From 08d44b9bdfd649007ef715601f08c5f0a3f44061 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Wed, 7 Oct 2026 20:46:29 -0700
Subject: [PATCH] Separate transfer, prediction and mediation in four community
graphs (batch107)
---
...illus_Thiamine_Ectomycorrhizal_SynCom.html | 139 ++-
...ulfide_Spring_Autotrophic_CPR_Biofilm.html | 142 ++-
...SynComBac10_Chicken_Intestinal_SynCom.html | 140 ++-
...ynCom_ARC_Peanut_Aflatoxin_Nodulation.html | 191 ++-
.../2026-10-08T032721Z-codex-f26eee.yaml | 28 +
.../2026-10-08T032721Z-codex-525fbf.yaml | 28 +
.../2026-10-08T033029Z-codex-a989db.yaml | 26 +
.../2026-10-08T032722Z-codex-28b659.yaml | 27 +
.../2026-10-08T032722Z-codex-9322a4.yaml | 27 +
...illus_Thiamine_Ectomycorrhizal_SynCom.yaml | 139 ++-
...ulfide_Spring_Autotrophic_CPR_Biofilm.yaml | 152 ++-
...SynComBac10_Chicken_Intestinal_SynCom.yaml | 125 +-
...ynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml | 157 ++-
reports/causal_graph_review/README.md | 25 +
.../adversarial-review-20261008-batch107.yaml | 299 +++++
.../cache-provenance-20261008-batch107.json | 114 ++
.../20261008-four-records-batch107.yaml | 789 ++++++++++++
reports/causal_graph_review/inventory.tsv | 8 +-
reports/causal_graph_review/summary.json | 10 +-
.../validation-20261008-batch107.json | 1096 +++++++++++++++++
tests/test_causal_review_batch107.py | 145 +++
tests/test_participating_taxa.py | 1 +
22 files changed, 3498 insertions(+), 310 deletions(-)
create mode 100644 history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml
create mode 100644 history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml
create mode 100644 history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml
create mode 100644 history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml
create mode 100644 history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261008-batch107.yaml
create mode 100644 reports/causal_graph_review/cache-provenance-20261008-batch107.json
create mode 100644 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
create mode 100644 reports/causal_graph_review/validation-20261008-batch107.json
create mode 100644 tests/test_causal_review_batch107.py
diff --git a/docs/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.html b/docs/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.html
index 3f9225140..05ac477cb 100644
--- a/docs/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.html
+++ b/docs/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.html
@@ -653,6 +653,11 @@ Ecological Interactions
aria-hidden="true" data-symbol="symbolPlus"
data-color="#edab12"> Colonization facilitation
+
+
@@ -662,7 +667,7 @@ Ecological Interactions
Fungal recruitment of the hyphae-associated bacterium
COLONIZATION_FACILITATION
- Suillus clintonianus secretes ureidosuccinic acid and pregnenolone that recruit Bacillus altitudinis B4 to the fungal mycelial surface, establishing the association.
+ Suillus clintonianus exudates attract Bacillus altitudinis B4 and support attachment to fungal hyphae. Ureidosuccinic acid promoted chemotaxis, whereas pregnenolone primarily enhanced swimming and swarming. Their separate effects support recruitment without showing that both compounds are equivalent chemoattractants or that no other exudate contributes.
Source Taxon: Suillus clintonianus
@@ -694,8 +699,7 @@ Fungal recruitment of the hyphae-associated bacterium
→ Ureidosuccinic acid stimulation of bacterial thiamine production
-
Recruitment of B. altitudinis B4 to the S. clintonianus mycelial surface precedes ureidosuccinic-acid stimulation of the recruited bacterium's thiamine biosynthesis.
-
+
HYPOTHESIZED/PARTIAL: recruitment establishes the close fungal-bacterial association in which fungal exudates can stimulate bacterial thiamine production. The authors propose this sequence, but recruitment was not isolated as a necessary mediator of the cue response; ureidosuccinic acid also acted in the separate bacterial assay.
@@ -718,6 +722,19 @@ Evidence
+
+
+
+ "However, pregnenolone could only improve the bacterial motility, including swimming and swarming of B. altitudinis B4"
+
+
+
@@ -725,9 +742,8 @@ Evidence
-
Ureidosuccinic acid secreted by S. clintonianus stimulates B. altitudinis B4 to increase biomass and upregulate thiamine biosynthesis genes, enhancing thiamine production.
+
Ureidosuccinic acid associated with S. clintonianus exudates increased B. altitudinis B4 growth, extracellular thiamine and expression of selected thiamine-metabolism genes in the tested assays. This is a measured metabolite response, not demonstrated uptake of ureidosuccinate as a carbon or nitrogen nutrient. The proposed precursor explanation and the benefit received by the bacterial partner remain unresolved.
Source Taxon: Suillus clintonianus
@@ -766,8 +782,7 @@
Ureidosuccinic acid stimulation of bacterial thiamine production
→ Thiamine provisioning fulfilling the fungal requirement
-
Ureidosuccinic acid-induced biomass increase and thiamine-gene upregulation in B. altitudinis B4 enhance the thiamine pool supplied to the thiamine-limited fungus.
-
+
Ureidosuccinic acid increased extracellular thiamine in the bacterial assay, supporting a greater vitamin supply available to the fungal recipient. Separate coculture and tracer observations support fungal acquisition of bacterial thiamine; they do not quantify what fraction of endogenous transfer is caused by this one exudate.
Evidence
+
+
+
+ "However, it remains unclear what benefits the bacteria gain in this consortium."
+
+
+
@@ -799,7 +827,7 @@ Evidence
Thiamine provisioning fulfilling the fungal requirement
CROSS_FEEDING
- Bacillus altitudinis B4 supplies thiamine that Suillus clintonianus absorbs, promoting fungal growth; the fungus cannot effectively obtain or synthesize thiamine on its own.
+ B. altitudinis B4 supplies thiamine that S. clintonianus acquires under thiamine-deficient conditions. Bacterial supernatant rescued fungal growth, and labeled thiamine derived from bacterial metabolites was detected in fungal hyphae, supporting actual bacterial-to-fungal vitamin transfer. Genomic evidence and vitamin-omission phenotypes support fungal thiamine auxotrophy; the biosynthetic annotation refers to the bacterial donor.
Source Taxon: Bacillus altitudinis B4
@@ -838,8 +866,7 @@ Thiamine provisioning fulfilling the fungal requirement
→ Enhanced ectomycorrhizal colonization of the pine host
-
Bacterially produced thiamine is absorbed by S. clintonianus to promote fungal growth, increasing ectomycorrhizal colonization of P. massoniana.
-
+
HYPOTHESIZED/PARTIAL: bacterial thiamine supports fungal growth and is proposed to contribute to the higher ectomycorrhizal colonization observed with B4 in the pot experiment. The vitamin-mediated route is supported across the assays but is not isolated as the exclusive mediator of the in-plant phenotype.
@@ -862,6 +889,19 @@ Evidence
+
+
+
+ "13C12-thiamine was detected within the S. clintonianus hyphae following their cultivation with metabolites from B. altitudinis B4"
+
+
+
@@ -871,7 +911,7 @@ Evidence
Enhanced ectomycorrhizal colonization of the pine host
MUTUALISM
- The bacterial thiamine supply promotes fungal growth and increases the ectomycorrhizal colonization rate of Suillus clintonianus in association with the host pine Pinus massoniana, completing a vitamin-mediated tripartite symbiosis.
+ The combined S. clintonianus-B4 treatment increased fungal relative biomass and ectomycorrhizal colonization compared with the fungus-only treatment. Pine dry weight, root activity and phosphorus content also increased, supporting a beneficial ectomycorrhizal association rather than colonization alone. B4 alone did not significantly improve seedling performance. The authors interpret this as support for fungal-host mutualism; the pot comparison does not isolate thiamine as the sole mediator or measure bidirectional host-fungal nutrient flux.
Source Taxon: Suillus clintonianus
@@ -915,6 +955,19 @@ Evidence
+
+
+
+ "the dry weight, root activity, and phosphorus content of P. massoniana were significantly greater in the combined treatment compared to the S. clintonianus-only treatment"
+
+
+
@@ -924,6 +977,60 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which parts of recruitment and pine improvement are specifically mediated by the identified fungal cues and bacterial thiamine?
+
+
Direct thiamine transfer and positive fungal/plant outcomes are retained. The source leaves bacterial benefit and cue mechanism unresolved, and the pot treatment does not isolate thiamine as the only driver. Retain the proposed sequence with these limits, without turning cue exposure into demonstrated nutrient consumption or universal reciprocity.
+
+
Attaches to: ecological_interactions#Fungal recruitment of the hyphae-associated bacterium, ecological_interactions#Ureidosuccinic acid stimulation of bacterial thiamine production, ecological_interactions#Thiamine provisioning fulfilling the fungal requirement, ecological_interactions#Enhanced ectomycorrhizal colonization of the pine host
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
However, it remains unclear what benefits the bacteria gain in this consortium.
+
The source explicitly leaves bacterial benefit unresolved; it does not establish reciprocal nutrient exchange.
+
+
+
13C12-thiamine was detected within the S. clintonianus hyphae following their cultivation with metabolites from B. altitudinis B4
+
The reported isotope observation directly supports transfer, beyond bulk supernatant depletion.
+
+
+
+
@@ -1424,7 +1531,7 @@ Evidence
var processes = [];
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1453,7 +1560,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "CROSS_FEEDING";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1466,7 +1573,7 @@ Evidence
processes.push("thiamine biosynthetic process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1508,7 +1615,7 @@ Evidence
processes.push("thiamine biosynthetic process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1546,7 +1653,7 @@ Evidence
processes.push("biological process involved in interspecies interaction between organisms");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
diff --git a/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html b/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html
index a86483893..c2516c96e 100644
--- a/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html
+++ b/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html
@@ -605,7 +605,7 @@ Ecological Interactions
Ecological interaction network for Sulfide Spring Autotrophic CPR-Hosting Biofilm
- 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 (commensalism).
+ 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.
@@ -613,8 +613,8 @@
Ecological Interactions
@@ -623,13 +623,10 @@ Ecological Interactions
-
Filamentous bacteria, likely Thiothrix, contain protein-encapsulated spherical elemental sulfur granules consistent with sulfur-oxidizing chemolithotrophy.
+
STXM and sulfur-edge spectroscopy show protein-associated elemental sulfur granules in filaments from the MS4 and MS11 spring biofilms, consistent with sulfur oxidation. The authors infer Thiothrix-like and Beggiatoa-related identities from the surrounding community evidence. HYPOTHESIZED/PARTIAL: the legacy canonical participant links do not identify the imaged cells, and NCBITaxon:1031 is not established for the MS4 lineage. These observations do not demonstrate commensalism or neutral effects on a host.
-
Source Taxon: Thiothrix
-
Participating Taxa:
@@ -669,16 +666,6 @@
Filamentous Sulfur Oxidation with Encapsulated S Granules
-
-
Downstream Effects:
-
-
-
→ CPR Episymbiosis with Filamentous Hosts
-
The chemolithotrophic Thiothrix- and Beggiatoa-like filaments are the sulfur-oxidizing biofilm structures near which ultra-small CPR-like episymbionts were imaged.
-
-
-
-
Evidence
@@ -690,7 +677,7 @@
Evidence
PMID:38273328
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix"
@@ -703,10 +690,9 @@ Evidence
-
STXM imaging reveals ultra-small cells near the surfaces of filamentous bacteria, suggesting CPR bacterial episymbionts attached to the sulfur-oxidizing hosts.
+
HYPOTHESIZED/PARTIAL: small cells occur near or on sulfur-bearing filaments, and the authors propose that some are CPR episymbionts. Attempts to identify CPR cells by FISH were unsuccessful, so the observed cells, their hosts and the fitness consequences remain unresolved. The source/target links retain legacy canonical cross-references for this proposed association; they do not verify a CPR-Thiothrix nivea pair. A possible cryptic sulfur-cycling symbiosis remains a source hypothesis, not demonstrated exchange.
Source Taxon: Candidate Phyla Radiation (CPR) bacteria
@@ -732,20 +718,23 @@
CPR Episymbiosis with Filamentous Hosts
-
-
Downstream Effects:
-
-
→ CPR Sulfur-Hydrogen Coupling
-
CPR attachment to sulfur-oxidizing filament surfaces places the CPR bacteria in the same cryptic sulfur-cycling biofilm where CPR hydrogenase and thiosulfate-conversion genes were predicted.
-
-
+
Evidence
+
+
+
+
+ "STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts"
+
+
@@ -756,7 +745,7 @@
Evidence
- SUPPORT (IN_VIVO)
- "STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts"
+ "our attempts to perform fluorescent in situ hybridization to determine CPR bacterial identity were unsuccessful due to low amount of material, so this inference remains tentative."
@@ -766,10 +755,9 @@ Evidence
-
Genome-resolved metagenomics predicts that CPR bacteria in the sulfide-spring biofilm contribute to cryptic sulfur and hydrogen cycling through Berkelbacteria and Moranbacteria electron-bifurcating group 3b [NiFe]-hydrogenases and Doudnabacteria thiosulfate-to-sulfite genes.
+
HYPOTHESIZED/PARTIAL: metagenomic gene content, genomic context and structural models suggest a potentially electron-bifurcating group 3b hydrogenase in Berkelbacteria/Moranbacteria and thiosulfate-conversion capacity in Doudnabacteria. These are lineage-specific predictions, not demonstrated enzyme activity, sulfur/hydrogen flux or a capacity shared by every CPR member. The authors suggest that such capacities could contribute to cryptic sulfur symbioses; neither a particular host nor metabolite exchange was experimentally resolved.
@@ -824,7 +812,7 @@
Evidence
PMID:38273328
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b"
@@ -837,7 +825,7 @@ Evidence
PMID:38273328
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite."
@@ -853,6 +841,60 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Can the imaged cells and canonical participant groundings be resolved before asserting a specific CPR-host metabolic interaction?
+
+
The dominant MS4 genome is reported as only 51% average amino-acid similarity to Thiothrix nivea, so the current species identifier is not validated. FISH did not resolve CPR identity. Proximity does not cause encoded metabolic potential; the two former spatial arrows are removed while preserving the observations and source hypotheses. Canonical taxonomy and graph references need a coordinated identity repair; this record remains needs_research.
+
+
Attaches to: ecological_interactions#Filamentous Sulfur Oxidation with Encapsulated S Granules, ecological_interactions#Putative CPR association with sulfur-oxidizing filaments, ecological_interactions#Predicted CPR sulfur and hydrogen metabolic capacity
+
+
+
+
+ 2 evidence item(s)
+
+
+
+
our attempts to perform fluorescent in situ hybridization to determine CPR bacterial identity were unsuccessful due to low amount of material, so this inference remains tentative.
+
States the unresolved identification boundary directly.
+
+
+
The most abundant species in MS4 shares genome-wide average 51% amino acid similarity with the sulfur-oxidizer Thiothrix nivea
+
The source describes similarity to a reference species, not identity as that species.
+
+
+
+
@@ -1069,7 +1111,7 @@ Environmental Factors
(function() {
var intId = "interaction:0";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1097,18 +1139,26 @@ Environmental Factors
});
- var srcKey = "Thiothrix";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Thiothrix",
+
+ "Beggiatoa"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:1";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1117,11 +1167,11 @@ Environmental Factors
processes.push("interspecies interaction between organisms");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "CPR Episymbiosis with Filamentous Hosts",
+ label: "Putative CPR association with sulfur-oxidizing filaments",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1146,7 +1196,7 @@ Environmental Factors
(function() {
var intId = "interaction:2";
- var intType = "COMMENSALISM";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1167,7 +1217,7 @@ Environmental Factors
nodes.push({
id: intId,
- label: "CPR Sulfur-Hydrogen Coupling",
+ label: "Predicted CPR sulfur and hydrogen metabolic capacity",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html b/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html
index 1a2260ce5..97d9e376b 100644
--- a/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html
+++ b/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html
@@ -594,7 +594,7 @@ Ecological Interactions
Ecological interaction network for SynComBac10 Chicken Intestinal SynCom
- 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, competition, colonization facilitation).
+ 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).
@@ -607,13 +607,8 @@
Ecological Interactions
-
-
@@ -621,10 +616,10 @@ Ecological Interactions
-
SynComBac10-derived metabolites, including staphyloferrin B from multiple SynCom members, are predicted to facilitate early establishment of segmented filamentous bacteria in the chicken intestine.
+
HYPOTHESIZED/PARTIAL: iNAP 2.0 predicted potential metabolite exchange from SynComBac10 to segmented filamentous bacteria, including the reported siderophore candidate. Culture-supernatant metabolomics corroborated production of a subset of predicted metabolites, but production is not measured transfer to SFB in the intestine. The source proposes cross-feeding as an explanation for SFB establishment and acknowledges alternative community effects.
@@ -667,7 +662,7 @@
SynCom-Stimulated SFB Cross-Feeding
→ SFB-Driven Th17 Immune Priming
-
SynComBac10 metabolite cross-feeding is the proposed mechanism for early SFB establishment, which then induces Th17 cell-mediated immune responses.
+
HYPOTHESIZED/PARTIAL: predicted nutrient provision may help account for the observed SFB establishment upstream of Th17 induction. The study supports SFB-associated immune induction, but does not establish the predicted exchange as its necessary upstream mediator.
Evidence
PMID:40266232
- - SUPPORT (COMPUTATIONAL)
+ - PARTIAL (COMPUTATIONAL)
"staphyloferrin B, a siderophore, could be provided from six SynComBac10 members (L. reuteri CML393, B. velezensis CML396, E. faecium CML291, M. funiformis CML154, R. lituseburensis CML137, and E. sp. CML138) to SFB"
+
+
+
+ "we performed metabolomic profiling of the bacterial culture supernatants, and ultimately, a total of 18 metabolites were confirmed"
+
+
+
@@ -697,9 +705,8 @@ Evidence
-
Segmented filamentous bacteria enriched after SynComBac10 exposure induce Th17 cell-mediated immune responses in the chicken gut.
+
SFB-associated intervention increased intestinal Th17 cells, supported by cellular profiling and flow cytometry, alongside the Th17 increase in SynComBac10-treated chickens. This is host immune induction, not a colonization-facilitation interaction. The specifically Th17 observation should not be represented only as regulation of innate immunity.
@@ -714,25 +721,14 @@
SFB-Driven Th17 Immune Priming
-
Biological Processes:
-
-
-
- regulation of innate immune response
- (GO:0045088 )
-
-
-
-
Downstream Effects:
-
→ SFB-Mediated Salmonella Resistance
-
Th17 immune priming by SFB supplies the host-mediated protective mechanism that increases resistance to Salmonella infection.
+
→ Host protection after SynComBac10 exposure
+
HYPOTHESIZED/PARTIAL: SFB-associated Th17 responses are proposed to contribute to the protective host outcomes after SynComBac10 exposure. The source explicitly leaves other immune and non-immune contributions open, so this is not an exclusive or experimentally isolated mediation claim.
@@ -755,16 +751,28 @@
Evidence
+
+
+
+ "The induction of Th17 cells after SFB spore inoculation was also evidenced by the flow cytometry results"
+
+
+
-
SFB-mediated immune responses protect the host from Salmonella infection in SynComBac10-treated chickens.
+
SynComBac10-treated chickens showed improved host growth, tissue and serum outcome measures in the reported Salmonella comparison. SFB-associated immune responses are a proposed contributor, not the sole established cause of protection. These host endpoints do not demonstrate reciprocal-negative competition between SFB and Salmonella, pathogen eradication, or a universal effect across hosts.
@@ -805,13 +813,26 @@
Evidence
PMID:40266232
- - SUPPORT (IN_VIVO)
+ - PARTIAL (IN_VIVO)
"SFB-enriched SynComBac10 chickens were highly resistant to Salmonella infection due to the SFB-mediated immune responses"
+
+
+
+ "the anti-Salmonella effect of SynComBac10 treatment may not be solely attributed to its induction of SFB colonization."
+
+
+
@@ -821,6 +842,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How much of the protective host outcome is mediated by predicted metabolite transfer and SFB-associated Th17 responses?
+
+
Retain the measured metabolite-production, immune and host-protection findings. The source does not establish recipient uptake of the predicted metabolites or exclusive mediation through SFB. This record-level repair adds no procedures, strain designs, pathogen enhancement mechanisms or optimization advice.
+
+
Attaches to: ecological_interactions#Predicted SynCom-to-SFB metabolite exchange, ecological_interactions#SFB-Driven Th17 Immune Priming, ecological_interactions#Host protection after SynComBac10 exposure
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
the anti-Salmonella effect of SynComBac10 treatment may not be solely attributed to its induction of SFB colonization.
+
States the source limitation on exclusive SFB mediation.
+
+
+
+
@@ -1054,11 +1114,11 @@ Evidence
processes.push("multi-organism process");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "SynCom-Stimulated SFB Cross-Feeding",
+ label: "Predicted SynCom-to-SFB metabolite exchange",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1086,16 +1146,12 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("regulation of innate immune response");
-
-
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1125,7 +1181,7 @@ Evidence
(function() {
var intId = "interaction:2";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1134,11 +1190,11 @@ Evidence
processes.push("defense response to bacterium");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "SFB-Mediated Salmonella Resistance",
+ label: "Host protection after SynComBac10 exposure",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.html b/docs/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.html
index e56d1d053..1d0b47569 100644
--- a/docs/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.html
+++ b/docs/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.html
@@ -661,7 +661,7 @@ Ecological Interactions
Ecological interaction network for SynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community
- 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 (competition, colonization facilitation).
+ 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 (colonization facilitation).
@@ -669,13 +669,13 @@
Ecological Interactions
@@ -684,13 +684,23 @@ Ecological Interactions
-
The four-strain community inhibits growth of the aflatoxin-producing fungus Aspergillus flavus and lowers peanut aflatoxin levels by 85.6% over four years of field trials, with the abstract additionally reporting that the community acts on multiple targets in the fungus.
-
+
The four-member ARC community inhibited A. flavus in the reported assays. In multi-year field comparisons, harvested peanuts showed lower aflatoxigenic fungal abundance, and the reported mean 85.6% aflatoxin reduction was measured after 12 months of natural storage. These protective outcomes do not demonstrate reciprocal-negative competition or resolve the individual inhibitory compounds.
+
+
Participating Taxa:
+
+ Bacillus (ARC strains Bl13-2C11, Ba13-20E05, Bm14-5G09),
+
+ Enterobacter (ARC strain El17-4B09),
+
+ Aspergillus flavus,
+
+ peanut
+
+
@@ -713,9 +723,8 @@
SynCom ARC Suppression of Aspergillus flavus
Downstream Effects:
-
→ Coupled Aflatoxin Prevention and Nodulation-Supported Yield
-
A. flavus suppression supplies the pathogen-control branch of ARC's coupled peanut field phenotype.
-
+
→ Concurrent aflatoxin reduction, nodulation and yield outcomes
+
HYPOTHESIZED/PARTIAL: fungal suppression contributes to the aflatoxin-control component of the combined protective phenotype. Its contribution to the joint nodulation and yield outcome is not isolated from the other effects of ARC.
Evidence
+
+
+
+ "After 12 months of natural storage, aflatoxin levels were reduced by an average of 85.6%"
+
+
+
@@ -747,12 +769,23 @@ Evidence
SynCom ARC Induction of Rhizobia-Legume Nodulation
COLONIZATION_FACILITATION
- Alongside pathogen suppression, the community enhances peanut nodulation and nitrogenase activity and keeps nodules active through to harvest, so the same consortium that antagonises the fungus facilitates colonisation by the nitrogen-fixing symbiont.
-
+ ARC enhanced peanut nodulation, nitrogenase activity and retention of active nodules. The laboratory comparison found no nodulation with ARC alone but more nodules when ARC accompanied rhizobia, supporting facilitation of the rhizobial-host association rather than nitrogen fixation by the four ARC members themselves. The source also reports increased rhizobial abundance; strain-specific persistence and the responsible compounds are not resolved.
+ Participating Taxa:
+
+ Bacillus (ARC strains Bl13-2C11, Ba13-20E05, Bm14-5G09),
+
+ Enterobacter (ARC strain El17-4B09),
+
+ Bradyrhizobium PHNZY-24-6,
+
+ peanut
+
+
+
@@ -780,9 +813,8 @@ SynCom ARC Induction of Rhizobia-Legume Nodulation
Downstream Effects:
-
→ Coupled Aflatoxin Prevention and Nodulation-Supported Yield
-
Enhanced rhizobia-legume nodulation supplies the nitrogen-fixation branch of ARC's coupled peanut field phenotype.
-
+
→ Concurrent aflatoxin reduction, nodulation and yield outcomes
+
HYPOTHESIZED/PARTIAL: enhanced rhizobial nodulation and nitrogenase activity are proposed to support the higher-yield phenotype alongside improved photosynthesis and carbon allocation. Parallel endpoints and omics associations do not isolate the contribution of nitrogen fixation or prove the proposed feedback quantitatively.
Evidence
+
+
+
+ "Laboratory tests showed ARC alone did not induce nodulation but promoted significantly more nodules when co-inoculated with rhizobia"
+
+
+
-
SynCom ARC joins A. flavus inhibition with rhizobia-legume nodulation induction, enhanced nitrogenase activity, retained active nodules, and improved photosynthesis and carbon supply, producing lower aflatoxin and higher yield without a super-nodulation penalty in field trials.
-
+
ARC-treated field systems combined reduced aflatoxin, greater nodulation and nitrogenase activity, retained active nodules, improved photosynthetic measures and higher yield. These positive outcomes support the reported multifunctional phenotype. The proposed carbon-nitrogen feedback and precise contributions of fungal inhibition versus rhizobial facilitation remain preliminary mechanisms, not an independently demonstrated feedback loop or host antifungal immune response.
@@ -827,12 +870,6 @@
Coupled Aflatoxin Prevention and Nodulation-Supported Yield
Biological Processes:
"SynCom ARC inhibits multiple targets in A. flavus, recruits and activates nodulation and nitrogen fixation in rhizobia and peanut, and improves photosynthesis and carbon supply for aflatoxin prevention and nodulation induction, balancing yield increase"
+
+
+
+ "Building upon the phenotypic effects and preliminary mechanisms revealed in this study"
+
+
+
@@ -882,6 +932,45 @@ Evidence
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which mechanisms quantitatively connect ARC suppression and rhizobial facilitation to the combined field phenotype?
+
+
The positive suppression, nodulation and yield findings remain. The study describes preliminary mechanisms and leaves specific compounds and host regulation unresolved. Retain qualified contributions rather than a demonstrated feedback or host-defense mechanism. Counter-selected candidates remain outside the interaction graph; no toxin-production methods or optimization instructions are added.
+
+
Attaches to: ecological_interactions#SynCom ARC Suppression of Aspergillus flavus, ecological_interactions#SynCom ARC Induction of Rhizobia-Legume Nodulation, ecological_interactions#Concurrent aflatoxin reduction, nodulation and yield outcomes
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
Building upon the phenotypic effects and preliminary mechanisms revealed in this study
+
The source distinguishes phenotypic effects from preliminary mechanistic interpretation.
+
+
+
+
@@ -1363,7 +1452,7 @@ Evidence
(function() {
var intId = "interaction:0";
- var intType = "COMPETITION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1372,7 +1461,7 @@ Evidence
processes.push("biological process involved in interspecies interaction between organisms");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1387,6 +1476,23 @@ Evidence
+ var participantKeys = [
+
+ "Bacillus (ARC strains Bl13-2C11, Ba13-20E05, Bm14-5G09)",
+
+ "Enterobacter (ARC strain El17-4B09)",
+
+ "Aspergillus flavus",
+
+ "peanut"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
@@ -1402,7 +1508,7 @@ Evidence
processes.push("nitrogen fixation");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
@@ -1417,18 +1523,33 @@ Evidence
+ var participantKeys = [
+
+ "Bacillus (ARC strains Bl13-2C11, Ba13-20E05, Bm14-5G09)",
+
+ "Enterobacter (ARC strain El17-4B09)",
+
+ "Bradyrhizobium PHNZY-24-6",
+
+ "peanut"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
+
})();
(function() {
var intId = "interaction:2";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
- processes.push("defense response to fungus");
-
processes.push("nodulation");
processes.push("nitrogen fixation");
@@ -1436,11 +1557,11 @@ Evidence
processes.push("photosynthesis");
- var evidenceCount = 1;
+ var evidenceCount = 2;
nodes.push({
id: intId,
- label: "Coupled Aflatoxin Prevention and Nodulation-Supported Yield",
+ label: "Concurrent aflatoxin reduction, nodulation and yield outcomes",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml b/history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml
new file mode 100644
index 000000000..70c3c2dce
--- /dev/null
+++ b/history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml
+ slug: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+session:
+ id: 2026-10-08T032721Z-codex-f26eee
+ timestamp: '2026-10-08T03:27:21Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1837
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain recruitment, distinguishing chemotaxis from motility and qualifying its
+ necessity for the cue response.; Retain the measured cue response without asserting nutrient
+ uptake or resolved bacterial benefit.; Preserve experimentally supported thiamine transfer
+ and growth rescue; qualify in-plant mediation.; Preserve fungal and host benefits and
+ the source mutualism interpretation without exclusive mediator or flux claims.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
diff --git a/history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml b/history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml
new file mode 100644
index 000000000..287dadf7b
--- /dev/null
+++ b/history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
+ slug: Sulfide_Spring_Autotrophic_CPR_Biofilm
+session:
+ id: 2026-10-08T032721Z-codex-525fbf
+ timestamp: '2026-10-08T03:27:21Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1838
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve sulfur-granule observations; remove commensalism and redundant source,
+ explicitly leaving species grounding unresolved.; Preserve the source episymbiosis hypothesis
+ without confirmed cell identity or fitness interpretation; remove the spatial causal arrow.;
+ Preserve lineage-specific genomic/structural predictions with provenance, not measured
+ flux or host exchange.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
diff --git a/history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml b/history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml
new file mode 100644
index 000000000..91a3fd8b9
--- /dev/null
+++ b/history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
+ slug: Sulfide_Spring_Autotrophic_CPR_Biofilm
+session:
+ id: 2026-10-08T033029Z-codex-a989db
+ timestamp: '2026-10-08T03:30:29Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1838
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ summary: Narrow Doudnabacteria sulfur-enzyme provenance to METABOLIC and AlphaFold2; HydDB
+ applies only to the separate hydrogenase prediction.
+ details: Adversarial correction after history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml.
+ The prior artifact remains byte-identical. HydDB classifies hydrogenases, not the separately
+ predicted sulfur enzymes. No biological topology or snippet change.
diff --git a/history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml b/history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml
new file mode 100644
index 000000000..7230577f8
--- /dev/null
+++ b/history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml
+ slug: SynComBac10_Chicken_Intestinal_SynCom
+session:
+ id: 2026-10-08T032722Z-codex-28b659
+ timestamp: '2026-10-08T03:27:22Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1839
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Preserve predicted exchange and measured metabolite production with iNAP provenance
+ and an explicitly partial upstream mechanism.; Preserve supported Th17 induction; remove
+ colonization typing and the mismatched innate-only GO annotation.; Preserve positive host-protection
+ endpoints without competition, eradication or exclusive SFB mediation.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
diff --git a/history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml b/history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml
new file mode 100644
index 000000000..d2248ad69
--- /dev/null
+++ b/history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml
+ slug: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+session:
+ id: 2026-10-08T032722Z-codex-9322a4
+ timestamp: '2026-10-08T03:27:22Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1840
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain protective fungal/aflatoxin endpoints with the storage-time boundary, without
+ reciprocal competition.; Retain rhizobia-dependent nodulation facilitation with participant
+ scope excluding the fungal target.; Retain combined positive outcomes, qualifying causal
+ coupling and removing misplaced colonization/host-defense typing.
+ details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
diff --git a/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml b/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml
index 9fe7a7dae..18ae36431 100644
--- a/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml
+++ b/kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml
@@ -122,8 +122,10 @@ taxonomy:
community-scale outcome.
ecological_interactions:
- name: Fungal recruitment of the hyphae-associated bacterium
- description: Suillus clintonianus secretes ureidosuccinic acid and pregnenolone that recruit
- Bacillus altitudinis B4 to the fungal mycelial surface, establishing the association.
+ description: Suillus clintonianus exudates attract Bacillus altitudinis B4 and support attachment to fungal hyphae.
+ Ureidosuccinic acid promoted chemotaxis, whereas pregnenolone primarily enhanced swimming and swarming. Their
+ separate effects support recruitment without showing that both compounds are equivalent chemoattractants or
+ that no other exudate contributes.
interaction_type: COLONIZATION_FACILITATION
scope: PAIRWISE
source_taxon:
@@ -147,22 +149,28 @@ ecological_interactions:
label: pregnenolone
downstream:
- target: Ureidosuccinic acid stimulation of bacterial thiamine production
- description: >
- Recruitment of B. altitudinis B4 to the S. clintonianus mycelial surface
- precedes ureidosuccinic-acid stimulation of the recruited bacterium's
- thiamine biosynthesis.
+ description: 'HYPOTHESIZED/PARTIAL: recruitment establishes the close fungal-bacterial association in which
+ fungal exudates can stimulate bacterial thiamine production. The authors propose this sequence, but recruitment
+ was not isolated as a necessary mediator of the cue response; ureidosuccinic acid also acted in the separate
+ bacterial assay.'
evidence:
- reference: PMID:41454778
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: S. clintonianus first secreted ureidosuccinic acid and pregnenolone, recruiting the
- hyphae-associated bacterium B. altitudinis B4 to the mycelial surface
- explanation: Supports fungal exudate-driven recruitment of the bacterium via ureidosuccinic acid
- and pregnenolone.
+ snippet: S. clintonianus first secreted ureidosuccinic acid and pregnenolone, recruiting the hyphae-associated
+ bacterium B. altitudinis B4 to the mycelial surface
+ explanation: Supports fungal exudate-driven recruitment of the bacterium via ureidosuccinic acid and pregnenolone.
+ - reference: PMID:41454778
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: However, pregnenolone could only improve the bacterial motility, including swimming and swarming of
+ B. altitudinis B4
+ explanation: Distinguishes the measured motility effect from the ureidosuccinate chemotaxis result.
- name: Ureidosuccinic acid stimulation of bacterial thiamine production
- description: Ureidosuccinic acid secreted by S. clintonianus stimulates B. altitudinis B4 to
- increase biomass and upregulate thiamine biosynthesis genes, enhancing thiamine production.
- interaction_type: CROSS_FEEDING
+ description: Ureidosuccinic acid associated with S. clintonianus exudates increased B. altitudinis B4 growth,
+ extracellular thiamine and expression of selected thiamine-metabolism genes in the tested assays. This is a
+ measured metabolite response, not demonstrated uptake of ureidosuccinate as a carbon or nitrogen nutrient. The
+ proposed precursor explanation and the benefit received by the bacterial partner remain unresolved.
scope: PAIRWISE
source_taxon:
preferred_term: Suillus clintonianus
@@ -186,21 +194,28 @@ ecological_interactions:
label: thiamine biosynthetic process
downstream:
- target: Thiamine provisioning fulfilling the fungal requirement
- description: >
- Ureidosuccinic acid-induced biomass increase and thiamine-gene
- upregulation in B. altitudinis B4 enhance the thiamine pool supplied to
- the thiamine-limited fungus.
+ description: Ureidosuccinic acid increased extracellular thiamine in the bacterial assay, supporting a greater
+ vitamin supply available to the fungal recipient. Separate coculture and tracer observations support fungal
+ acquisition of bacterial thiamine; they do not quantify what fraction of endogenous transfer is caused by
+ this one exudate.
evidence:
- reference: PMID:41454778
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: the ureidosuccinic acid secreted by S. clintonianus further stimulated B. altitudinis B4
- to enhance thiamine production
- explanation: Supports fungal ureidosuccinic acid as the cue that upregulates bacterial thiamine
- biosynthesis.
+ snippet: the ureidosuccinic acid secreted by S. clintonianus further stimulated B. altitudinis B4 to enhance
+ thiamine production
+ explanation: Supports fungal ureidosuccinic acid as the cue that upregulates bacterial thiamine biosynthesis.
+ - reference: PMID:41454778
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: However, it remains unclear what benefits the bacteria gain in this consortium.
+ explanation: The source explicitly leaves bacterial benefit unresolved; it does not establish reciprocal nutrient
+ exchange.
- name: Thiamine provisioning fulfilling the fungal requirement
- description: Bacillus altitudinis B4 supplies thiamine that Suillus clintonianus absorbs, promoting
- fungal growth; the fungus cannot effectively obtain or synthesize thiamine on its own.
+ description: B. altitudinis B4 supplies thiamine that S. clintonianus acquires under thiamine-deficient conditions.
+ Bacterial supernatant rescued fungal growth, and labeled thiamine derived from bacterial metabolites was detected
+ in fungal hyphae, supporting actual bacterial-to-fungal vitamin transfer. Genomic evidence and vitamin-omission
+ phenotypes support fungal thiamine auxotrophy; the biosynthetic annotation refers to the bacterial donor.
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -225,21 +240,27 @@ ecological_interactions:
label: thiamine biosynthetic process
downstream:
- target: Enhanced ectomycorrhizal colonization of the pine host
- description: >
- Bacterially produced thiamine is absorbed by S. clintonianus to promote
- fungal growth, increasing ectomycorrhizal colonization of P. massoniana.
+ description: 'HYPOTHESIZED/PARTIAL: bacterial thiamine supports fungal growth and is proposed to contribute
+ to the higher ectomycorrhizal colonization observed with B4 in the pot experiment. The vitamin-mediated route
+ is supported across the assays but is not isolated as the exclusive mediator of the in-plant phenotype.'
evidence:
- reference: PMID:41454778
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: S. clintonianus absorbed the thiamine secreted by the B. altitudinis B4, promoting
- fungal growth
- explanation: Supports thiamine cross-feeding from bacterium to fungus and the resulting fungal
- growth benefit.
+ snippet: S. clintonianus absorbed the thiamine secreted by the B. altitudinis B4, promoting fungal growth
+ explanation: Supports thiamine cross-feeding from bacterium to fungus and the resulting fungal growth benefit.
+ - reference: PMID:41454778
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 13C12-thiamine was detected within the S. clintonianus hyphae following their cultivation with metabolites
+ from B. altitudinis B4
+ explanation: The reported isotope observation directly supports transfer, beyond bulk supernatant depletion.
- name: Enhanced ectomycorrhizal colonization of the pine host
- description: The bacterial thiamine supply promotes fungal growth and increases the ectomycorrhizal
- colonization rate of Suillus clintonianus in association with the host pine Pinus massoniana,
- completing a vitamin-mediated tripartite symbiosis.
+ description: The combined S. clintonianus-B4 treatment increased fungal relative biomass and ectomycorrhizal colonization
+ compared with the fungus-only treatment. Pine dry weight, root activity and phosphorus content also increased,
+ supporting a beneficial ectomycorrhizal association rather than colonization alone. B4 alone did not significantly
+ improve seedling performance. The authors interpret this as support for fungal-host mutualism; the pot comparison
+ does not isolate thiamine as the sole mediator or measure bidirectional host-fungal nutrient flux.
interaction_type: MUTUALISM
scope: PAIRWISE
source_taxon:
@@ -261,10 +282,15 @@ ecological_interactions:
- reference: PMID:41454778
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: promoting fungal growth and increasing the colonization rate in association with Pinus
- massoniana
- explanation: Supports increased ectomycorrhizal colonization of the pine host as the outcome of
- the thiamine cross-feeding.
+ snippet: promoting fungal growth and increasing the colonization rate in association with Pinus massoniana
+ explanation: Supports increased ectomycorrhizal colonization of the pine host as the outcome of the thiamine
+ cross-feeding.
+ - reference: PMID:41454778
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: the dry weight, root activity, and phosphorus content of P. massoniana were significantly greater in
+ the combined treatment compared to the S. clintonianus-only treatment
+ explanation: Supports the host benefit that accompanies the increased fungal biomass and colonization.
growth_media:
- name: Potato dextrose agar, ectomycorrhizal fungal isolation and culture
composition:
@@ -464,3 +490,42 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this thiamine cross-feeding
ectomycorrhizal community.
+discussions:
+- discussion_id: suillus-cue-transfer-and-plant-mediation
+ prompt: Which parts of recruitment and pine improvement are specifically mediated by the identified fungal cues
+ and bacterial thiamine?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Fungal recruitment of the hyphae-associated bacterium
+ - ecological_interactions#Ureidosuccinic acid stimulation of bacterial thiamine production
+ - ecological_interactions#Thiamine provisioning fulfilling the fungal requirement
+ - ecological_interactions#Enhanced ectomycorrhizal colonization of the pine host
+ rationale: Direct thiamine transfer and positive fungal/plant outcomes are retained. The source leaves bacterial
+ benefit and cue mechanism unresolved, and the pot treatment does not isolate thiamine as the only driver. Retain
+ the proposed sequence with these limits, without turning cue exposure into demonstrated nutrient consumption
+ or universal reciprocity.
+ evidence:
+ - reference: PMID:41454778
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: However, it remains unclear what benefits the bacteria gain in this consortium.
+ explanation: The source explicitly leaves bacterial benefit unresolved; it does not establish reciprocal nutrient
+ exchange.
+ - reference: PMID:41454778
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: 13C12-thiamine was detected within the S. clintonianus hyphae following their cultivation with metabolites
+ from B. altitudinis B4
+ explanation: The reported isotope observation directly supports transfer, beyond bulk supernatant depletion.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T03:27:19Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain recruitment, distinguishing chemotaxis from motility and qualifying its necessity for the cue
+ response.; Retain the measured cue response without asserting nutrient uptake or resolved bacterial benefit.;
+ Preserve experimentally supported thiamine transfer and growth rescue; qualify in-plant mediation.; Preserve
+ fungal and host benefits and the source mutualism interpretation without exclusive mediator or flux claims.
+ Issue#1837; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ llm_assisted: true
diff --git a/kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml b/kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
index f0cb2cad6..38d827dee 100644
--- a/kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
+++ b/kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
@@ -170,10 +170,11 @@ related_ingredients:
explanation: Attributes hydrogen cycling roles to the biofilm CPR bacteria.
ecological_interactions:
- name: Filamentous Sulfur Oxidation with Encapsulated S Granules
- description: Filamentous bacteria, likely Thiothrix, contain
- protein-encapsulated spherical elemental sulfur granules consistent with
- sulfur-oxidizing chemolithotrophy.
- interaction_type: COMMENSALISM
+ description: 'STXM and sulfur-edge spectroscopy show protein-associated elemental sulfur granules in filaments
+ from the MS4 and MS11 spring biofilms, consistent with sulfur oxidation. The authors infer Thiothrix-like and
+ Beggiatoa-related identities from the surrounding community evidence. HYPOTHESIZED/PARTIAL: the legacy canonical
+ participant links do not identify the imaged cells, and NCBITaxon:1031 is not established for the MS4 lineage.
+ These observations do not demonstrate commensalism or neutral effects on a host.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Thiothrix
@@ -184,11 +185,6 @@ ecological_interactions:
term:
id: NCBITaxon:1021
label: Beggiatoa
- source_taxon:
- preferred_term: Thiothrix
- term:
- id: NCBITaxon:1031
- label: Thiothrix nivea
metabolites:
- preferred_term: sulfide
term:
@@ -203,25 +199,20 @@ ecological_interactions:
term:
id: GO:0006790
label: sulfur compound metabolic process
- downstream:
- - target: CPR Episymbiosis with Filamentous Hosts
- description: The chemolithotrophic Thiothrix- and Beggiatoa-like filaments
- are the sulfur-oxidizing biofilm structures near which ultra-small
- CPR-like episymbionts were imaged.
evidence:
- reference: PMID:38273328
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VIVO
- snippet: filamentous bacteria contain protein-encapsulated spherical
- elemental sulfur granules, indicating that they are sulfur oxidizers,
- likely Thiothrix
- explanation: Supports the curated sulfur-oxidizing role of the filamentous
- Thiothrix-like bacteria.
-- name: CPR Episymbiosis with Filamentous Hosts
- description: STXM imaging reveals ultra-small cells near the surfaces of
- filamentous bacteria, suggesting CPR bacterial episymbionts attached to the
- sulfur-oxidizing hosts.
- interaction_type: COMMENSALISM
+ snippet: filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that
+ they are sulfur oxidizers, likely Thiothrix
+ explanation: Supports sulfur-containing filaments and a likely taxonomic interpretation, not identification
+ as Thiothrix nivea or an organism-to-organism fitness relationship.
+- name: Putative CPR association with sulfur-oxidizing filaments
+ description: 'HYPOTHESIZED/PARTIAL: small cells occur near or on sulfur-bearing filaments, and the authors propose
+ that some are CPR episymbionts. Attempts to identify CPR cells by FISH were unsuccessful, so the observed cells,
+ their hosts and the fitness consequences remain unresolved. The source/target links retain legacy canonical
+ cross-references for this proposed association; they do not verify a CPR-Thiothrix nivea pair. A possible cryptic
+ sulfur-cycling symbiosis remains a source hypothesis, not demonstrated exchange.'
scope: PAIRWISE
source_taxon:
preferred_term: Candidate Phyla Radiation (CPR) bacteria
@@ -238,24 +229,26 @@ ecological_interactions:
term:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
- downstream:
- - target: CPR Sulfur-Hydrogen Coupling
- description: CPR attachment to sulfur-oxidizing filament surfaces places
- the CPR bacteria in the same cryptic sulfur-cycling biofilm where
- CPR hydrogenase and thiosulfate-conversion genes were predicted.
evidence:
+ - reference: PMID:38273328
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial
+ episymbionts
+ explanation: Supports a tentative identity/association inference from imaging, not confirmed CPR-host identities
+ or commensalism.
- reference: PMID:38273328
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: STXM imaging revealed ultra-small cells near the surfaces of
- filamentous bacteria that may be CPR bacterial episymbionts
- explanation: Supports the proposed CPR episymbiotic association.
-- name: CPR Sulfur-Hydrogen Coupling
- description: Genome-resolved metagenomics predicts that CPR bacteria in the
- sulfide-spring biofilm contribute to cryptic sulfur and hydrogen cycling
- through Berkelbacteria and Moranbacteria electron-bifurcating group 3b
- [NiFe]-hydrogenases and Doudnabacteria thiosulfate-to-sulfite genes.
- interaction_type: COMMENSALISM
+ snippet: our attempts to perform fluorescent in situ hybridization to determine CPR bacterial identity were
+ unsuccessful due to low amount of material, so this inference remains tentative.
+ explanation: States the unresolved identification boundary directly.
+- name: Predicted CPR sulfur and hydrogen metabolic capacity
+ description: 'HYPOTHESIZED/PARTIAL: metagenomic gene content, genomic context and structural models suggest a
+ potentially electron-bifurcating group 3b hydrogenase in Berkelbacteria/Moranbacteria and thiosulfate-conversion
+ capacity in Doudnabacteria. These are lineage-specific predictions, not demonstrated enzyme activity, sulfur/hydrogen
+ flux or a capacity shared by every CPR member. The authors suggest that such capacities could contribute to
+ cryptic sulfur symbioses; neither a particular host nor metabolite exchange was experimentally resolved.'
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: Candidate Phyla Radiation (CPR) bacteria
@@ -282,18 +275,39 @@ ecological_interactions:
label: sulfur compound metabolic process
evidence:
- reference: PMID:38273328
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: Berkelbacteria and Moranbacteria in the same biofilm sample are predicted
- to have a novel electron bifurcating group 3b
+ snippet: Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron
+ bifurcating group 3b
explanation: Supports predicted CPR hydrogenases linked to sulfur metabolism.
+ computational_provenance:
+ prediction_type: OTHER
+ tools:
+ - tool_name: METABOLIC
+ role: Functional annotation of metagenomic bins
+ - tool_name: HydDB
+ role: Reference classification of hydrogenases with HMM and genomic-context evidence
+ - tool_name: AlphaFold2
+ role: Multimer structural modeling of putative complexes
+ model_source: Genome-resolved metagenomic bins from the Alum Rock springs
+ parameters: Gene content, genomic context, homology and structural predictions; no flux simulation or measured
+ exchange.
- reference: PMID:38273328
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that
- may convert thiosulfate to sulfite.
- explanation: Supports a predicted thiosulfate-to-sulfite conversion route in
- the CPR sulfur cycle.
+ snippet: One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert
+ thiosulfate to sulfite.
+ explanation: Supports a predicted thiosulfate-to-sulfite conversion route in the CPR sulfur cycle.
+ computational_provenance:
+ prediction_type: OTHER
+ tools:
+ - tool_name: METABOLIC
+ role: Functional annotation of metagenomic bins
+ - tool_name: AlphaFold2
+ role: Multimer structural modeling of putative complexes
+ model_source: Genome-resolved metagenomic bins from the Alum Rock springs
+ parameters: Gene content, genomic context, homology and structural predictions; no flux simulation or measured
+ exchange.
environmental_factors:
- name: Sulfide-rich groundwater
value: deeply sourced sulfide-rich spring water
@@ -331,3 +345,47 @@ rare_earth_elements_present: []
metal_relevance: NOT_APPLICABLE
metal_notes: No metal or rare earth element processing role is curated for this
sulfide-spring biofilm.
+discussions:
+- discussion_id: spring-unresolved-cell-identity-and-metabolic-coupling
+ prompt: Can the imaged cells and canonical participant groundings be resolved before asserting a specific CPR-host
+ metabolic interaction?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Filamentous Sulfur Oxidation with Encapsulated S Granules
+ - ecological_interactions#Putative CPR association with sulfur-oxidizing filaments
+ - ecological_interactions#Predicted CPR sulfur and hydrogen metabolic capacity
+ rationale: The dominant MS4 genome is reported as only 51% average amino-acid similarity to Thiothrix nivea, so
+ the current species identifier is not validated. FISH did not resolve CPR identity. Proximity does not cause
+ encoded metabolic potential; the two former spatial arrows are removed while preserving the observations and
+ source hypotheses. Canonical taxonomy and graph references need a coordinated identity repair; this record remains
+ needs_research.
+ evidence:
+ - reference: PMID:38273328
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: our attempts to perform fluorescent in situ hybridization to determine CPR bacterial identity were
+ unsuccessful due to low amount of material, so this inference remains tentative.
+ explanation: States the unresolved identification boundary directly.
+ - reference: PMID:38273328
+ supports: SUPPORT
+ evidence_source: COMPUTATIONAL
+ snippet: The most abundant species in MS4 shares genome-wide average 51% amino acid similarity with the sulfur-oxidizer
+ Thiothrix nivea
+ explanation: The source describes similarity to a reference species, not identity as that species.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T03:27:20Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve sulfur-granule observations; remove commensalism and redundant source, explicitly leaving species
+ grounding unresolved.; Preserve the source episymbiosis hypothesis without confirmed cell identity or fitness
+ interpretation; remove the spatial causal arrow.; Preserve lineage-specific genomic/structural predictions with
+ provenance, not measured flux or host exchange. Issue#1838; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ llm_assisted: true
+- timestamp: '2026-10-08T03:30:28Z'
+ curator: codex
+ action: CORRECT_EVIDENCE_PROVENANCE
+ changes: Narrow Doudnabacteria sulfur-enzyme provenance to METABOLIC and AlphaFold2; HydDB applies only to the
+ separate hydrogenase prediction. Adversarial follow-up to Issue1838; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ llm_assisted: true
diff --git a/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml b/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml
index 9ea495f7f..df1a9e102 100644
--- a/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml
+++ b/kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml
@@ -97,10 +97,12 @@ taxonomy:
explanation: Identifies Salmonella Typhimurium as a pathogen tested against the stable
SynComBac10 consortium.
ecological_interactions:
-- name: SynCom-Stimulated SFB Cross-Feeding
- description: SynComBac10-derived metabolites, including staphyloferrin B from multiple SynCom
- members, are predicted to facilitate early establishment of segmented filamentous bacteria in
- the chicken intestine.
+- name: Predicted SynCom-to-SFB metabolite exchange
+ description: 'HYPOTHESIZED/PARTIAL: iNAP 2.0 predicted potential metabolite exchange from SynComBac10 to segmented
+ filamentous bacteria, including the reported siderophore candidate. Culture-supernatant metabolomics corroborated
+ production of a subset of predicted metabolites, but production is not measured transfer to SFB in the intestine.
+ The source proposes cross-feeding as an explanation for SFB establishment and acknowledges alternative community
+ effects.'
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
participating_taxa:
@@ -124,48 +126,65 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: SFB-Driven Th17 Immune Priming
- description: SynComBac10 metabolite cross-feeding is the proposed mechanism for early SFB
- establishment, which then induces Th17 cell-mediated immune responses.
+ description: 'HYPOTHESIZED/PARTIAL: predicted nutrient provision may help account for the observed SFB establishment
+ upstream of Th17 induction. The study supports SFB-associated immune induction, but does not establish the
+ predicted exchange as its necessary upstream mediator.'
evidence:
- reference: PMID:40266232
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: COMPUTATIONAL
- snippet: staphyloferrin B, a siderophore, could be provided from six SynComBac10 members
- (L. reuteri CML393, B. velezensis CML396, E. faecium CML291, M. funiformis CML154,
- R. lituseburensis CML137, and E. sp. CML138) to SFB
- explanation: In-silico transfer analysis predicts staphyloferrin B as an iron-scavenging
- metabolite supplied by six SynComBac10 members to SFB.
+ snippet: staphyloferrin B, a siderophore, could be provided from six SynComBac10 members (L. reuteri CML393,
+ B. velezensis CML396, E. faecium CML291, M. funiformis CML154, R. lituseburensis CML137, and E. sp. CML138)
+ to SFB
+ explanation: Supports a predicted donor-recipient route, not experimentally traced in-host transfer.
+ computational_provenance:
+ prediction_type: METABOLIC_INTERACTION_SIMULATION
+ tools:
+ - tool_name: iNAP
+ tool_version: '2.0'
+ role: Prediction of potentially transferable metabolites
+ model_source: Metabolic information from SynComBac10 member and reconstructed SFB genomes
+ parameters: Potential transfer prediction; supernatant metabolite detection is separate evidence and does
+ not measure recipient uptake.
+ - reference: PMID:40266232
+ supports: SUPPORT
+ evidence_source: IN_VITRO
+ snippet: we performed metabolomic profiling of the bacterial culture supernatants, and ultimately, a total of
+ 18 metabolites were confirmed
+ explanation: Preserves the positive metabolite-detection result without equating production with transfer.
- name: SFB-Driven Th17 Immune Priming
- description: Segmented filamentous bacteria enriched after SynComBac10 exposure induce Th17
- cell-mediated immune responses in the chicken gut.
- interaction_type: COLONIZATION_FACILITATION
+ description: SFB-associated intervention increased intestinal Th17 cells, supported by cellular profiling and
+ flow cytometry, alongside the Th17 increase in SynComBac10-treated chickens. This is host immune induction,
+ not a colonization-facilitation interaction. The specifically Th17 observation should not be represented only
+ as regulation of innate immunity.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: segmented filamentous bacteria
term:
id: NCBITaxon:49082
label: Candidatus Neoarthromitus
- biological_processes:
- - preferred_term: regulation of innate immune response
- term:
- id: GO:0045088
- label: regulation of innate immune response
downstream:
- - target: SFB-Mediated Salmonella Resistance
- description: Th17 immune priming by SFB supplies the host-mediated protective mechanism that
- increases resistance to Salmonella infection.
+ - target: Host protection after SynComBac10 exposure
+ description: 'HYPOTHESIZED/PARTIAL: SFB-associated Th17 responses are proposed to contribute to the protective
+ host outcomes after SynComBac10 exposure. The source explicitly leaves other immune and non-immune contributions
+ open, so this is not an exclusive or experimentally isolated mediation claim.'
evidence:
- reference: PMID:40266232
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SFB), which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance
- to Salmonella infection
- explanation: SynComBac10-promoted SFB growth is reported upstream of Th17 immune responses
- and Salmonella resistance.
-- name: SFB-Mediated Salmonella Resistance
- description: SFB-mediated immune responses protect the host from Salmonella infection in
- SynComBac10-treated chickens.
- interaction_type: COMPETITION
+ snippet: SFB), which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella
+ infection
+ explanation: SynComBac10-promoted SFB growth is reported upstream of Th17 immune responses and Salmonella resistance.
+ - reference: PMID:40266232
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: The induction of Th17 cells after SFB spore inoculation was also evidenced by the flow cytometry results
+ explanation: Supports the positive cellular immune endpoint beyond transcript association.
+- name: Host protection after SynComBac10 exposure
+ description: SynComBac10-treated chickens showed improved host growth, tissue and serum outcome measures in the
+ reported Salmonella comparison. SFB-associated immune responses are a proposed contributor, not the sole established
+ cause of protection. These host endpoints do not demonstrate reciprocal-negative competition between SFB and
+ Salmonella, pathogen eradication, or a universal effect across hosts.
scope: COMMUNITY_LEVEL
participating_taxa:
- preferred_term: segmented filamentous bacteria
@@ -182,13 +201,19 @@ ecological_interactions:
id: GO:0042742
label: defense response to bacterium
evidence:
+ - reference: PMID:40266232
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: SFB-enriched SynComBac10 chickens were highly resistant to Salmonella infection due to the SFB-mediated
+ immune responses
+ explanation: The authors attribute host protection to SFB immunity, but explicitly qualify exclusive attribution
+ in the discussion.
- reference: PMID:40266232
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SFB-enriched SynComBac10 chickens were highly resistant to Salmonella infection due to
- the SFB-mediated immune responses
- explanation: Supports SFB-mediated host immunity as the resistance mechanism that suppresses
- Salmonella infection in SynComBac10-treated chickens.
+ snippet: the anti-Salmonella effect of SynComBac10 treatment may not be solely attributed to its induction of
+ SFB colonization.
+ explanation: States the source limitation on exclusive SFB mediation.
environmental_factors:
- name: early-life gut SynCom exposure
value: Chickens were exposed early in life to SynComBac10 and evaluated for gut maturation and Salmonella
@@ -239,3 +264,33 @@ growth_media:
evidence_source: IN_VITRO
snippet: absolute abundance of 10 strains in GAM medium
explanation: GAM (Gifu Anaerobic Medium) used to culture the 10-member consortium.
+discussions:
+- discussion_id: chicken-predicted-transfer-and-nonexclusive-protection
+ prompt: How much of the protective host outcome is mediated by predicted metabolite transfer and SFB-associated
+ Th17 responses?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Predicted SynCom-to-SFB metabolite exchange
+ - ecological_interactions#SFB-Driven Th17 Immune Priming
+ - ecological_interactions#Host protection after SynComBac10 exposure
+ rationale: Retain the measured metabolite-production, immune and host-protection findings. The source does not
+ establish recipient uptake of the predicted metabolites or exclusive mediation through SFB. This record-level
+ repair adds no procedures, strain designs, pathogen enhancement mechanisms or optimization advice.
+ evidence:
+ - reference: PMID:40266232
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: the anti-Salmonella effect of SynComBac10 treatment may not be solely attributed to its induction of
+ SFB colonization.
+ explanation: States the source limitation on exclusive SFB mediation.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T03:27:20Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Preserve predicted exchange and measured metabolite production with iNAP provenance and an explicitly
+ partial upstream mechanism.; Preserve supported Th17 induction; remove colonization typing and the mismatched
+ innate-only GO annotation.; Preserve positive host-protection endpoints without competition, eradication or
+ exclusive SFB mediation. Issue#1839; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ llm_assisted: true
diff --git a/kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml b/kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml
index af9e3b482..cae51cd41 100644
--- a/kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml
+++ b/kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml
@@ -192,11 +192,10 @@ taxonomy:
explanation: Names peanut as the host and the nodulation endpoint measured in it.
ecological_interactions:
- name: SynCom ARC Suppression of Aspergillus flavus
- description: >
- The four-strain community inhibits growth of the aflatoxin-producing fungus Aspergillus flavus
- and lowers peanut aflatoxin levels by 85.6% over four years of field trials, with the abstract
- additionally reporting that the community acts on multiple targets in the fungus.
- interaction_type: COMPETITION
+ description: The four-member ARC community inhibited A. flavus in the reported assays. In multi-year field comparisons,
+ harvested peanuts showed lower aflatoxigenic fungal abundance, and the reported mean 85.6% aflatoxin reduction
+ was measured after 12 months of natural storage. These protective outcomes do not demonstrate reciprocal-negative
+ competition or resolve the individual inhibitory compounds.
scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: biological process involved in interspecies interaction between organisms
@@ -204,23 +203,45 @@ ecological_interactions:
id: GO:0044419
label: biological process involved in interspecies interaction between organisms
downstream:
- - target: Coupled Aflatoxin Prevention and Nodulation-Supported Yield
- description: >
- A. flavus suppression supplies the pathogen-control branch of ARC's coupled
- peanut field phenotype.
+ - target: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ description: 'HYPOTHESIZED/PARTIAL: fungal suppression contributes to the aflatoxin-control component of the
+ combined protective phenotype. Its contribution to the joint nodulation and yield outcome is not isolated
+ from the other effects of ARC.'
evidence:
- reference: PMID:42099455
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom ARC inhibits A. flavus growth and reduces peanut aflatoxin levels by 85.6% in 4
- year field trials
- explanation: Supports community-level antagonism of the pathogen with a quantified field
- outcome.
+ snippet: SynCom ARC inhibits A. flavus growth and reduces peanut aflatoxin levels by 85.6% in 4 year field trials
+ explanation: Supports community-level antagonism of the pathogen with a quantified field outcome.
+ - reference: PMID:42099455
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: After 12 months of natural storage, aflatoxin levels were reduced by an average of 85.6%
+ explanation: Locates the quantitative aflatoxin endpoint after storage rather than asserting an immediate field-stage
+ reduction.
+ participating_taxa:
+ - preferred_term: Bacillus (ARC strains Bl13-2C11, Ba13-20E05, Bm14-5G09)
+ term:
+ id: NCBITaxon:1386
+ label: Bacillus
+ - preferred_term: Enterobacter (ARC strain El17-4B09)
+ term:
+ id: NCBITaxon:547
+ label: Enterobacter
+ - preferred_term: Aspergillus flavus
+ term:
+ id: NCBITaxon:5059
+ label: Aspergillus flavus
+ - preferred_term: peanut
+ term:
+ id: NCBITaxon:3818
+ label: Arachis hypogaea
- name: SynCom ARC Induction of Rhizobia-Legume Nodulation
- description: >
- Alongside pathogen suppression, the community enhances peanut nodulation and nitrogenase
- activity and keeps nodules active through to harvest, so the same consortium that antagonises
- the fungus facilitates colonisation by the nitrogen-fixing symbiont.
+ description: ARC enhanced peanut nodulation, nitrogenase activity and retention of active nodules. The laboratory
+ comparison found no nodulation with ARC alone but more nodules when ARC accompanied rhizobia, supporting facilitation
+ of the rhizobial-host association rather than nitrogen fixation by the four ARC members themselves. The source
+ also reports increased rhizobial abundance; strain-specific persistence and the responsible compounds are not
+ resolved.
interaction_type: COLONIZATION_FACILITATION
scope: COMMUNITY_LEVEL
biological_processes:
@@ -233,31 +254,48 @@ ecological_interactions:
id: GO:0009399
label: nitrogen fixation
downstream:
- - target: Coupled Aflatoxin Prevention and Nodulation-Supported Yield
- description: >
- Enhanced rhizobia-legume nodulation supplies the nitrogen-fixation branch
- of ARC's coupled peanut field phenotype.
+ - target: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ description: 'HYPOTHESIZED/PARTIAL: enhanced rhizobial nodulation and nitrogenase activity are proposed to support
+ the higher-yield phenotype alongside improved photosynthesis and carbon allocation. Parallel endpoints and
+ omics associations do not isolate the contribution of nitrogen fixation or prove the proposed feedback quantitatively.'
evidence:
- reference: PMID:42099455
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom ARC enhances peanut nodulation and nitrogenase activity, retains active nodules
- at harvest
- explanation: Supports facilitation of the rhizobia-legume symbiosis as a community-level effect
- distinct from the antifungal activity.
-- name: Coupled Aflatoxin Prevention and Nodulation-Supported Yield
- description: >
- SynCom ARC joins A. flavus inhibition with rhizobia-legume nodulation
- induction, enhanced nitrogenase activity, retained active nodules, and
- improved photosynthesis and carbon supply, producing lower aflatoxin and
- higher yield without a super-nodulation penalty in field trials.
- interaction_type: COLONIZATION_FACILITATION
+ snippet: SynCom ARC enhances peanut nodulation and nitrogenase activity, retains active nodules at harvest
+ explanation: Supports facilitation of the rhizobia-legume symbiosis as a community-level effect distinct from
+ the antifungal activity.
+ - reference: PMID:42099455
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Laboratory tests showed ARC alone did not induce nodulation but promoted significantly more nodules
+ when co-inoculated with rhizobia
+ explanation: Distinguishes facilitation of rhizobia-dependent nodulation from nodulation by ARC alone.
+ participating_taxa:
+ - preferred_term: Bacillus (ARC strains Bl13-2C11, Ba13-20E05, Bm14-5G09)
+ term:
+ id: NCBITaxon:1386
+ label: Bacillus
+ - preferred_term: Enterobacter (ARC strain El17-4B09)
+ term:
+ id: NCBITaxon:547
+ label: Enterobacter
+ - preferred_term: Bradyrhizobium PHNZY-24-6
+ term:
+ id: NCBITaxon:374
+ label: Bradyrhizobium
+ - preferred_term: peanut
+ term:
+ id: NCBITaxon:3818
+ label: Arachis hypogaea
+- name: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ description: ARC-treated field systems combined reduced aflatoxin, greater nodulation and nitrogenase activity,
+ retained active nodules, improved photosynthetic measures and higher yield. These positive outcomes support
+ the reported multifunctional phenotype. The proposed carbon-nitrogen feedback and precise contributions of fungal
+ inhibition versus rhizobial facilitation remain preliminary mechanisms, not an independently demonstrated feedback
+ loop or host antifungal immune response.
scope: COMMUNITY_LEVEL
biological_processes:
- - preferred_term: defense response to fungus
- term:
- id: GO:0050832
- label: defense response to fungus
- preferred_term: nodulation
term:
id: GO:0009877
@@ -271,16 +309,19 @@ ecological_interactions:
id: GO:0015979
label: photosynthesis
evidence:
+ - reference: PMID:42099455
+ supports: PARTIAL
+ evidence_source: IN_VIVO
+ snippet: SynCom ARC inhibits multiple targets in A. flavus, recruits and activates nodulation and nitrogen fixation
+ in rhizobia and peanut, and improves photosynthesis and carbon supply for aflatoxin prevention and nodulation
+ induction, balancing yield increase
+ explanation: The source proposes coupling of several measured outcomes; it does not isolate each mediator or
+ quantify the proposed feedback.
- reference: PMID:42099455
supports: SUPPORT
evidence_source: IN_VIVO
- snippet: SynCom ARC inhibits multiple targets in A. flavus, recruits and activates nodulation
- and nitrogen fixation in rhizobia and peanut, and improves photosynthesis and carbon supply
- for aflatoxin prevention and nodulation induction, balancing yield increase
- explanation: >
- Supports the field outcome as a coupled product of pathogen inhibition,
- rhizobial activation, peanut nitrogen fixation, and improved
- photosynthetic carbon supply.
+ snippet: Building upon the phenotypic effects and preliminary mechanisms revealed in this study
+ explanation: The source distinguishes phenotypic effects from preliminary mechanistic interpretation.
environmental_factors:
- name: Multi-year multi-site field trial
value: 4 years; 325 sites across 19 provinces
@@ -434,3 +475,33 @@ cultivation_setup:
snippet: "The final concentrations of A. flavus was 5\xD7105 spores/mL and that of the bacterial strain\
\ was 1\xD7107 colony-forming units (CFU)/mL."
explanation: Gives what was inoculated at what density.
+discussions:
+- discussion_id: arc-protective-endpoints-versus-causal-coupling
+ prompt: Which mechanisms quantitatively connect ARC suppression and rhizobial facilitation to the combined field
+ phenotype?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#SynCom ARC Suppression of Aspergillus flavus
+ - ecological_interactions#SynCom ARC Induction of Rhizobia-Legume Nodulation
+ - ecological_interactions#Concurrent aflatoxin reduction, nodulation and yield outcomes
+ rationale: The positive suppression, nodulation and yield findings remain. The study describes preliminary mechanisms
+ and leaves specific compounds and host regulation unresolved. Retain qualified contributions rather than a demonstrated
+ feedback or host-defense mechanism. Counter-selected candidates remain outside the interaction graph; no toxin-production
+ methods or optimization instructions are added.
+ evidence:
+ - reference: PMID:42099455
+ supports: SUPPORT
+ evidence_source: IN_VIVO
+ snippet: Building upon the phenotypic effects and preliminary mechanisms revealed in this study
+ explanation: The source distinguishes phenotypic effects from preliminary mechanistic interpretation.
+ posed_by: codex
+curation_history:
+- timestamp: '2026-10-08T03:27:20Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain protective fungal/aflatoxin endpoints with the storage-time boundary, without reciprocal competition.;
+ Retain rhizobia-dependent nodulation facilitation with participant scope excluding the fungal target.; Retain
+ combined positive outcomes, qualifying causal coupling and removing misplaced colonization/host-defense typing.
+ Issue#1840; reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 0cfef3086..d55e0cfe4 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -1284,3 +1284,28 @@ full-text absence is asserted. No new topology, Edison spend or pathogen
enhancement procedures are introduced. Repairs #1829-#1832 await protected-main
merge; non-graph #1833 stays open. Self-review is not independent approval or
corpus completion.
+
+## Batch107: Transfer, Prediction And Mediation
+
+[Decisions](decisions/20261008-four-records-batch107.yaml),
+[validation](validation-20261008-batch107.json),
+[cache provenance](cache-provenance-20261008-batch107.json) and
+[self-adversarial review](adversarial-review-20261008-batch107.yaml) cover the
+Suillus-Bacillus thiamine, sulfide-spring CPR, chicken SynComBac10 and peanut
+SynCom ARC records. All thirteen nodes remain; seven existing directions are
+qualified and two spatial arrows removed. Direct bacterial-to-fungal vitamin
+transfer and positive host/plant outcomes remain distinct from inferred
+exchange, encoded metabolic capacity and unisolated causal mediation.
+The spring record remains `needs_research`: legacy species groundings exceed
+the source evidence and require coordinated identity curation under #1841.
+The self-adversarial pass corrected HydDB attribution on sulfur-enzyme evidence;
+five append-only histories preserve both the initial edit and the correction.
+A control/mutation/restore probe confirms that the regression test rejects
+reintroducing that provenance error, without changing canonical files.
+All final gates were rerun after that correction; the interrupted preliminary
+verification is archived, not counted as a completed pass.
+Primary read spans and source limits are recorded. All caches and non-graph raw
+blocks remain unchanged, not recertified. No new topology, Edison spend,
+pathogen-enhancement or toxin-production procedures are introduced.
+Repairs #1837-#1840 await protected-main merge; identity #1841 stays open.
+Self-review is not independent approval or corpus completion.
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch107.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch107.yaml
new file mode 100644
index 000000000..7b57990a8
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch107.yaml
@@ -0,0 +1,299 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 2d931aca3afcab956c0eba9661e09344479ad2c7
+scope:
+- kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml
+- kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
+- kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml
+- kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch107.json
+findings:
+- issue: 1837
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate Suillus recruitment and vitamin transfer from untested causal mediation
+ disposition: Close only after protected-main merge.
+- issue: 1838
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate sulfide-spring imaging and predicted metabolism from commensalism and spatial arrows
+ disposition: Close only after protected-main merge.
+- issue: 1839
+ severity: P2
+ status: addressed_in_this_change
+ finding: Qualify SynComBac10 predicted exchange and immune mediation without losing host protection
+ disposition: Close only after protected-main merge.
+- issue: 1840
+ severity: P2
+ status: addressed_in_this_change
+ finding: Bound ARC outcome graph to protective assays and distinguish nodulation from aggregate yield
+ disposition: Close only after protected-main merge.
+- issue: 1841
+ severity: P2
+ status: open_identity_follow_up
+ finding: Resolve sulfide-spring Thiothrix participant identity before certifying its causal graph
+ disposition: Coordinated canonical and graph identity curation required; record remains needs_research.
+adversarial_correction:
+ issue: 1838
+ finding: HydDB incorrectly listed on the separate sulfur-enzyme evidence
+ resolution: Narrow Doudnabacteria sulfur-enzyme provenance to METABOLIC and AlphaFold2; HydDB applies only to
+ the separate hydrogenase prediction.
+ initial_history: history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml
+ correction_history: history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml
+ initial_history_sha256: fbfb65d6b1cc316f1cbc9c90b6f419ab00b9b295e8d76a5ee208e428d3020606
+superseded_verification:
+ report: /private/tmp/communitymech-batch107/pre-correction-validation.json
+ sha256: f415569eea83f28f133dc7e6669d0af61386ee53175453a4f358ff140d9324fa
+ log_directory: /private/tmp/communitymech-batch107/verification-pre-correction
+ original_log_directory: /private/tmp/communitymech-batch107/verification
+ status: Interrupted for factual provenance correction;not a final pass
+ exec_session: 77092
+ exit_code: 130
+adversarial_checks:
+- 'Whole original targets and changed graph/discussion diffs reviewed. All 13 original nodes and nine directions
+ have dispositions: retain 13 nodes and seven qualified existing directions, remove two spatial arrows and rename
+ five nodes. No new topology or Edison spend.'
+- 'Challenge removal versus lost evidence: retain demonstrated bacterial-to-fungal vitamin transfer, fungal/host
+ benefits, sulfur-granule imaging, tentative CPR associations and lineage-specific predictions, immune induction
+ and protective host/plant outcomes. Preserve qualified source hypotheses rather than rejecting positive observations.'
+- 'Suillus: distinguish ureidosuccinate chemotaxis from pregnenolone motility. Cue response does not establish nutrient
+ uptake or resolved bacterial benefit. Labeled thiamine in fungal hyphae supports direct transfer; preserve CROSS_FEEDING
+ and host mutualism interpretation. Qualify recruitment necessity and exclusive in-plant vitamin mediation. Preserve
+ thiamine-free P20 and prior #583 context.'
+- 'Spring: remove unestablished commensalism and spatial arrows. Proximity does not cause attachment or encoded
+ metabolic capacity. Failed FISH leaves imaged-cell identity tentative; predicted genes and structures are not
+ measured flux or exchange. The legacy Thiothrix species grounding exceeds the source 51% average amino-acid similarity
+ and is explicitly uncertified. Keep needs_research under #1841, not completed review.'
+- 'Adversarial correction: HydDB was initially copied onto sulfur-enzyme provenance. Narrow that evidence to METABOLIC
+ and AlphaFold2; retain HydDB only for hydrogenases. Add a second spring curation event and fifth append-only history
+ without rewriting the first. Interrupt the first verification with SIGINT/exit130 for this factual correction,
+ archive its partial report/logs and run all final gates afresh. This was not a timeout. A separate in-memory control/mutation/restore
+ probe passes, rejects reinserting HydDB at the exact tool-set assertion, then passes again; canonical files remain
+ unchanged.'
+- 'Chicken: iNAP2.0 predicted exchange and measured supernatant metabolites do not prove recipient uptake or exclusive
+ mediation. Preserve supported immune induction and host protection; remove mismatched colonization/competition
+ typing and innate-only GO annotation. Keep both existing directions explicitly partial. No pathogen-enhancement
+ procedures, challenge protocols, strain-selection advice or genetic designs are added.'
+- 'ARC: retain reduced aflatoxin after 12 months of storage, not an immediate field endpoint. ARC alone did not
+ induce nodulation; preserve the rhizobia-dependent comparison and identity-only node scopes. Remove reciprocal-competition
+ and aggregate colonization/host-defense annotations. Parallel positive endpoints and omics do not isolate the
+ proposed carbon/nitrogen feedback. Preserve #300/#307 counter-selection and #653 supplement context; no toxin-production
+ or optimization procedures.'
+- Twenty-five graph and six discussion quotations match fresh primary text and unchanged caches. Four independently
+ retrieved primary XML sources have bounded actual read spans recorded in the ledger. No figure-pixel, separate-supplement,
+ raw-data or full-pipeline certification. Cache headers with abstract_only labels can contain body text; no cache
+ imports or global absence claims. Literal matching is distinct from entailment.
+- Four guarded initial writes plus one guarded provenance correction produce five append-only histories. All 456
+ other records, all 923 caches, non-graph raw blocks and prior history/decision files remain byte-identical. No
+ schema, validator, census-threshold or runtime-rule changes. The global participant census is unchanged; legacy
+ spring identity links are not certified.
+- Eight focused tests and 967 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks
+ and all five histories validate. The network retains 56 baseline warnings and zero structural defects. Deterministic
+ rendering and exact HTML parsing cover 456 pages, 1372 node descriptions and 543 arrows, not screenshots. Plain
+ just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+- 'Repair issues #1837-#1840 are addressed but remain open until protected-main merge. Identity #1841 stays open.
+ Existing license #949, loader #1703 and DOI-cache case #1091 are not certified. Denied and unanswered Edison scopes
+ remain untouched. Self-review is not independent approval; no artificial CI, protection bypass or premature branch
+ deletion.'
+- Corpus status is 341 reviewed, 68 pending and 51 needs_research, not completion. Postcommit docs-current and exact-head
+ publication require separate receipts and are not preasserted here.
+correction_regression_proof:
+ report:
+ test: tests/test_causal_review_batch107.py
+ test_function: test_computational_evidence_stays_on_predictions_not_discussion_schema
+ control: PASS
+ mutation: Reinsert HydDB only into the sulfur-enzyme evidence tool list in memory.
+ mutation_applied: true
+ mutation_result: AssertionError at exact tool-set assertion
+ assertion_line: 62
+ restored_control: PASS
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml: 69551869693ec797fb080f10747bdacd590e9686cdcdb93ff8c47a2e20880a18
+ kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml: 5d3a32811ff6817ac9002bd39f79c53511fa76bc15d97a9adca897220471f235
+ kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml: 3b6f0e648eb199d8139c7d790034e88f471e3fa5a3f0212ed55a60280921a6e6
+ kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml: 8128a35b7336eb6a0e2da4768e456cd12e84db5632b771708a70f07d6bebd5b5
+ tests/test_causal_review_batch107.py: 0be0b34da158fcb6b9a9d4788949d1615d42ad26ecf19168905a06fc5b17bed6
+ artifact: /private/tmp/communitymech-batch107/correction-regression-proof.json
+ sha256: b278410c408d405162797ffcf004375e29d1785ec7cef7cdd62e0335f9f36dc2
+verification:
+ combined_regressions: 967 passed in 327.16s (0:05:27)
+ new_regression_tests: 8
+ total_recorded_gate_outputs: 42
+ primary_graph_snippet_proof:
+ graph_quotations: 25
+ new_discussion_quotations: 6
+ fresh_primary_literal_matches: 31
+ all_cached_literal_matches: 31
+ retained_nodes: 13
+ removed_nodes: 0
+ retained_arrows: 7
+ removed_arrows: 2
+ new_nodes_or_directions: 0
+ scope: All reviewed quotations match fresh primary text and unchanged caches; source entailment separately reviewed.
+ Four bounded main-text reviews,not whole-paper/supplement/figure/raw-data certification.
+ references: Four full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal
+ matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks.
+ Loader1703 not certified.
+ snippet_counts_by_record:
+ kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml:
+ MATCH: 17
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml:
+ MATCH: 15
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml:
+ MATCH: 24
+ RENDERING: 1
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 8977
+ categories:
+ MATCH: 8840
+ RENDERING: 21
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 39
+ NOCONTENT: 76
+ caveat: Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ interpretation: All13nodes retained,seven existing directions qualified,two spatial arrows removed. All56existing
+ warnings unchanged;zero structural defects. Spring species identity remains unresolved1841 despite structural
+ validity.
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml: deb7c0eb9394c0e4a810507a75e20c88b029c9c7ca8a4851d078b4aaad0c9940
+ tests/test_causal_review_batch107.py: 0be0b34da158fcb6b9a9d4788949d1615d42ad26ecf19168905a06fc5b17bed6
+ tests/test_participating_taxa.py: 5a52c3d54ae981f49fd187531e19c8c8b8788473e16465f1dce59b1a6c2e9aad
+ tests/test_community_level_connectivity_credit.py: 383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c
+ reports/causal_graph_review/cache-provenance-20261008-batch107.json: 9a031575c6dc1d75f998b819cc7e46122344adb49eeedb2344741ab5fed0112c
+ kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml: 69551869693ec797fb080f10747bdacd590e9686cdcdb93ff8c47a2e20880a18
+ kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml: 5d3a32811ff6817ac9002bd39f79c53511fa76bc15d97a9adca897220471f235
+ kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml: 3b6f0e648eb199d8139c7d790034e88f471e3fa5a3f0212ed55a60280921a6e6
+ kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml: 8128a35b7336eb6a0e2da4768e456cd12e84db5632b771708a70f07d6bebd5b5
+ history_sha256:
+ history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml: e7c9aa698811f6fce4db925bdf63a60bc85abd74ade9364acaba69059a718b66
+ history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml: fbfb65d6b1cc316f1cbc9c90b6f419ab00b9b295e8d76a5ee208e428d3020606
+ history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml: daefa0855186be3a47d742a0fc8b98810b750c109e9c620db4a0bedd8edd3384
+ history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml: ecbebf388c21f1a3c40d2514705e19a0ba1662b7679107100dcc746a9ba15596
+ history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml: 339045fc453118baa32f96de53db2bc1bf8681bd303d382bbbb9ed46cbe17493
+ unchanged_records: 456
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 822
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing-node evidence/semantics repair,seven existing directions retained,two spatial arrows
+ removed;identity1841needs coordinated curation,not new-topology generation.
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 403
+ mixed: 128
+ community_level_only: 275
+ taxa: 1544
+ credited_solely_by_the_rule: 1270
+ current:
+ records: 460
+ with_community_level: 403
+ mixed: 128
+ community_level_only: 275
+ taxa: 1544
+ credited_solely_by_the_rule: 1270
+ delta:
+ records: 0
+ with_community_level: 0
+ mixed: 0
+ community_level_only: 0
+ taxa: 0
+ credited_solely_by_the_rule: 0
+ interpretation: ARC suppression/nodulation observations gain canonical identity-only scope. The combined endpoint
+ still encompasses the system;global census unchanged. Spring legacy identity links are explicitly uncertified.
+ No census thresholds or audit rules changed.
+corpus:
+ records: 460
+ nodes: 1386
+ edges: 551
+ review_status_counts:
+ needs_research: 51
+ pending: 68
+ reviewed: 341
+lint_limitation: Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies
+ unchanged. Not a complete embedding runtime.
+limitations:
+- Fresh both-root baseline before source reads:460records,923caches,56existing warnings,zero structural defects.
+ Whole four targets and all13nodes/9directions reviewed. Retain13nodes/7existing directions,remove2spatial arrows,rename5nodes.
+ No new topology or Edison submission/spend.
+- Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60
+ and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662 read;
+ chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract; ARC extracted
+ main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data or full-pipeline
+ certification.
+- Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text
+ review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has two
+ existing cache representations; no new cache imports. Large single-line cache output was truncated and is not
+ claimed as read. No license949,loader1703 or DOI-case1091 certification.
+- Suillus:preserve demonstrated bacterial-to-fungal thiamine transfer,auxotrophy rescue,recruitment and fungal/plant
+ benefits. Distinguish pregnenolone motility from ureidosuccinate chemotaxis. Remove nutrient-consumption typing
+ from cue response; preserve host mutualism interpretation but not measured host-fungal flux or exclusive thiamine
+ mediation. Thiamine-free P20 and prior583 context remain unchanged.
+- Spring:preserve sulfur-granule imaging,putative CPR association and lineage-specific metabolic predictions. Remove
+ unestablished commensalism and both spatial arrows; add bounded genomic/structural provenance. Current canonical
+ NCBITaxon:1031 link exceeds the source51%amino-acid similarity; legacy references remain explicitly uncertified
+ pending coordinated identity repair1841. This record remains needs_research rather than being counted fully reviewed.
+- Chicken:preserve measured immune induction,metabolite-production evidence and host protection. Predicted iNAP2.0
+ exchange is not measured recipient transfer; protective association is not exclusive mediation. Remove colonization/competition
+ typing and misplaced innate-only GO annotation. Evidence correction only; no new pathogen enhancement,genetic
+ designs,strain-selection advice,challenge methods,growth optimization or causal mechanisms.
+- ARC:preserve protective fungal,nodulation,photosynthesis and yield outcomes. Attach85.6%aflatoxin decrease to12months
+ storage and retain the rhizobia-dependent nodulation boundary. Remove reciprocal-competition and aggregate-colonization/host-defense
+ annotations; narrow separate node participants. Both outcome-contribution directions remain qualified,not isolated
+ mechanisms or a proven feedback loop. Prior300/307counter-selection and653supplement provenance remain unchanged.
+ No toxin-production procedures or optimization advice.
+- Graph repairs1837-1840remain open until protected-main merge. Identity1841remains open after repair merge. Fresh
+ all-state issue-title/body search matched653/583/307/304/300; all five bodies read. Scoped local search includes
+ ignored/hidden files,excluding.git/docs/site/references_cache and credentials; relevant caches separately covered.
+ PRs/comments not exhaustively searched. No reusable taxon match found in ignored/hidden-inclusive kb/taxa search
+ for the reviewed taxa/IDs.
+- Only graphs,new focused discussions and curation events change. All456other records,923caches,non-graph raw blocks
+ and prior histories/decisions preserved. No schema,validator,threshold or runtime-rule changes. Spring remaining
+ identity uncertainty is explicit; other non-graph taxonomy,abundance,role,cultivation and evidence claims are
+ not recertified. Self-review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered
+ Edison scopes untouched. Validation/publication are not preasserted.
+- Self-adversarial review corrected a too-broad computational tool chain before publication:HydDB removed from Doudnabacteria
+ sulfur-enzyme provenance and retained for hydrogenases. A fifth append-only history and second spring curation
+ event preserve the initial entry unchanged. Initial verification was deliberately interrupted with SIGINT/exit130
+ for this factual correction,not a timeout,and its partial logs are archived;all final gates run afresh.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch107.json b/reports/causal_graph_review/cache-provenance-20261008-batch107.json
new file mode 100644
index 000000000..b7a20d8c9
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch107.json
@@ -0,0 +1,114 @@
+{
+ "changes": [],
+ "unchanged_cache_files": 923,
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch107/arc-metadata.json": "243c7ec12677ace786ed8c24ab04368552bae147f51be7492e3b3d6066b585c4",
+ "/private/tmp/communitymech-batch107/arc-primary.txt": "45274786c15ca06c2a01283691fd22a4c652cd40403f07a92d6e59da954cd92e",
+ "/private/tmp/communitymech-batch107/arc-primary.xml": "bb4c534cc823bfcb837c13b6a075a97ec048ee08b81ed97d48b74f759a64ffa4",
+ "/private/tmp/communitymech-batch107/baseline.json": "2e02db0cebfc1d13f0a10ad4f47ab0bd0778fe9ac236ddad667ebb5e28aeec52",
+ "/private/tmp/communitymech-batch107/chicken-metadata.json": "f48ba18d3c7689680f4fc924c6242ac72d46f3892be4934b9cb06707034e3d51",
+ "/private/tmp/communitymech-batch107/chicken-primary.txt": "9092ee825b832e4fa71e79862a3635880465b10f957c7a3b00aa0b223b5eb3bf",
+ "/private/tmp/communitymech-batch107/chicken-primary.xml": "61f675010caab7d60942a57b1f1a4d54e54b4b05efdbab19f70d12a00387980d",
+ "/private/tmp/communitymech-batch107/dedup-local-current.txt": "83f33a0c26dd2bd43f1e1ef955e06f096147d600bcc306dd33bd86bee4af1f5f",
+ "/private/tmp/communitymech-batch107/issue-dedup-current.json": "218e392ea3f23bb630bc060c1235b090c79148c89e95b0e012458c9cae8540c3",
+ "/private/tmp/communitymech-batch107/primary-manifest.json": "0c4114e4b83e51489ae02cf7336b467ffa37454d4b6c5c4961778b1833f95dab",
+ "/private/tmp/communitymech-batch107/spring-metadata.json": "8a1459c1212f4136ba8097058ed37af82624ae9f56742a2c57ede76db7f70c86",
+ "/private/tmp/communitymech-batch107/spring-primary.txt": "0140358180e01a111d0e4bf949bec128a5d74ed3bf27e10ad891df75d5cd6a6b",
+ "/private/tmp/communitymech-batch107/spring-primary.xml": "09a2d4f1d6d96b23af8f3d15619852e2f7953caa7aa15f954e71f6db8019b541",
+ "/private/tmp/communitymech-batch107/suillus-metadata.json": "8761d1a578bf6f4f866e2627cb7459f6b3096c60fcf87f65a663f705d549ac36",
+ "/private/tmp/communitymech-batch107/suillus-primary.txt": "0a1231d39da69f2fc4c87970fbf5671094282a6f0c9d6f385dcb325b46dddce1",
+ "/private/tmp/communitymech-batch107/suillus-primary.xml": "0fa12fd23362bdc788f15ff2c752d40eaa63e076fbc8d4dd4168ec914326c2c6",
+ "references_cache/PMID_38273328.md": "a7cc4c5561b4a8b33686c68ca4f7939331f5d78b256794b4561d10330c52c675",
+ "references_cache/PMID_40266232.txt": "bf18b8e042d72b4084df724a26ea7c3bae9236d1e267c17a29961ff1eeb5f3ec",
+ "references_cache/PMID_41454778.md": "c5750137a6f5de73953126f714e07c45ffba7367d9b55c7ea0a680dc9b527809",
+ "references_cache/PMID_42099455.txt": "b94e222a0aea5e54f856ab247d4682ef0238739bf8daafd9f8da411294577344"
+ },
+ "source_access": {
+ "retrieval_manifest": {
+ "suillus": {
+ "reference": "PMID:41454778",
+ "title": "Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis.",
+ "pmid": "41454778",
+ "pmcid": "PMC12815266",
+ "doi": "10.1093/ismejo/wraf290",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12815266/fullTextXML",
+ "metadata": "/private/tmp/communitymech-batch107/suillus-metadata.json",
+ "source": "/private/tmp/communitymech-batch107/suillus-primary.xml",
+ "source_sha256": "0fa12fd23362bdc788f15ff2c752d40eaa63e076fbc8d4dd4168ec914326c2c6",
+ "extracted_body": "/private/tmp/communitymech-batch107/suillus-primary.txt",
+ "body_sha256": "0a1231d39da69f2fc4c87970fbf5671094282a6f0c9d6f385dcb325b46dddce1",
+ "body_lines": 697,
+ "scope": "XML retrieved, not yet read. Extracted abstract and main text; no figure pixels, supplements or raw data certification.",
+ "license": "\u00a9 The Author(s) 2026. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.",
+ "fulltext_error": null
+ },
+ "spring": {
+ "reference": "PMID:38273328",
+ "title": "Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism.",
+ "pmid": "38273328",
+ "pmcid": "PMC10811913",
+ "doi": "10.1186/s40168-023-01704-w",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10811913/fullTextXML",
+ "metadata": "/private/tmp/communitymech-batch107/spring-metadata.json",
+ "source": "/private/tmp/communitymech-batch107/spring-primary.xml",
+ "source_sha256": "09a2d4f1d6d96b23af8f3d15619852e2f7953caa7aa15f954e71f6db8019b541",
+ "extracted_body": "/private/tmp/communitymech-batch107/spring-primary.txt",
+ "body_sha256": "0140358180e01a111d0e4bf949bec128a5d74ed3bf27e10ad891df75d5cd6a6b",
+ "body_lines": 952,
+ "scope": "XML retrieved, not yet read. Extracted abstract and main text; no figure pixels, supplements or raw data certification.",
+ "license": "\u00a9 The Author(s) 2024Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.",
+ "fulltext_error": null
+ },
+ "chicken": {
+ "reference": "PMID:40266232",
+ "title": "Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.",
+ "pmid": "40266232",
+ "pmcid": "PMC12527353",
+ "doi": "10.1093/ismejo/wraf076",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12527353/fullTextXML",
+ "metadata": "/private/tmp/communitymech-batch107/chicken-metadata.json",
+ "source": "/private/tmp/communitymech-batch107/chicken-primary.xml",
+ "source_sha256": "61f675010caab7d60942a57b1f1a4d54e54b4b05efdbab19f70d12a00387980d",
+ "extracted_body": "/private/tmp/communitymech-batch107/chicken-primary.txt",
+ "body_sha256": "9092ee825b832e4fa71e79862a3635880465b10f957c7a3b00aa0b223b5eb3bf",
+ "body_lines": 522,
+ "scope": "XML retrieved, not yet read. Extracted abstract and non-methods text only for protective-outcome and evidence-metadata review. No operational methods, enhancement advice or new mechanisms to curate.",
+ "license": "\u00a9 The Author(s) 2025. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.2025https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.",
+ "fulltext_error": null
+ },
+ "arc": {
+ "reference": "PMID:42099455",
+ "title": "Microbial synthetic community ARC prevents aflatoxin and increases rhizobia-legume nodulation couplingly.",
+ "pmid": "42099455",
+ "pmcid": "PMC13147931",
+ "doi": "10.1002/imt2.70125",
+ "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13147931/fullTextXML",
+ "metadata": "/private/tmp/communitymech-batch107/arc-metadata.json",
+ "source": "/private/tmp/communitymech-batch107/arc-primary.xml",
+ "source_sha256": "bb4c534cc823bfcb837c13b6a075a97ec048ee08b81ed97d48b74f759a64ffa4",
+ "extracted_body": "/private/tmp/communitymech-batch107/arc-primary.txt",
+ "body_sha256": "45274786c15ca06c2a01283691fd22a4c652cd40403f07a92d6e59da954cd92e",
+ "body_lines": 217,
+ "scope": "XML retrieved, not yet read. Extracted abstract and non-methods text only for protective-outcome and evidence-metadata review. No operational methods, enhancement advice or new mechanisms to curate.",
+ "license": "\u00a9 2026 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.",
+ "fulltext_error": null
+ }
+ },
+ "actual_read_scope": [
+ "Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60 and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662 read; chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract; ARC extracted main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data or full-pipeline certification.",
+ "Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has two existing cache representations; no new cache imports. Large single-line cache output was truncated and is not claimed as read. No license949,loader1703 or DOI-case1091 certification."
+ ]
+ },
+ "limitations": [
+ "Fresh both-root baseline before source reads:460records,923caches,56existing warnings,zero structural defects. Whole four targets and all13nodes/9directions reviewed. Retain13nodes/7existing directions,remove2spatial arrows,rename5nodes. No new topology or Edison submission/spend.",
+ "Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60 and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662 read; chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract; ARC extracted main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data or full-pipeline certification.",
+ "Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has two existing cache representations; no new cache imports. Large single-line cache output was truncated and is not claimed as read. No license949,loader1703 or DOI-case1091 certification.",
+ "Suillus:preserve demonstrated bacterial-to-fungal thiamine transfer,auxotrophy rescue,recruitment and fungal/plant benefits. Distinguish pregnenolone motility from ureidosuccinate chemotaxis. Remove nutrient-consumption typing from cue response; preserve host mutualism interpretation but not measured host-fungal flux or exclusive thiamine mediation. Thiamine-free P20 and prior583 context remain unchanged.",
+ "Spring:preserve sulfur-granule imaging,putative CPR association and lineage-specific metabolic predictions. Remove unestablished commensalism and both spatial arrows; add bounded genomic/structural provenance. Current canonical NCBITaxon:1031 link exceeds the source51%amino-acid similarity; legacy references remain explicitly uncertified pending coordinated identity repair1841. This record remains needs_research rather than being counted fully reviewed.",
+ "Chicken:preserve measured immune induction,metabolite-production evidence and host protection. Predicted iNAP2.0 exchange is not measured recipient transfer; protective association is not exclusive mediation. Remove colonization/competition typing and misplaced innate-only GO annotation. Evidence correction only; no new pathogen enhancement,genetic designs,strain-selection advice,challenge methods,growth optimization or causal mechanisms.",
+ "ARC:preserve protective fungal,nodulation,photosynthesis and yield outcomes. Attach85.6%aflatoxin decrease to12months storage and retain the rhizobia-dependent nodulation boundary. Remove reciprocal-competition and aggregate-colonization/host-defense annotations; narrow separate node participants. Both outcome-contribution directions remain qualified,not isolated mechanisms or a proven feedback loop. Prior300/307counter-selection and653supplement provenance remain unchanged. No toxin-production procedures or optimization advice.",
+ "Graph repairs1837-1840remain open until protected-main merge. Identity1841remains open after repair merge. Fresh all-state issue-title/body search matched653/583/307/304/300; all five bodies read. Scoped local search includes ignored/hidden files,excluding.git/docs/site/references_cache and credentials; relevant caches separately covered. PRs/comments not exhaustively searched. No reusable taxon match found in ignored/hidden-inclusive kb/taxa search for the reviewed taxa/IDs.",
+ "Only graphs,new focused discussions and curation events change. All456other records,923caches,non-graph raw blocks and prior histories/decisions preserved. No schema,validator,threshold or runtime-rule changes. Spring remaining identity uncertainty is explicit; other non-graph taxonomy,abundance,role,cultivation and evidence claims are not recertified. Self-review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication are not preasserted.",
+ "Self-adversarial review corrected a too-broad computational tool chain before publication:HydDB removed from Doudnabacteria sulfur-enzyme provenance and retained for hydrogenases. A fifth append-only history and second spring curation event preserve the initial entry unchanged. Initial verification was deliberately interrupted with SIGINT/exit130 for this factual correction,not a timeout,and its partial logs are archived;all final gates run afresh."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
new file mode 100644
index 000000000..0c9980db0
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
@@ -0,0 +1,789 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 2d931aca3afcab956c0eba9661e09344479ad2c7
+baseline_commit: 2d931aca3afcab956c0eba9661e09344479ad2c7
+base_tree: 9bb3e7d09f2a5234432adf83c9509773b19635a4
+pre_source_baseline_sha256: 2e02db0cebfc1d13f0a10ad4f47ab0bd0778fe9ac236ddad667ebb5e28aeec52
+issues:
+- 1837
+- 1838
+- 1839
+- 1840
+unresolved_research_issues:
+- 1841
+unresolved_non_graph_issues: []
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 1087
+ matching_issues:
+ - 653
+ - 583
+ - 307
+ - 304
+ - 300
+ ignored_hidden_local_search: true
+source_access:
+ retrieval_manifest:
+ suillus:
+ reference: PMID:41454778
+ title: Ectomycorrhizal fungi recruit hyphae-associated bacteria that metabolize thiamine to promote pine symbiosis.
+ pmid: '41454778'
+ pmcid: PMC12815266
+ doi: 10.1093/ismejo/wraf290
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12815266/fullTextXML
+ metadata: /private/tmp/communitymech-batch107/suillus-metadata.json
+ source: /private/tmp/communitymech-batch107/suillus-primary.xml
+ source_sha256: 0fa12fd23362bdc788f15ff2c752d40eaa63e076fbc8d4dd4168ec914326c2c6
+ extracted_body: /private/tmp/communitymech-batch107/suillus-primary.txt
+ body_sha256: 0a1231d39da69f2fc4c87970fbf5671094282a6f0c9d6f385dcb325b46dddce1
+ body_lines: 697
+ scope: XML retrieved, not yet read. Extracted abstract and main text; no figure pixels, supplements or raw
+ data certification.
+ license: "\xA9 The Author(s) 2026. Published by Oxford University Press on behalf of the International Society\
+ \ for Microbial Ecology.This is an Open Access article distributed under the terms of the Creative Commons\
+ \ Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse,\
+ \ distribution, and reproduction in any medium, provided the original work is properly cited."
+ fulltext_error: null
+ spring:
+ reference: PMID:38273328
+ title: Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur
+ and hydrogen metabolism.
+ pmid: '38273328'
+ pmcid: PMC10811913
+ doi: 10.1186/s40168-023-01704-w
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10811913/fullTextXML
+ metadata: /private/tmp/communitymech-batch107/spring-metadata.json
+ source: /private/tmp/communitymech-batch107/spring-primary.xml
+ source_sha256: 09a2d4f1d6d96b23af8f3d15619852e2f7953caa7aa15f954e71f6db8019b541
+ extracted_body: /private/tmp/communitymech-batch107/spring-primary.txt
+ body_sha256: 0140358180e01a111d0e4bf949bec128a5d74ed3bf27e10ad891df75d5cd6a6b
+ body_lines: 952
+ scope: XML retrieved, not yet read. Extracted abstract and main text; no figure pixels, supplements or raw
+ data certification.
+ license: "\xA9 The Author(s) 2024Open Access This article is licensed under a Creative Commons Attribution\
+ \ 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any\
+ \ medium or format, as long as you give appropriate credit to the original author(s) and the source, provide\
+ \ a link to the Creative Commons licence, and indicate if changes were made. The images or other third party\
+ \ material in this article are included in the article's Creative Commons licence, unless indicated otherwise\
+ \ in a credit line to the material. If material is not included in the article's Creative Commons licence\
+ \ and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will\
+ \ need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.\
+ \ The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/)\
+ \ applies to the data made available in this article, unless otherwise stated in a credit line to the data."
+ fulltext_error: null
+ chicken:
+ reference: PMID:40266232
+ title: Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella
+ immunity mediated by segmented filamentous bacteria.
+ pmid: '40266232'
+ pmcid: PMC12527353
+ doi: 10.1093/ismejo/wraf076
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12527353/fullTextXML
+ metadata: /private/tmp/communitymech-batch107/chicken-metadata.json
+ source: /private/tmp/communitymech-batch107/chicken-primary.xml
+ source_sha256: 61f675010caab7d60942a57b1f1a4d54e54b4b05efdbab19f70d12a00387980d
+ extracted_body: /private/tmp/communitymech-batch107/chicken-primary.txt
+ body_sha256: 9092ee825b832e4fa71e79862a3635880465b10f957c7a3b00aa0b223b5eb3bf
+ body_lines: 522
+ scope: XML retrieved, not yet read. Extracted abstract and non-methods text only for protective-outcome and
+ evidence-metadata review. No operational methods, enhancement advice or new mechanisms to curate.
+ license: "\xA9 The Author(s) 2025. Published by Oxford University Press on behalf of the International Society\
+ \ for Microbial Ecology.2025https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed\
+ \ under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/),\
+ \ which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original\
+ \ work is properly cited."
+ fulltext_error: null
+ arc:
+ reference: PMID:42099455
+ title: Microbial synthetic community ARC prevents aflatoxin and increases rhizobia-legume nodulation couplingly.
+ pmid: '42099455'
+ pmcid: PMC13147931
+ doi: 10.1002/imt2.70125
+ url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13147931/fullTextXML
+ metadata: /private/tmp/communitymech-batch107/arc-metadata.json
+ source: /private/tmp/communitymech-batch107/arc-primary.xml
+ source_sha256: bb4c534cc823bfcb837c13b6a075a97ec048ee08b81ed97d48b74f759a64ffa4
+ extracted_body: /private/tmp/communitymech-batch107/arc-primary.txt
+ body_sha256: 45274786c15ca06c2a01283691fd22a4c652cd40403f07a92d6e59da954cd92e
+ body_lines: 217
+ scope: XML retrieved, not yet read. Extracted abstract and non-methods text only for protective-outcome and
+ evidence-metadata review. No operational methods, enhancement advice or new mechanisms to curate.
+ license: "\xA9 2026 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta\
+ \ Science.https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of\
+ \ the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction\
+ \ in any medium, provided the original work is properly cited."
+ fulltext_error: null
+ actual_read_scope:
+ - Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60
+ and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662
+ read; chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract;
+ ARC extracted main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data
+ or full-pipeline certification.
+ - Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text
+ review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has
+ two existing cache representations; no new cache imports. Large single-line cache output was truncated and is
+ not claimed as read. No license949,loader1703 or DOI-case1091 certification.
+primary_artifacts:
+ /private/tmp/communitymech-batch107/arc-metadata.json: 243c7ec12677ace786ed8c24ab04368552bae147f51be7492e3b3d6066b585c4
+ /private/tmp/communitymech-batch107/arc-primary.txt: 45274786c15ca06c2a01283691fd22a4c652cd40403f07a92d6e59da954cd92e
+ /private/tmp/communitymech-batch107/arc-primary.xml: bb4c534cc823bfcb837c13b6a075a97ec048ee08b81ed97d48b74f759a64ffa4
+ /private/tmp/communitymech-batch107/baseline.json: 2e02db0cebfc1d13f0a10ad4f47ab0bd0778fe9ac236ddad667ebb5e28aeec52
+ /private/tmp/communitymech-batch107/chicken-metadata.json: f48ba18d3c7689680f4fc924c6242ac72d46f3892be4934b9cb06707034e3d51
+ /private/tmp/communitymech-batch107/chicken-primary.txt: 9092ee825b832e4fa71e79862a3635880465b10f957c7a3b00aa0b223b5eb3bf
+ /private/tmp/communitymech-batch107/chicken-primary.xml: 61f675010caab7d60942a57b1f1a4d54e54b4b05efdbab19f70d12a00387980d
+ /private/tmp/communitymech-batch107/dedup-local-current.txt: 83f33a0c26dd2bd43f1e1ef955e06f096147d600bcc306dd33bd86bee4af1f5f
+ /private/tmp/communitymech-batch107/issue-dedup-current.json: 218e392ea3f23bb630bc060c1235b090c79148c89e95b0e012458c9cae8540c3
+ /private/tmp/communitymech-batch107/primary-manifest.json: 0c4114e4b83e51489ae02cf7336b467ffa37454d4b6c5c4961778b1833f95dab
+ /private/tmp/communitymech-batch107/spring-metadata.json: 8a1459c1212f4136ba8097058ed37af82624ae9f56742a2c57ede76db7f70c86
+ /private/tmp/communitymech-batch107/spring-primary.txt: 0140358180e01a111d0e4bf949bec128a5d74ed3bf27e10ad891df75d5cd6a6b
+ /private/tmp/communitymech-batch107/spring-primary.xml: 09a2d4f1d6d96b23af8f3d15619852e2f7953caa7aa15f954e71f6db8019b541
+ /private/tmp/communitymech-batch107/suillus-metadata.json: 8761d1a578bf6f4f866e2627cb7459f6b3096c60fcf87f65a663f705d549ac36
+ /private/tmp/communitymech-batch107/suillus-primary.txt: 0a1231d39da69f2fc4c87970fbf5671094282a6f0c9d6f385dcb325b46dddce1
+ /private/tmp/communitymech-batch107/suillus-primary.xml: 0fa12fd23362bdc788f15ff2c752d40eaa63e076fbc8d4dd4168ec914326c2c6
+ references_cache/PMID_38273328.md: a7cc4c5561b4a8b33686c68ca4f7939331f5d78b256794b4561d10330c52c675
+ references_cache/PMID_40266232.txt: bf18b8e042d72b4084df724a26ea7c3bae9236d1e267c17a29961ff1eeb5f3ec
+ references_cache/PMID_41454778.md: c5750137a6f5de73953126f714e07c45ffba7367d9b55c7ea0a680dc9b527809
+ references_cache/PMID_42099455.txt: b94e222a0aea5e54f856ab247d4682ef0238739bf8daafd9f8da411294577344
+primary_graph_snippet_count: 25
+snippet_checks:
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Fungal recruitment of the hyphae-associated bacterium
+ evidence_index: 0
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Fungal recruitment of the hyphae-associated bacterium
+ evidence_index: 1
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Ureidosuccinic acid stimulation of bacterial thiamine production
+ evidence_index: 0
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Ureidosuccinic acid stimulation of bacterial thiamine production
+ evidence_index: 1
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Thiamine provisioning fulfilling the fungal requirement
+ evidence_index: 0
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Thiamine provisioning fulfilling the fungal requirement
+ evidence_index: 1
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Enhanced ectomycorrhizal colonization of the pine host
+ evidence_index: 0
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: Enhanced ectomycorrhizal colonization of the pine host
+ evidence_index: 1
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: Filamentous Sulfur Oxidation with Encapsulated S Granules
+ evidence_index: 0
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: Putative CPR association with sulfur-oxidizing filaments
+ evidence_index: 0
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: Putative CPR association with sulfur-oxidizing filaments
+ evidence_index: 1
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: Predicted CPR sulfur and hydrogen metabolic capacity
+ evidence_index: 0
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: Predicted CPR sulfur and hydrogen metabolic capacity
+ evidence_index: 1
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: Predicted SynCom-to-SFB metabolite exchange
+ evidence_index: 0
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: Predicted SynCom-to-SFB metabolite exchange
+ evidence_index: 1
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: SFB-Driven Th17 Immune Priming
+ evidence_index: 0
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: SFB-Driven Th17 Immune Priming
+ evidence_index: 1
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: Host protection after SynComBac10 exposure
+ evidence_index: 0
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: Host protection after SynComBac10 exposure
+ evidence_index: 1
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: SynCom ARC Suppression of Aspergillus flavus
+ evidence_index: 0
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: SynCom ARC Suppression of Aspergillus flavus
+ evidence_index: 1
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: SynCom ARC Induction of Rhizobia-Legume Nodulation
+ evidence_index: 0
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: SynCom ARC Induction of Rhizobia-Legume Nodulation
+ evidence_index: 1
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ evidence_index: 0
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ evidence_index: 1
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+discussion_snippet_checks:
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: suillus-cue-transfer-and-plant-mediation
+ evidence_index: 0
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom
+ node: suillus-cue-transfer-and-plant-mediation
+ evidence_index: 1
+ reference: PMID:41454778
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/suillus-primary.txt
+ cache_artifact: references_cache/PMID_41454778.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: spring-unresolved-cell-identity-and-metabolic-coupling
+ evidence_index: 0
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: Sulfide_Spring_Autotrophic_CPR_Biofilm
+ node: spring-unresolved-cell-identity-and-metabolic-coupling
+ evidence_index: 1
+ reference: PMID:38273328
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/spring-primary.txt
+ cache_artifact: references_cache/PMID_38273328.md
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynComBac10_Chicken_Intestinal_SynCom
+ node: chicken-predicted-transfer-and-nonexclusive-protection
+ evidence_index: 0
+ reference: PMID:40266232
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/chicken-primary.txt
+ cache_artifact: references_cache/PMID_40266232.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+- record: SynCom_ARC_Peanut_Aflatoxin_Nodulation
+ node: arc-protective-endpoints-versus-causal-coupling
+ evidence_index: 0
+ reference: PMID:42099455
+ cache_matched: true
+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch107/arc-primary.txt
+ cache_artifact: references_cache/PMID_42099455.txt
+ scope: Normalized literal match to fresh primary text and unchanged cache; entailment reviewed separately.
+cache_changes: []
+edison:
+ required_for_this_repair: false
+ required_for_unresolved_extensions: false
+ provider_submissions: 0
+ credits_spent: 0
+ dry_runs: []
+ repair_scope: Existing-node evidence/semantics repair,seven existing directions retained,two spatial arrows removed;identity1841needs
+ coordinated curation,not new-topology generation.
+limitations:
+- Fresh both-root baseline before source reads:460records,923caches,56existing warnings,zero structural defects.
+ Whole four targets and all13nodes/9directions reviewed. Retain13nodes/7existing directions,remove2spatial arrows,rename5nodes.
+ No new topology or Edison submission/spend.
+- Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60
+ and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662 read;
+ chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract; ARC extracted
+ main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data or full-pipeline
+ certification.
+- Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text
+ review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has two
+ existing cache representations; no new cache imports. Large single-line cache output was truncated and is not
+ claimed as read. No license949,loader1703 or DOI-case1091 certification.
+- Suillus:preserve demonstrated bacterial-to-fungal thiamine transfer,auxotrophy rescue,recruitment and fungal/plant
+ benefits. Distinguish pregnenolone motility from ureidosuccinate chemotaxis. Remove nutrient-consumption typing
+ from cue response; preserve host mutualism interpretation but not measured host-fungal flux or exclusive thiamine
+ mediation. Thiamine-free P20 and prior583 context remain unchanged.
+- Spring:preserve sulfur-granule imaging,putative CPR association and lineage-specific metabolic predictions. Remove
+ unestablished commensalism and both spatial arrows; add bounded genomic/structural provenance. Current canonical
+ NCBITaxon:1031 link exceeds the source51%amino-acid similarity; legacy references remain explicitly uncertified
+ pending coordinated identity repair1841. This record remains needs_research rather than being counted fully reviewed.
+- Chicken:preserve measured immune induction,metabolite-production evidence and host protection. Predicted iNAP2.0
+ exchange is not measured recipient transfer; protective association is not exclusive mediation. Remove colonization/competition
+ typing and misplaced innate-only GO annotation. Evidence correction only; no new pathogen enhancement,genetic
+ designs,strain-selection advice,challenge methods,growth optimization or causal mechanisms.
+- ARC:preserve protective fungal,nodulation,photosynthesis and yield outcomes. Attach85.6%aflatoxin decrease to12months
+ storage and retain the rhizobia-dependent nodulation boundary. Remove reciprocal-competition and aggregate-colonization/host-defense
+ annotations; narrow separate node participants. Both outcome-contribution directions remain qualified,not isolated
+ mechanisms or a proven feedback loop. Prior300/307counter-selection and653supplement provenance remain unchanged.
+ No toxin-production procedures or optimization advice.
+- Graph repairs1837-1840remain open until protected-main merge. Identity1841remains open after repair merge. Fresh
+ all-state issue-title/body search matched653/583/307/304/300; all five bodies read. Scoped local search includes
+ ignored/hidden files,excluding.git/docs/site/references_cache and credentials; relevant caches separately covered.
+ PRs/comments not exhaustively searched. No reusable taxon match found in ignored/hidden-inclusive kb/taxa search
+ for the reviewed taxa/IDs.
+- Only graphs,new focused discussions and curation events change. All456other records,923caches,non-graph raw blocks
+ and prior histories/decisions preserved. No schema,validator,threshold or runtime-rule changes. Spring remaining
+ identity uncertainty is explicit; other non-graph taxonomy,abundance,role,cultivation and evidence claims are
+ not recertified. Self-review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered
+ Edison scopes untouched. Validation/publication are not preasserted.
+- Self-adversarial review corrected a too-broad computational tool chain before publication:HydDB removed from Doudnabacteria
+ sulfur-enzyme provenance and retained for hydrogenases. A fifth append-only history and second spring curation
+ event preserve the initial entry unchanged. Initial verification was deliberately interrupted with SIGINT/exit130
+ for this factual correction,not a timeout,and its partial logs are archived;all final gates run afresh.
+records:
+- path: kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml
+ id: CommunityMech:000312
+ original_sha256: aa951b219710a3b699cd561d2fed9a7d10a2dfd49e90745957d0ce68093fcd30
+ record_sha256: 69551869693ec797fb080f10747bdacd590e9686cdcdb93ff8c47a2e20880a18
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification.
+ summary: Retain recruitment, distinguishing chemotaxis from motility and qualifying its necessity for the cue
+ response.; Retain the measured cue response without asserting nutrient uptake or resolved bacterial benefit.;
+ Preserve experimentally supported thiamine transfer and growth rescue; qualify in-plant mediation.; Preserve
+ fungal and host benefits and the source mutualism interpretation without exclusive mediator or flux claims.
+ node_decisions:
+ - node: Fungal recruitment of the hyphae-associated bacterium
+ rationale: Retain recruitment, distinguishing chemotaxis from motility and qualifying its necessity for the
+ cue response.
+ - node: Ureidosuccinic acid stimulation of bacterial thiamine production
+ rationale: Retain the measured cue response without asserting nutrient uptake or resolved bacterial benefit.
+ - node: Thiamine provisioning fulfilling the fungal requirement
+ rationale: Preserve experimentally supported thiamine transfer and growth rescue; qualify in-plant mediation.
+ - node: Enhanced ectomycorrhizal colonization of the pine host
+ rationale: Preserve fungal and host benefits and the source mutualism interpretation without exclusive mediator
+ or flux claims.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id001
+ source: Fungal recruitment of the hyphae-associated bacterium
+ target: Ureidosuccinic acid stimulation of bacterial thiamine production
+ description: 'Recruitment of B. altitudinis B4 to the S. clintonianus mycelial surface precedes ureidosuccinic-acid
+ stimulation of the recruited bacterium''s thiamine biosynthesis.
+
+ '
+ - &id003
+ source: Ureidosuccinic acid stimulation of bacterial thiamine production
+ target: Thiamine provisioning fulfilling the fungal requirement
+ description: 'Ureidosuccinic acid-induced biomass increase and thiamine-gene upregulation in B. altitudinis
+ B4 enhance the thiamine pool supplied to the thiamine-limited fungus.
+
+ '
+ - &id005
+ source: Thiamine provisioning fulfilling the fungal requirement
+ target: Enhanced ectomycorrhizal colonization of the pine host
+ description: 'Bacterially produced thiamine is absorbed by S. clintonianus to promote fungal growth, increasing
+ ectomycorrhizal colonization of P. massoniana.
+
+ '
+ edges_after:
+ - &id002
+ source: Fungal recruitment of the hyphae-associated bacterium
+ target: Ureidosuccinic acid stimulation of bacterial thiamine production
+ description: 'HYPOTHESIZED/PARTIAL: recruitment establishes the close fungal-bacterial association in which
+ fungal exudates can stimulate bacterial thiamine production. The authors propose this sequence, but recruitment
+ was not isolated as a necessary mediator of the cue response; ureidosuccinic acid also acted in the separate
+ bacterial assay.'
+ - &id004
+ source: Ureidosuccinic acid stimulation of bacterial thiamine production
+ target: Thiamine provisioning fulfilling the fungal requirement
+ description: Ureidosuccinic acid increased extracellular thiamine in the bacterial assay, supporting a greater
+ vitamin supply available to the fungal recipient. Separate coculture and tracer observations support fungal
+ acquisition of bacterial thiamine; they do not quantify what fraction of endogenous transfer is caused by
+ this one exudate.
+ - &id006
+ source: Thiamine provisioning fulfilling the fungal requirement
+ target: Enhanced ectomycorrhizal colonization of the pine host
+ description: 'HYPOTHESIZED/PARTIAL: bacterial thiamine supports fungal growth and is proposed to contribute
+ to the higher ectomycorrhizal colonization observed with B4 in the pot experiment. The vitamin-mediated route
+ is supported across the assays but is not isolated as the exclusive mediator of the in-plant phenotype.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ - before: *id003
+ after: *id004
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ - before: *id005
+ after: *id006
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:41454778
+ issues:
+ - 1837
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml
+- path: kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml
+ id: CommunityMech:000222
+ original_sha256: bdde368007b748fab8102646934b696e16102c0adffbd28df7fef6aa382c32a0
+ record_sha256: 5d3a32811ff6817ac9002bd39f79c53511fa76bc15d97a9adca897220471f235
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification.
+ summary: Preserve sulfur-granule observations; remove commensalism and redundant source, explicitly leaving species
+ grounding unresolved.; Preserve the source episymbiosis hypothesis without confirmed cell identity or fitness
+ interpretation; remove the spatial causal arrow.; Preserve lineage-specific genomic/structural predictions with
+ provenance, not measured flux or host exchange.
+ node_decisions:
+ - node: Filamentous Sulfur Oxidation with Encapsulated S Granules
+ rationale: Preserve sulfur-granule observations; remove commensalism and redundant source, explicitly leaving
+ species grounding unresolved.
+ - node: Putative CPR association with sulfur-oxidizing filaments
+ rationale: Preserve the source episymbiosis hypothesis without confirmed cell identity or fitness interpretation;
+ remove the spatial causal arrow.
+ - node: Predicted CPR sulfur and hydrogen metabolic capacity
+ rationale: Preserve lineage-specific genomic/structural predictions with provenance, not measured flux or host
+ exchange. HydDB is attached only to the hydrogenase evidence, not the sulfur-enzyme prediction.
+ removed_node_decisions: []
+ renamed_nodes:
+ CPR Episymbiosis with Filamentous Hosts: Putative CPR association with sulfur-oxidizing filaments
+ CPR Sulfur-Hydrogen Coupling: Predicted CPR sulfur and hydrogen metabolic capacity
+ edges_before:
+ - source: Filamentous Sulfur Oxidation with Encapsulated S Granules
+ target: CPR Episymbiosis with Filamentous Hosts
+ description: The chemolithotrophic Thiothrix- and Beggiatoa-like filaments are the sulfur-oxidizing biofilm
+ structures near which ultra-small CPR-like episymbionts were imaged.
+ - source: CPR Episymbiosis with Filamentous Hosts
+ target: CPR Sulfur-Hydrogen Coupling
+ description: CPR attachment to sulfur-oxidizing filament surfaces places the CPR bacteria in the same cryptic
+ sulfur-cycling biofilm where CPR hydrogenase and thiosulfate-conversion genes were predicted.
+ edges_after: []
+ retained_edge_decisions: []
+ removed_edge_decisions:
+ - source: Filamentous Sulfur Oxidation with Encapsulated S Granules
+ target: CPR Episymbiosis with Filamentous Hosts
+ description: The chemolithotrophic Thiothrix- and Beggiatoa-like filaments are the sulfur-oxidizing biofilm
+ structures near which ultra-small CPR-like episymbionts were imaged.
+ rationale: Spatial association does not establish a causal transition; attachment does not cause encoded metabolic
+ capacity. Preserve observations and source hypotheses without a false arrow.
+ - source: CPR Episymbiosis with Filamentous Hosts
+ target: CPR Sulfur-Hydrogen Coupling
+ description: CPR attachment to sulfur-oxidizing filament surfaces places the CPR bacteria in the same cryptic
+ sulfur-cycling biofilm where CPR hydrogenase and thiosulfate-conversion genes were predicted.
+ rationale: Spatial association does not establish a causal transition; attachment does not cause encoded metabolic
+ capacity. Preserve observations and source hypotheses without a false arrow.
+ references:
+ - PMID:38273328
+ issues:
+ - 1838
+ - 1841
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 2
+ history_files:
+ - history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml
+ - history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml
+ remaining_requirement: Resolve canonical Thiothrix/Beggiatoa lineage and imaged-cell identity boundaries with
+ the graph references; current species links are not certified. Issue1841 remains open.
+- path: kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml
+ id: CommunityMech:000127
+ original_sha256: 660c1b3de9165421c53f76fdee1ef9609e6101d50ab1850fbc68c52ea474b563
+ record_sha256: 3b6f0e648eb199d8139c7d790034e88f471e3fa5a3f0212ed55a60280921a6e6
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification.
+ summary: Preserve predicted exchange and measured metabolite production with iNAP provenance and an explicitly
+ partial upstream mechanism.; Preserve supported Th17 induction; remove colonization typing and the mismatched
+ innate-only GO annotation.; Preserve positive host-protection endpoints without competition, eradication or
+ exclusive SFB mediation.
+ node_decisions:
+ - node: Predicted SynCom-to-SFB metabolite exchange
+ rationale: Preserve predicted exchange and measured metabolite production with iNAP provenance and an explicitly
+ partial upstream mechanism.
+ - node: SFB-Driven Th17 Immune Priming
+ rationale: Preserve supported Th17 induction; remove colonization typing and the mismatched innate-only GO annotation.
+ - node: Host protection after SynComBac10 exposure
+ rationale: Preserve positive host-protection endpoints without competition, eradication or exclusive SFB mediation.
+ removed_node_decisions: []
+ renamed_nodes:
+ SynCom-Stimulated SFB Cross-Feeding: Predicted SynCom-to-SFB metabolite exchange
+ SFB-Mediated Salmonella Resistance: Host protection after SynComBac10 exposure
+ edges_before:
+ - &id007
+ source: SynCom-Stimulated SFB Cross-Feeding
+ target: SFB-Driven Th17 Immune Priming
+ description: SynComBac10 metabolite cross-feeding is the proposed mechanism for early SFB establishment, which
+ then induces Th17 cell-mediated immune responses.
+ - &id009
+ source: SFB-Driven Th17 Immune Priming
+ target: SFB-Mediated Salmonella Resistance
+ description: Th17 immune priming by SFB supplies the host-mediated protective mechanism that increases resistance
+ to Salmonella infection.
+ edges_after:
+ - &id008
+ source: Predicted SynCom-to-SFB metabolite exchange
+ target: SFB-Driven Th17 Immune Priming
+ description: 'HYPOTHESIZED/PARTIAL: predicted nutrient provision may help account for the observed SFB establishment
+ upstream of Th17 induction. The study supports SFB-associated immune induction, but does not establish the
+ predicted exchange as its necessary upstream mediator.'
+ - &id010
+ source: SFB-Driven Th17 Immune Priming
+ target: Host protection after SynComBac10 exposure
+ description: 'HYPOTHESIZED/PARTIAL: SFB-associated Th17 responses are proposed to contribute to the protective
+ host outcomes after SynComBac10 exposure. The source explicitly leaves other immune and non-immune contributions
+ open, so this is not an exclusive or experimentally isolated mediation claim.'
+ retained_edge_decisions:
+ - before: *id007
+ after: *id008
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ - before: *id009
+ after: *id010
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:40266232
+ issues:
+ - 1839
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml
+- path: kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml
+ id: CommunityMech:000314
+ original_sha256: 525ba5f6ae9b8d78451ffcb4dbb58a652c5c82897b96e88727eceb528b3391ac
+ record_sha256: 8128a35b7336eb6a0e2da4768e456cd12e84db5632b771708a70f07d6bebd5b5
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml
+ scope: Whole record and all existing nodes/directions; graph/evidence repair, not whole-record certification.
+ summary: Retain protective fungal/aflatoxin endpoints with the storage-time boundary, without reciprocal competition.;
+ Retain rhizobia-dependent nodulation facilitation with participant scope excluding the fungal target.; Retain
+ combined positive outcomes, qualifying causal coupling and removing misplaced colonization/host-defense typing.
+ node_decisions:
+ - node: SynCom ARC Suppression of Aspergillus flavus
+ rationale: Retain protective fungal/aflatoxin endpoints with the storage-time boundary, without reciprocal competition.
+ - node: SynCom ARC Induction of Rhizobia-Legume Nodulation
+ rationale: Retain rhizobia-dependent nodulation facilitation with participant scope excluding the fungal target.
+ - node: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ rationale: Retain combined positive outcomes, qualifying causal coupling and removing misplaced colonization/host-defense
+ typing.
+ removed_node_decisions: []
+ renamed_nodes:
+ Coupled Aflatoxin Prevention and Nodulation-Supported Yield: Concurrent aflatoxin reduction, nodulation and
+ yield outcomes
+ edges_before:
+ - &id011
+ source: SynCom ARC Suppression of Aspergillus flavus
+ target: Coupled Aflatoxin Prevention and Nodulation-Supported Yield
+ description: 'A. flavus suppression supplies the pathogen-control branch of ARC''s coupled peanut field phenotype.
+
+ '
+ - &id013
+ source: SynCom ARC Induction of Rhizobia-Legume Nodulation
+ target: Coupled Aflatoxin Prevention and Nodulation-Supported Yield
+ description: 'Enhanced rhizobia-legume nodulation supplies the nitrogen-fixation branch of ARC''s coupled peanut
+ field phenotype.
+
+ '
+ edges_after:
+ - &id012
+ source: SynCom ARC Suppression of Aspergillus flavus
+ target: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ description: 'HYPOTHESIZED/PARTIAL: fungal suppression contributes to the aflatoxin-control component of the
+ combined protective phenotype. Its contribution to the joint nodulation and yield outcome is not isolated
+ from the other effects of ARC.'
+ - &id014
+ source: SynCom ARC Induction of Rhizobia-Legume Nodulation
+ target: Concurrent aflatoxin reduction, nodulation and yield outcomes
+ description: 'HYPOTHESIZED/PARTIAL: enhanced rhizobial nodulation and nitrogenase activity are proposed to support
+ the higher-yield phenotype alongside improved photosynthesis and carbon allocation. Parallel endpoints and
+ omics associations do not isolate the contribution of nitrogen fixation or prove the proposed feedback quantitatively.'
+ retained_edge_decisions:
+ - before: *id011
+ after: *id012
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ - before: *id013
+ after: *id014
+ rationale: Existing direction retained with assay-specific support and explicit mediation limits.
+ removed_edge_decisions: []
+ references:
+ - PMID:42099455
+ issues:
+ - 1840
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml
+adversarial_correction:
+ issue: 1838
+ finding: HydDB incorrectly listed on the separate sulfur-enzyme evidence
+ resolution: Narrow Doudnabacteria sulfur-enzyme provenance to METABOLIC and AlphaFold2; HydDB applies only to
+ the separate hydrogenase prediction.
+ initial_history: history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml
+ correction_history: history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml
+ initial_history_sha256: fbfb65d6b1cc316f1cbc9c90b6f419ab00b9b295e8d76a5ee208e428d3020606
+superseded_verification:
+ report: /private/tmp/communitymech-batch107/pre-correction-validation.json
+ sha256: f415569eea83f28f133dc7e6669d0af61386ee53175453a4f358ff140d9324fa
+ log_directory: /private/tmp/communitymech-batch107/verification-pre-correction
+ original_log_directory: /private/tmp/communitymech-batch107/verification
+ status: Interrupted for factual provenance correction;not a final pass
+ exec_session: 77092
+ exit_code: 130
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index e5d0f8056..56d401549 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -388,10 +388,10 @@ kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml C
kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml CommunityMech:000254 3f9b3c0e30a8f745ccaa24400d3523ef7306000486ab5e1b5c05a0cf3f877e27 4 1 81.2 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml CommunityMech:000335 4ef09a74970615b914a26247da7f2919234df7487a087c51923c41dea1a9042c 4 2 90.0 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
kb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml CommunityMech:000251 0f750d563e028d6b70a47ac876aec68e29bef5b87eae6ec06ba34630e43e6bd9 4 2 100.0 reports/causal_graph_review/decisions/20261008-four-records-batch106.yaml reviewed
-kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml CommunityMech:000312 aa951b219710a3b699cd561d2fed9a7d10a2dfd49e90745957d0ce68093fcd30 4 3 100.0 pending
-kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml CommunityMech:000222 bdde368007b748fab8102646934b696e16102c0adffbd28df7fef6aa382c32a0 3 2 100.0 pending
-kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml CommunityMech:000127 660c1b3de9165421c53f76fdee1ef9609e6101d50ab1850fbc68c52ea474b563 3 2 100.0 pending
-kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml CommunityMech:000314 525ba5f6ae9b8d78451ffcb4dbb58a652c5c82897b96e88727eceb528b3391ac 3 2 100.0 pending
+kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml CommunityMech:000312 69551869693ec797fb080f10747bdacd590e9686cdcdb93ff8c47a2e20880a18 4 3 97.5 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml reviewed
+kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml CommunityMech:000222 5d3a32811ff6817ac9002bd39f79c53511fa76bc15d97a9adca897220471f235 3 0 65.0 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml needs_research
+kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml CommunityMech:000127 3b6f0e648eb199d8139c7d790034e88f471e3fa5a3f0212ed55a60280921a6e6 3 2 91.7 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml reviewed
+kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml CommunityMech:000314 8128a35b7336eb6a0e2da4768e456cd12e84db5632b771708a70f07d6bebd5b5 3 2 93.3 reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml reviewed
kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml CommunityMech:000278 ffe0f5e7381d820061ccfe30ec1b71277c3e88866519bcc52389537d4bc85123 3 2 100.0 pending
kb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml CommunityMech:000285 6bc229bfcabb16639d9a7ffd085739421b0f38be95cc85cd66aaf80ecc70b9c5 5 3 100.0 pending
kb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml CommunityMech:000302 83b3d7091d48bc228128b3266d84d6f9fe3d4d596befb02d76136cbab8d2e24b 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index d33342c98..dedf364d7 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": 1386,
- "edges": 553,
+ "edges": 551,
"records_without_nodes": 10,
- "records_without_edges": 182,
+ "records_without_edges": 183,
"review_status_counts": {
- "needs_research": 50,
- "pending": 72,
- "reviewed": 338
+ "needs_research": 51,
+ "pending": 68,
+ "reviewed": 341
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch107.json b/reports/causal_graph_review/validation-20261008-batch107.json
new file mode 100644
index 000000000..c2a0413b0
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch107.json
@@ -0,0 +1,1096 @@
+{
+ "base_commit": "2d931aca3afcab956c0eba9661e09344479ad2c7",
+ "scope": [
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch107.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/focused.log",
+ "log_sha256": "f41086e8776e0ac73a11c58150afcf40275e9d54b9c7b70faad30187378bc82a",
+ "output_tail": "........ [100%]\n8 passed in 14.91s\n"
+ },
+ {
+ "check": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch107/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-strict.tsv",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-strict.log",
+ "log_sha256": "70b04b9446ee6035894889d8e38aad52be88d63662ffd39a4a8b41b8cd2c5f18",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch107/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-batch107/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-references.log",
+ "log_sha256": "1a6bddb2d723e844551e23978fbf0947cd37511ad07afd9c3a55593eed17658a",
+ "output_tail": "Validating kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.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/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.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": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-snippets.log",
+ "log_sha256": "c72869c3cfa80d3275b80461e8b721727d9e301213f59836200303704b4482a6",
+ "output_tail": "# 27 evidence snippets scanned across 1 files\n MATCH 27\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-rank.log",
+ "log_sha256": "8b0b5497ce69fbeb99a8e9d2fa02351e2526735f5393deefe073a4bbd33f7409",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000312\",\n \"name\": \"Suillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\",\n \"score\": 97.5,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 4,\n \"downstream_edges\": 3,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom/2026-10-08T032721Z-codex-f26eee.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch107/Sulfide_Spring_Autotrophic_CPR_Biofilm-strict.tsv",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-strict.log",
+ "log_sha256": "3365e1d35fc9826b5d13fcd5fc5c396e5ff3d837b650b804242c442dbf4e1b46",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch107/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-batch107/Sulfide_Spring_Autotrophic_CPR_Biofilm-strict.tsv\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-references.log",
+ "log_sha256": "6bd9f9070bc466a43ebc1647e8a1b6b0f76d2aa679fc3c03c5ee0a8708c08c39",
+ "output_tail": "Validating kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.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/Sulfide_Spring_Autotrophic_CPR_Biofilm.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": "Sulfide_Spring_Autotrophic_CPR_Biofilm-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-snippets.log",
+ "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+ "output_tail": "# 17 evidence snippets scanned across 1 files\n MATCH 17\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-rank.log",
+ "log_sha256": "ea92a730ede9fdbf2bef4fb55eae7fee8ff53fb59074936aff62fb8f74933bcb",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000222\",\n \"name\": \"Sulfide Spring Autotrophic CPR-Hosting Biofilm\",\n \"score\": 65.0,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 0,\n \"interaction_evidence\": 5,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"downstream\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T032721Z-codex-525fbf.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Sulfide_Spring_Autotrophic_CPR_Biofilm-history-1",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Sulfide_Spring_Autotrophic_CPR_Biofilm/2026-10-08T033029Z-codex-a989db.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/Sulfide_Spring_Autotrophic_CPR_Biofilm-history-1.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynComBac10_Chicken_Intestinal_SynCom-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynComBac10_Chicken_Intestinal_SynCom-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch107/SynComBac10_Chicken_Intestinal_SynCom-strict.tsv",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-strict.log",
+ "log_sha256": "f1dd81d90f311b09294869bd666ca2cc4cf6bfc411fa2f9fd158549bec54a108",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch107/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-batch107/SynComBac10_Chicken_Intestinal_SynCom-strict.tsv\n"
+ },
+ {
+ "check": "SynComBac10_Chicken_Intestinal_SynCom-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SynComBac10_Chicken_Intestinal_SynCom-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-references.log",
+ "log_sha256": "bb3a2a92bce78ad287f28f46ae712b5a96963f3217bedae53a1b8daf3ff13ea1",
+ "output_tail": "Validating kb/communities/SynComBac10_Chicken_Intestinal_SynCom.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/SynComBac10_Chicken_Intestinal_SynCom.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": "SynComBac10_Chicken_Intestinal_SynCom-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-snippets.log",
+ "log_sha256": "826e9c1ef5038bfe5995c8f56b27f9f6d8418cb9a40f124b1547f2d75876c305",
+ "output_tail": "# 15 evidence snippets scanned across 1 files\n MATCH 15\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "SynComBac10_Chicken_Intestinal_SynCom-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-rank.log",
+ "log_sha256": "03df6d841eca2257618abe0bc540feab685e4d0688a6293c89196cf69bdb2cd5",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000127\",\n \"name\": \"SynComBac10 Chicken Intestinal SynCom\",\n \"score\": 91.7,\n \"taxonomy\": 3,\n \"connected_taxa\": 3,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "SynComBac10_Chicken_Intestinal_SynCom-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SynComBac10_Chicken_Intestinal_SynCom/2026-10-08T032722Z-codex-28b659.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynComBac10_Chicken_Intestinal_SynCom-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch107/SynCom_ARC_Peanut_Aflatoxin_Nodulation-strict.tsv",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-strict.log",
+ "log_sha256": "c8d0bb98a53f4c673d1420c9e5868014ecfce5c1bac5a60fba24fd159a2be080",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch107/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-batch107/SynCom_ARC_Peanut_Aflatoxin_Nodulation-strict.tsv\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-references.log",
+ "log_sha256": "a67d4a292d83cbbb36b363a36ded08736b278a8136fd851ca60cd7d3b39f0deb",
+ "output_tail": "Validating kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-snippets.log",
+ "log_sha256": "c9f381dbb19f92a2794c60960d7047d1e74637f587b4266fdba89a29ad817e36",
+ "output_tail": "# 25 evidence snippets scanned across 1 files\n MATCH 24\n RENDERING 1\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n 1 kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-rank.log",
+ "log_sha256": "0cfa574f46be467488d0bb7cd81bf7e435574c69113d4350330fbcbc4ed53437",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000314\",\n \"name\": \"SynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\",\n \"score\": 93.3,\n \"taxonomy\": 5,\n \"connected_taxa\": 5,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 6,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "SynCom_ARC_Peanut_Aflatoxin_Nodulation-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/SynCom_ARC_Peanut_Aflatoxin_Nodulation/2026-10-08T032722Z-codex-9322a4.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/SynCom_ARC_Peanut_Aflatoxin_Nodulation-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-batch107/verification/inventory.log",
+ "log_sha256": "d61b836596bc691699c00e59d65f07f8468d35dbe4a1b76f1734ed11652ef268",
+ "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\": 1386,\n \"edges\": 551,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 183,\n \"review_status_counts\": {\n \"needs_research\": 51,\n \"pending\": 68,\n \"reviewed\": 341\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-batch107/verification/network.log",
+ "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+ "output_tail": " \"total_genomes\": 17191,\n \"is_reclassified\": false,\n \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n },\n \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"mexZ\"\n },\n \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n \"evidence\": [\n {\n \"reference\": \"PMID:42153623\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "just-network-json",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_codes": [
+ 2
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/just-network-json.log",
+ "log_sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/rank-all.log",
+ "log_sha256": "4c56af46d790f6da656a55382a12058542527bc825bbd502842ff08a609c53eb",
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RDK17 Terephthalic-acid Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n408\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n410\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t4\t2\t4\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_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"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/render.log",
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+ "output_tail": "unitymech-causal-batch107/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 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Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch107/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch107/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch107/docs/index.html\n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "exit_code": 0,
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Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 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/private/tmp/communitymech-causal-batch107/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch107/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch107/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch107/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch107/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch106')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/connectivity-survey.log",
+ "log_sha256": "38a12f49cbc88c7b8677195d203bbd2c525ef38242aa0ab91633314f37a45aa7",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch100.py",
+ "tests/test_causal_review_batch101.py",
+ "tests/test_causal_review_batch102.py",
+ "tests/test_causal_review_batch103.py",
+ "tests/test_causal_review_batch104.py",
+ "tests/test_causal_review_batch105.py",
+ "tests/test_causal_review_batch106.py",
+ "tests/test_causal_review_batch107.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch47.py",
+ "tests/test_causal_review_batch48.py",
+ "tests/test_causal_review_batch49.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch50.py",
+ "tests/test_causal_review_batch51.py",
+ "tests/test_causal_review_batch52.py",
+ "tests/test_causal_review_batch53.py",
+ "tests/test_causal_review_batch54.py",
+ "tests/test_causal_review_batch55.py",
+ "tests/test_causal_review_batch56.py",
+ "tests/test_causal_review_batch57.py",
+ "tests/test_causal_review_batch58.py",
+ "tests/test_causal_review_batch59.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch60.py",
+ "tests/test_causal_review_batch61.py",
+ "tests/test_causal_review_batch62.py",
+ "tests/test_causal_review_batch63.py",
+ "tests/test_causal_review_batch64.py",
+ "tests/test_causal_review_batch65.py",
+ "tests/test_causal_review_batch66.py",
+ "tests/test_causal_review_batch67.py",
+ "tests/test_causal_review_batch68.py",
+ "tests/test_causal_review_batch69.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch70.py",
+ "tests/test_causal_review_batch71.py",
+ "tests/test_causal_review_batch72.py",
+ "tests/test_causal_review_batch73.py",
+ "tests/test_causal_review_batch74.py",
+ "tests/test_causal_review_batch75.py",
+ "tests/test_causal_review_batch76.py",
+ "tests/test_causal_review_batch77.py",
+ "tests/test_causal_review_batch78.py",
+ "tests/test_causal_review_batch79.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch80.py",
+ "tests/test_causal_review_batch81.py",
+ "tests/test_causal_review_batch82.py",
+ "tests/test_causal_review_batch83.py",
+ "tests/test_causal_review_batch84.py",
+ "tests/test_causal_review_batch85.py",
+ "tests/test_causal_review_batch86.py",
+ "tests/test_causal_review_batch87.py",
+ "tests/test_causal_review_batch88.py",
+ "tests/test_causal_review_batch89.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_causal_review_batch90.py",
+ "tests/test_causal_review_batch91.py",
+ "tests/test_causal_review_batch92.py",
+ "tests/test_causal_review_batch93.py",
+ "tests/test_causal_review_batch94.py",
+ "tests/test_causal_review_batch95.py",
+ "tests/test_causal_review_batch96.py",
+ "tests/test_causal_review_batch97.py",
+ "tests/test_causal_review_batch98.py",
+ "tests/test_causal_review_batch99.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/regressions.log",
+ "log_sha256": "4355d4b1ecca0347b508d6184ae8092ccc56de449e25060a84fb19f1edbb59c3",
+ "output_tail": "........................................................................ [ 7%]\n........................................................................ [ 14%]\n........................................................................ [ 22%]\n........................................................................ [ 29%]\n........................................................................ [ 37%]\n........................................................................ [ 44%]\n........................................................................ [ 52%]\n........................................................................ [ 59%]\n........................................................................ [ 67%]\n........................................................................ [ 74%]\n........................................................................ [ 81%]\n........................................................................ [ 89%]\n........................................................................ [ 96%]\n............................... [100%]\n967 passed in 327.16s (0:05:27)\n"
+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/just-lint.log",
+ "log_sha256": "8ec8eaa802a2b2a2f07856cd5d87abdfb7a6ed7e5158546fc2bb878a12e9bca1",
+ "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n360 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+ },
+ {
+ "check": "mypy-explicit-runtime",
+ "command": [
+ "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+ "--no-incremental",
+ "--python-executable",
+ "/private/tmp/communitymech-batch100/lint-env/bin/python",
+ "src/"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/mypy-explicit-runtime.log",
+ "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+ "output_tail": "Success: no issues found in 49 source files\n"
+ },
+ {
+ "check": "audit-snippets-all",
+ "command": [
+ "just",
+ "audit-snippets"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/audit-snippets-all.log",
+ "log_sha256": "3e3bcd640f461e0181110b528949ee7dd5a94f57b70d83fdd31cd8437d7b87d1",
+ "output_tail": "# 8977 evidence snippets scanned across 460 files\n MATCH 8840\n RENDERING 21\n ASSEMBLED 1\n WEAK 0\n MISMATCH 39\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch107/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh both-root baseline before source reads:460records,923caches,56existing warnings,zero structural defects. Whole four targets and all13nodes/9directions reviewed. Retain13nodes/7existing directions,remove2spatial arrows,rename5nodes. No new topology or Edison submission/spend.",
+ "Four primary EuropePMC XML sources independently retrieved with CC BY4.0 metadata. Suillus abstract/introduction1-60 and results/discussion242-503 read; spring abstract/background1-65,methods193-268,results270-485 and513-662 read; chicken bounded immune/protection/prediction results260-393 and discussion427-522 read, plus abstract; ARC extracted main text1-217 read. Other spans were indexed or not read. No figure-pixel,separate-supplement,raw-data or full-pipeline certification.",
+ "Existing caches used for headers,bounded context and normalized quote checks,not exhaustive duplicated full-text review. Suillus cache is PMID_41454778.md and contains body text despite abstract_only metadata. Chicken has two existing cache representations; no new cache imports. Large single-line cache output was truncated and is not claimed as read. No license949,loader1703 or DOI-case1091 certification.",
+ "Suillus:preserve demonstrated bacterial-to-fungal thiamine transfer,auxotrophy rescue,recruitment and fungal/plant benefits. Distinguish pregnenolone motility from ureidosuccinate chemotaxis. Remove nutrient-consumption typing from cue response; preserve host mutualism interpretation but not measured host-fungal flux or exclusive thiamine mediation. Thiamine-free P20 and prior583 context remain unchanged.",
+ "Spring:preserve sulfur-granule imaging,putative CPR association and lineage-specific metabolic predictions. Remove unestablished commensalism and both spatial arrows; add bounded genomic/structural provenance. Current canonical NCBITaxon:1031 link exceeds the source51%amino-acid similarity; legacy references remain explicitly uncertified pending coordinated identity repair1841. This record remains needs_research rather than being counted fully reviewed.",
+ "Chicken:preserve measured immune induction,metabolite-production evidence and host protection. Predicted iNAP2.0 exchange is not measured recipient transfer; protective association is not exclusive mediation. Remove colonization/competition typing and misplaced innate-only GO annotation. Evidence correction only; no new pathogen enhancement,genetic designs,strain-selection advice,challenge methods,growth optimization or causal mechanisms.",
+ "ARC:preserve protective fungal,nodulation,photosynthesis and yield outcomes. Attach85.6%aflatoxin decrease to12months storage and retain the rhizobia-dependent nodulation boundary. Remove reciprocal-competition and aggregate-colonization/host-defense annotations; narrow separate node participants. Both outcome-contribution directions remain qualified,not isolated mechanisms or a proven feedback loop. Prior300/307counter-selection and653supplement provenance remain unchanged. No toxin-production procedures or optimization advice.",
+ "Graph repairs1837-1840remain open until protected-main merge. Identity1841remains open after repair merge. Fresh all-state issue-title/body search matched653/583/307/304/300; all five bodies read. Scoped local search includes ignored/hidden files,excluding.git/docs/site/references_cache and credentials; relevant caches separately covered. PRs/comments not exhaustively searched. No reusable taxon match found in ignored/hidden-inclusive kb/taxa search for the reviewed taxa/IDs.",
+ "Only graphs,new focused discussions and curation events change. All456other records,923caches,non-graph raw blocks and prior histories/decisions preserved. No schema,validator,threshold or runtime-rule changes. Spring remaining identity uncertainty is explicit; other non-graph taxonomy,abundance,role,cultivation and evidence claims are not recertified. Self-review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication are not preasserted.",
+ "Self-adversarial review corrected a too-broad computational tool chain before publication:HydDB removed from Doudnabacteria sulfur-enzyme provenance and retained for hydrogenases. A fifth append-only history and second spring curation event preserve the initial entry unchanged. Initial verification was deliberately interrupted with SIGINT/exit130 for this factual correction,not a timeout,and its partial logs are archived;all final gates run afresh."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml": {
+ "MATCH": 27,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml": {
+ "MATCH": 17,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml": {
+ "MATCH": 15,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml": {
+ "MATCH": 24,
+ "RENDERING": 1,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 456,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 61,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "required_for_unresolved_extensions": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "dry_runs": [],
+ "repair_scope": "Existing-node evidence/semantics repair,seven existing directions retained,two spatial arrows removed;identity1841needs coordinated curation,not new-topology generation."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch107/arc-metadata.json": "243c7ec12677ace786ed8c24ab04368552bae147f51be7492e3b3d6066b585c4",
+ "/private/tmp/communitymech-batch107/arc-primary.txt": "45274786c15ca06c2a01283691fd22a4c652cd40403f07a92d6e59da954cd92e",
+ "/private/tmp/communitymech-batch107/arc-primary.xml": "bb4c534cc823bfcb837c13b6a075a97ec048ee08b81ed97d48b74f759a64ffa4",
+ "/private/tmp/communitymech-batch107/baseline.json": "2e02db0cebfc1d13f0a10ad4f47ab0bd0778fe9ac236ddad667ebb5e28aeec52",
+ "/private/tmp/communitymech-batch107/chicken-metadata.json": "f48ba18d3c7689680f4fc924c6242ac72d46f3892be4934b9cb06707034e3d51",
+ "/private/tmp/communitymech-batch107/chicken-primary.txt": "9092ee825b832e4fa71e79862a3635880465b10f957c7a3b00aa0b223b5eb3bf",
+ "/private/tmp/communitymech-batch107/chicken-primary.xml": "61f675010caab7d60942a57b1f1a4d54e54b4b05efdbab19f70d12a00387980d",
+ "/private/tmp/communitymech-batch107/dedup-local-current.txt": "83f33a0c26dd2bd43f1e1ef955e06f096147d600bcc306dd33bd86bee4af1f5f",
+ "/private/tmp/communitymech-batch107/issue-dedup-current.json": "218e392ea3f23bb630bc060c1235b090c79148c89e95b0e012458c9cae8540c3",
+ "/private/tmp/communitymech-batch107/primary-manifest.json": "0c4114e4b83e51489ae02cf7336b467ffa37454d4b6c5c4961778b1833f95dab",
+ "/private/tmp/communitymech-batch107/spring-metadata.json": "8a1459c1212f4136ba8097058ed37af82624ae9f56742a2c57ede76db7f70c86",
+ "/private/tmp/communitymech-batch107/spring-primary.txt": "0140358180e01a111d0e4bf949bec128a5d74ed3bf27e10ad891df75d5cd6a6b",
+ "/private/tmp/communitymech-batch107/spring-primary.xml": "09a2d4f1d6d96b23af8f3d15619852e2f7953caa7aa15f954e71f6db8019b541",
+ "/private/tmp/communitymech-batch107/suillus-metadata.json": "8761d1a578bf6f4f866e2627cb7459f6b3096c60fcf87f65a663f705d549ac36",
+ "/private/tmp/communitymech-batch107/suillus-primary.txt": "0a1231d39da69f2fc4c87970fbf5671094282a6f0c9d6f385dcb325b46dddce1",
+ "/private/tmp/communitymech-batch107/suillus-primary.xml": "0fa12fd23362bdc788f15ff2c752d40eaa63e076fbc8d4dd4168ec914326c2c6",
+ "references_cache/PMID_38273328.md": "a7cc4c5561b4a8b33686c68ca4f7939331f5d78b256794b4561d10330c52c675",
+ "references_cache/PMID_40266232.txt": "bf18b8e042d72b4084df724a26ea7c3bae9236d1e267c17a29961ff1eeb5f3ec",
+ "references_cache/PMID_41454778.md": "c5750137a6f5de73953126f714e07c45ffba7367d9b55c7ea0a680dc9b527809",
+ "references_cache/PMID_42099455.txt": "b94e222a0aea5e54f856ab247d4682ef0238739bf8daafd9f8da411294577344"
+ },
+ "immutable_prior_history_and_decision_files": 822,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 25,
+ "new_discussion_quotations": 6,
+ "fresh_primary_literal_matches": 31,
+ "all_cached_literal_matches": 31,
+ "retained_nodes": 13,
+ "removed_nodes": 0,
+ "retained_arrows": 7,
+ "removed_arrows": 2,
+ "new_nodes_or_directions": 0,
+ "scope": "All reviewed quotations match fresh primary text and unchanged caches; source entailment separately reviewed. Four bounded main-text reviews,not whole-paper/supplement/figure/raw-data certification."
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "interpretation": "All13nodes retained,seven existing directions qualified,two spatial arrows removed. All56existing warnings unchanged;zero structural defects. Spring species identity remains unresolved1841 despite structural validity."
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1372,
+ "arrows": 543
+ },
+ "render_scope": "Deterministic rendering and exact HTML-description parser,not screenshots;postcommit docs-current separately required.",
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 403,
+ "mixed": 128,
+ "community_level_only": 275,
+ "taxa": 1544,
+ "credited_solely_by_the_rule": 1270
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 403,
+ "mixed": 128,
+ "community_level_only": 275,
+ "taxa": 1544,
+ "credited_solely_by_the_rule": 1270
+ }
+ },
+ "delta": {
+ "records": 0,
+ "with_community_level": 0,
+ "mixed": 0,
+ "community_level_only": 0,
+ "taxa": 0,
+ "credited_solely_by_the_rule": 0
+ },
+ "interpretation": "ARC suppression/nodulation observations gain canonical identity-only scope. The combined endpoint still encompasses the system;global census unchanged. Spring legacy identity links are explicitly uncertified. No census thresholds or audit rules changed."
+ },
+ "lint_limitation": "Plain just-lint passed;explicit-runtime no-incremental mypy additionally checked.",
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked typing tools;project dependencies unchanged. Not a complete embedding runtime."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 8977,
+ "categories": {
+ "MATCH": 8840,
+ "RENDERING": 21,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 39,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification;literal matches are not entailment.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1386,
+ "edges": 551,
+ "records_without_nodes": 10,
+ "records_without_edges": 183,
+ "review_status_counts": {
+ "needs_research": 51,
+ "pending": 68,
+ "reviewed": 341
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml": "deb7c0eb9394c0e4a810507a75e20c88b029c9c7ca8a4851d078b4aaad0c9940",
+ "tests/test_causal_review_batch107.py": "0be0b34da158fcb6b9a9d4788949d1615d42ad26ecf19168905a06fc5b17bed6",
+ "tests/test_participating_taxa.py": "5a52c3d54ae981f49fd187531e19c8c8b8788473e16465f1dce59b1a6c2e9aad",
+ "tests/test_community_level_connectivity_credit.py": "383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c",
+ "reports/causal_graph_review/cache-provenance-20261008-batch107.json": "9a031575c6dc1d75f998b819cc7e46122344adb49eeedb2344741ab5fed0112c",
+ "kb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml": "69551869693ec797fb080f10747bdacd590e9686cdcdb93ff8c47a2e20880a18",
+ "kb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml": "5d3a32811ff6817ac9002bd39f79c53511fa76bc15d97a9adca897220471f235",
+ "kb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml": "3b6f0e648eb199d8139c7d790034e88f471e3fa5a3f0212ed55a60280921a6e6",
+ "kb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml": "8128a35b7336eb6a0e2da4768e456cd12e84db5632b771708a70f07d6bebd5b5"
+ },
+ "pre_research_baseline": {
+ "base_commit": "2d931aca3afcab956c0eba9661e09344479ad2c7",
+ "base_tree": "9bb3e7d09f2a5234432adf83c9509773b19635a4",
+ "research_worktree": "/private/tmp/communitymech-causal-batch106",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch107/baseline-rank.log",
+ "sha256": "004958f841cc787feb3888ad2d6ef78df5129af7486a591c05cb6dbb6ee9c94c"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch107/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch107/baseline-network.log",
+ "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch107/baseline-downstream.log",
+ "sha256": "9f56ab08e9883a7bbfda3b1e2f9fdd2d91333c5e0e3d193adcc4bcdbe1037985"
+ }
+ ],
+ "baseline_sha256": "2e02db0cebfc1d13f0a10ad4f47ab0bd0778fe9ac236ddad667ebb5e28aeec52"
+ },
+ "reference_validator_caveat": "Four full-record CLI and local snippet checks on macOS,not Linux;DOI-cache case1091 remains. Literal matches do not establish entailment;per-source read limits recorded. CLI Total checks counts issues,not checks. Loader1703 not certified.",
+ "status": "verified_existing_graph_repairs_with_source_access_limits",
+ "total_recorded_gate_outputs": 42
+}
diff --git a/tests/test_causal_review_batch107.py b/tests/test_causal_review_batch107.py
new file mode 100644
index 000000000..6f7548df1
--- /dev/null
+++ b/tests/test_causal_review_batch107.py
@@ -0,0 +1,145 @@
+"""Keep direct transfer and protective outcomes distinct from inferred mediation."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch107.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+
+
+def test_suillus_preserves_direct_transfer_and_host_benefit():
+ _, _, docs = records()
+ recruit, cue, vitamin, host = docs[0]["ecological_interactions"]
+ assert recruit["interaction_type"] == "COLONIZATION_FACILITATION"
+ assert "primarily enhanced swimming and swarming" in recruit["description"]
+ assert "interaction_type" not in cue
+ assert vitamin["interaction_type"] == "CROSS_FEEDING"
+ assert "13C12-thiamine" in vitamin["evidence"][1]["snippet"]
+ assert host["interaction_type"] == "MUTUALISM"
+ assert "dry weight, root activity, and phosphorus" in host["evidence"][1]["snippet"]
+ assert all(
+ n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ for n in [recruit, vitamin]
+ )
+ assert cue["downstream"][0]["target"] == vitamin["name"]
+
+
+def test_spring_keeps_observations_without_spatial_causation_or_commensalism():
+ _, rows, docs = records()
+ nodes = docs[1]["ecological_interactions"]
+ assert len(nodes) == 3
+ assert all("interaction_type" not in n and not n.get("downstream") for n in nodes)
+ assert "protein-associated elemental sulfur granules" in nodes[0]["description"]
+ assert "source_taxon" not in nodes[0]
+ assert "FISH" in nodes[1]["description"]
+ assert len(rows[1]["removed_edge_decisions"]) == 2
+
+
+def test_spring_identity_gap_cannot_be_counted_as_completed_review():
+ ledger, rows, docs = records()
+ assert rows[1]["status"] == "needs_research"
+ assert ledger["unresolved_research_issues"] == [1841]
+ assert 1841 in rows[1]["issues"]
+ assert "not established" in docs[1]["ecological_interactions"][0]["description"]
+ assert "51%" in docs[1]["discussions"][-1]["rationale"]
+ assert "not verify" in docs[1]["ecological_interactions"][1]["description"]
+
+
+def test_computational_evidence_stays_on_predictions_not_discussion_schema():
+ _, _, docs = records()
+ spring = docs[1]["ecological_interactions"][2]
+ for index, e in enumerate(spring["evidence"]):
+ assert e["supports"] == "PARTIAL" and e["evidence_source"] == "COMPUTATIONAL"
+ expected = {"METABOLIC", "AlphaFold2"} | ({"HydDB"} if index == 0 else set())
+ assert {t["tool_name"] for t in e["computational_provenance"]["tools"]} == expected
+ exchange = docs[2]["ecological_interactions"][0]
+ assert exchange["evidence"][0]["supports"] == "PARTIAL"
+ assert exchange["evidence"][0]["computational_provenance"]["tools"][0]["tool_version"] == "2.0"
+ assert exchange["evidence"][1]["evidence_source"] == "IN_VITRO"
+ assert all(
+ "computational_provenance" not in e
+ for d in docs
+ for x in d["discussions"]
+ for e in x["evidence"]
+ )
+
+
+def test_chicken_preserves_immune_and_protective_outcomes_without_exclusive_mediation():
+ _, _, docs = records()
+ exchange, immune, protection = docs[2]["ecological_interactions"]
+ assert exchange["interaction_type"] == "CROSS_FEEDING"
+ assert "interaction_type" not in immune and "biological_processes" not in immune
+ assert "flow cytometry" in immune["evidence"][1]["snippet"]
+ assert "interaction_type" not in protection
+ assert "may not be solely attributed" in protection["evidence"][1]["snippet"]
+ assert immune["downstream"][0]["target"] == protection["name"]
+ assert all(
+ n["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+ for n in [exchange, immune]
+ )
+
+
+def test_arc_preserves_rhizobia_boundary_and_poststorage_aflatoxin_endpoint():
+ _, _, docs = records()
+ doc = docs[3]
+ suppression, nodulation, outcome = doc["ecological_interactions"]
+ assert "interaction_type" not in suppression
+ assert "After 12 months of natural storage" in suppression["evidence"][1]["snippet"]
+ assert nodulation["interaction_type"] == "COLONIZATION_FACILITATION"
+ assert "ARC alone did not induce nodulation" in nodulation["evidence"][1]["snippet"]
+ assert "interaction_type" not in outcome
+ assert "GO:0050832" not in [p["term"]["id"] for p in outcome["biological_processes"]]
+ assert len(doc["engineering_design"]["counter_selection"]) == 1
+ assert doc["engineering_design"]["counter_selection"][0]["excluded_count"] == 3
+ for node, indexes in [(suppression, [0, 1, 3, 4]), (nodulation, [0, 1, 2, 4])]:
+ assert node["participating_taxa"] == [
+ {k: doc["taxonomy"][i]["taxon_term"][k] for k in ["preferred_term", "term"]}
+ for i in indexes
+ ]
+ assert node["downstream"][0]["target"] == outcome["name"]
+ assert node["downstream"][0]["description"].startswith("HYPOTHESIZED/PARTIAL:")
+
+
+def test_all_original_nodes_and_directions_have_dispositions_without_extensions():
+ ledger, rows, docs = records()
+ assert sum(len(d["ecological_interactions"]) for d in docs) == 13
+ assert sum(len(r["edges_before"]) for r in rows) == 9
+ assert sum(len(r["edges_after"]) for r in rows) == 7
+ assert sum(len(r["removed_edge_decisions"]) for r in rows) == 2
+ assert sum(len(r["renamed_nodes"]) for r in rows) == 5
+ assert not any(r["removed_node_decisions"] for r in rows)
+ assert ledger["edison"]["provider_submissions"] == 0
+ assert ledger["edison"]["credits_spent"] == 0
+ for row in rows:
+ assert len(row["retained_edge_decisions"]) == len(row["edges_after"])
+
+
+def test_review_hashes_histories_and_non_graph_boundaries_are_explicit():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ assert [r["status"] for r in rows] == ["reviewed", "needs_research", "reviewed", "reviewed"]
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert set(row["allowed_changed_fields"]) == {
+ "ecological_interactions",
+ "discussions",
+ "curation_history",
+ }
+ expected_events = 2 if row["id"] == "CommunityMech:000222" else 1
+ assert len(row["history_files"]) == row["curation_events_added"] == expected_events
+ assert (ROOT / row["history_files"][0]).exists()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ assert all(
+ e["target"] in names
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ )
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index d8ccda173..d45b22057 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -415,6 +415,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml",
"Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
"SynComBac10_Chicken_Intestinal_SynCom.yaml",
+ "SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml",
"SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml",
"SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml",
"Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml",