2f 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -251,9 +251,11 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"EcoFAB_Ring_Trial_SynCom17.yaml",
"Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.yaml",
"Electrostimulated_Toluene_Methanogenic_Microbiota.yaml",
+ "Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.yaml",
"Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml",
"Ecoli_GL10_XL12_D_Lactate_Mixed_Sugar_SynCom.yaml",
"Ecoli_K12_MG1655_Arg_Met_CrossFeeding_Coculture.yaml",
+ "Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml",
"Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.yaml",
"Episymbiotic_CPR_DPANN_Groundwater_Community.yaml",
"Eucalyptus_Nursery_FiveStrain_Inoculant_SynCom.yaml",