From c727c0587e7bd5f75ea758f852a5ca9676a30f28 Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Thu, 8 Oct 2026 02:22:31 -0700
Subject: [PATCH] Qualify thermophilic syntrophy mechanisms and assay contrasts
(batch114)
---
...rmobacter_Acetate_Oxidation_Coculture.html | 61 +-
...ldococcus_Hyperthermophilic_Syntrophy.html | 117 ++-
.../2026-10-08T090644Z-codex-512c88.yaml | 28 +
.../2026-10-08T090644Z-codex-4fdbb0.yaml | 29 +
...rmobacter_Acetate_Oxidation_Coculture.yaml | 93 +-
...ldococcus_Hyperthermophilic_Syntrophy.yaml | 119 ++-
reports/causal_graph_review/README.md | 26 +
.../adversarial-review-20261008-batch114.yaml | 288 +++++++
.../cache-provenance-20261008-batch114.json | 281 ++++++
.../20261008-two-records-batch114.yaml | 601 +++++++++++++
reports/causal_graph_review/inventory.tsv | 4 +-
reports/causal_graph_review/summary.json | 4 +-
.../validation-20261008-batch114.json | 807 ++++++++++++++++++
tests/test_causal_review_batch109.py | 8 +-
tests/test_causal_review_batch114.py | 131 +++
...est_community_level_connectivity_credit.py | 6 +-
tests/test_participating_taxa.py | 1 +
17 files changed, 2490 insertions(+), 114 deletions(-)
create mode 100644 history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml
create mode 100644 history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml
create mode 100644 reports/causal_graph_review/adversarial-review-20261008-batch114.yaml
create mode 100644 reports/causal_graph_review/cache-provenance-20261008-batch114.json
create mode 100644 reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
create mode 100644 reports/causal_graph_review/validation-20261008-batch114.json
create mode 100644 tests/test_causal_review_batch114.py
diff --git a/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html b/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
index 602dbc056..a564a6124 100644
--- a/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
+++ b/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
@@ -621,7 +621,7 @@ Ecological Interactions
Syntrophic Acetate Oxidation by Thermacetogenium
SYNTROPHY
- T. phaeum oxidizes acetate in coculture through the reversible CO dehydrogenase/ acetyl-CoA pathway, producing reduced carriers that require removal by the methanogenic partner for favorable syntrophic growth.
+ T. phaeum PB oxidizes acetate in the studied syntrophic coculture with M. thermautotrophicus TM. Enzyme activities and substrate-switch experiments support reversible use of the CO dehydrogenase/acetyl-CoA (Wood-Ljungdahl) pathway. Removal of reduced products supports acetate oxidation; this does not assert obligate partnership on other substrates, since T. phaeum also grows acetogenically in pure culture. Hydrogen and formate are extracellular electron-carrier candidates, not a claim that intracellular cofactors are passed between cells. The detailed formate-linked energy-conservation mechanism remains a model.
Source Taxon: Thermacetogenium phaeum PB
@@ -674,8 +674,7 @@ Syntrophic Acetate Oxidation by Thermacetogenium
→ Hydrogenotrophic Methanogenesis by Methanothermobacter
-
T. phaeum acetate oxidation produces low-concentration reduced carriers that M. thermautotrophicus consumes during hydrogenotrophic methanogenesis.
-
+
Acetate oxidation by T. phaeum supplies reduced products for the methanogenic partner, coupling acetate conversion to methane formation. Hydrogen consumption is supported by the TM/PB coculture experiments; PARTIAL for the partition of electron flow between hydrogen and formate and the specific formate-producing energy-conservation model. This is not direct acetate utilization by the methanogen.
@@ -717,7 +716,7 @@ Evidence
PMID:31849917
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"yielding formate as reduced product"
@@ -733,7 +732,7 @@ Evidence
Hydrogenotrophic Methanogenesis by Methanothermobacter
SYNTROPHY
- M. thermautotrophicus TM consumes low-concentration hydrogen and carbon dioxide during syntrophic growth and expresses methanogenesis machinery adapted to coculture conditions.
+ M. thermautotrophicus TM consumes hydrogen during acetate-fed coculture with T. phaeum PB, supporting product removal and methane formation. The 2002 TM/PB experiment maintained 20 to 80 Pa hydrogen and detected mcr/MRI rather than mrt/MRII expression in coculture; other assayed methanogenesis genes were expressed in both culture modes. This is not a universal activation of all methanogenesis genes or evidence of obligate dependence on PB. TM can also use formate; the hydrogenotrophic designation does not exclude formate-supported electron transfer. The separate DeltaH/butyrate coculture is not the PB/TM system.
Source Taxon: Methanothermobacter thermautotrophicus TM
@@ -815,7 +814,7 @@ Evidence
- SUPPORT (IN_VITRO)
- "catalyzing the final step of methanogenesis"
+ "only the mcr gene"
@@ -825,10 +824,10 @@ Evidence
-
Proteomic and enzyme evidence supports a reversed electron transport mechanism in T. phaeum that produces formate for transfer to the methanogenic partner.
+
PARTIAL: formate involvement in T. phaeum PB to M. thermautotrophicus TM electron transfer is supported by the partner-comparison literature discussed in the 2019 study, not dismissed as a genomic conjecture. The 2019 proteome and enzyme assays support a quinone-linked formate dehydrogenase and methyl-THF oxidation machinery. HYPOTHESIZED: their coupling through reverse electron transport, an ATP-supported proton gradient and ATP-independent acetate activation. Proton-gradient coupling and physiological acetate reduction were not demonstrated there. Neither the exact in vivo formate flux nor its fraction of total transferred electrons is established by these enzyme assays.
Source Taxon: Thermacetogenium phaeum PB
@@ -871,8 +870,7 @@
Formate Transfer to the Methanogenic Partner
→ Hydrogenotrophic Methanogenesis by Methanothermobacter
-
Formate and reducing equivalents generated by T. phaeum are transferred to the methanogenic partner that completes syntrophic acetate oxidation.
-
+
PARTIAL: formate produced by T. phaeum can supply reducing equivalents to the formate-utilizing TM partner for methanogenesis, while removal helps maintain favorable acetate oxidation. HYPOTHESIZED for the specific proton-coupled production mechanism; this arrow does not establish its in vivo flux or convert formate utilization into hydrogen-only metabolism.
Evidence
PMID:31849917
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"transferred to the methanogenic partner"
@@ -952,6 +950,45 @@ Associated Datasets
+
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ How much electron transfer uses formate, and which proton-coupled steps operate during PB/TM acetate oxidation?
+
+
The formate-transfer interpretation is supported, but enzyme/proteome results do not establish the complete energy budget or in vivo electron partition. The 2019 study explicitly leaves proton coupling and physiological acetate reduction unresolved. Preserve these distinctions when interpreting the two incoming methanogenesis arrows. Non-graph assay-condition followup remains issue #1890.
+
+
Attaches to: ecological_interactions#Syntrophic Acetate Oxidation by Thermacetogenium, ecological_interactions#Hydrogenotrophic Methanogenesis by Methanothermobacter, ecological_interactions#Formate-Linked Syntrophic Electron Transfer
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
transferred to the methanogenic partner
+
Authors interpret formate as a transferred product; the quoted conclusion does not itself measure interspecies flux or validate all proposed coupling steps.
+
+
+
+
@@ -1602,7 +1639,7 @@ Evidence
nodes.push({
id: intId,
- label: "Formate Transfer to the Methanogenic Partner",
+ label: "Formate-Linked Syntrophic Electron Transfer",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
diff --git a/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html b/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html
index 8a12e06a8..16237c9fe 100644
--- a/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html
+++ b/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html
@@ -585,7 +585,7 @@ Ecological Interactions
Ecological interaction network for Thermotoga-Methanocaldococcus Hyperthermophilic Syntrophy
- Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy, 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 (syntrophy).
@@ -598,8 +598,8 @@
Ecological Interactions
@@ -610,7 +610,7 @@ Ecological Interactions
Interspecies Hydrogen Transfer
SYNTROPHY
- T. maritima produces hydrogen during fermentative growth, and M. jannaschii consumes transferred hydrogen as a hydrogenotrophic methanogen, allowing the coculture to sustain higher T. maritima cell densities than monoculture.
+ T. maritima produces hydrogen during fermentation, and hydrogen consumption by M. jannaschii supports methanogenesis while relieving bacterial product inhibition. The 1997 study reported a tenfold bacterial density increase at 85 C and methanogen growth without external H2/CO2. The separate 2006 study reported a three- to fivefold density increase under its own conditions. These are assay-specific effects, not a single universal fold change or obligate mutual dependence under all conditions; T. maritima also grew in monoculture.
Source Taxon: Thermotoga maritima MSB8
@@ -663,7 +663,7 @@ Interspecies Hydrogen Transfer
→ Coculture-Associated Aggregation and Transcriptome Shift
-
Sustained interspecies hydrogen transfer places T. maritima in the methanogenic coculture state that changes its transcriptome and promotes EPS-based aggregation.
+
PARTIAL: hydrogen removal relieves growth inhibition and enables the higher-density coculture context in which aggregation and altered growth-phase transcription were observed. Hydrogen-removal comparisons support a contribution to physiology, but do not selectively demonstrate mediation of every EPS or transcript response by hydrogen transfer alone. Growth phase, population density and culture/gas-handling conditions remain part of this causal interpretation.
@@ -719,16 +719,19 @@ Evidence
-
Physical separation prevented establishment of the coculture, indicating that close spatial proximity is important for hydrogen transfer between the fermentative bacterium and methanogenic archaeon.
+
PARTIAL: the 1997 coculture failed to establish when partners were separated by a dialysis membrane, and the methanogen occurred in larger cell sorts. These observations support the importance of spatial proximity in that assay. They do not demonstrate direct cell contact as obligatory, a specific molecular adhesion mechanism, or directional colonization facilitation by the archaeon. Hydrogen transport and metabolic-rate effects were also modeled, rather than all directly measured.
-
Source Taxon: Methanocaldococcus jannaschii DSM 2661
+
Participating Taxa:
-
Target Taxon: Thermotoga maritima MSB8
+ Thermotoga maritima MSB8,
+
+ Methanocaldococcus jannaschii DSM 2661
+
+
@@ -760,7 +763,7 @@
Spatially Proximate Methanogenic Coculture
→ Interspecies Hydrogen Transfer
-
Close spatial proximity allows transferred hydrogen to reach M. jannaschii and establish the methanogenic coculture.
+
PARTIAL: proximity can reduce the transport distance for hydrogen from the fermenter to the methanogen, helping establish hydrogen-transfer syntrophy. Failure across a dialysis membrane and size-fraction association support this interpretation, but do not uniquely identify diffusion distance, direct contact or a specific attachment mechanism as the cause.
Evidence
PMID:18636642
- - SUPPORT (IN_VITRO)
+ - PARTIAL (IN_VITRO)
"suggesting the importance of spatial proximity"
@@ -803,16 +806,19 @@ Evidence
-
Methanogenic coculture altered the T. maritima transcriptome and promoted exopolysaccharide-based cell aggregates, linking syntrophic interaction to community structure and bacterial physiology.
+
T. maritima aggregation and transcription changed with growth phase in methanogenic coculture. In the 2006 study, 292 genes changed at least twofold from mid-log to early stationary phase within coculture, versus 24 for that transition within monoculture; these are not 292 genes in a direct coculture-versus-monoculture contrast. EPS-based aggregates were prominent during mid-log growth and diminished during stationary phase. Proposed sigma-factor, ppGpp and EPS-remodeling mechanisms are interpretations, not demonstrated regulatory necessity. The phenotype is not an additional measured metabolite-transfer event from bacterium to archaeon.
-
Source Taxon: Thermotoga maritima MSB8
+
Participating Taxa:
-
Target Taxon: Methanocaldococcus jannaschii DSM 2661
+ Thermotoga maritima MSB8,
+
+ Methanocaldococcus jannaschii DSM 2661
+
+
@@ -935,6 +941,45 @@
Associated Datasets
+ Knowledge gaps & discussions (1)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which proximity and hydrogen-removal effects specifically mediate aggregation and the bacterial transcript response?
+
+
Dialysis separation, hydrogen-removal comparisons and growth-phase observations support the existing qualified links, but do not isolate every step. Density-matched and gas-handling-matched comparisons would help distinguish hydrogen transfer from other coculture effects. The 1997 and 2006 assay conditions must remain separate; non-graph metadata followup remains issue #1891.
+
+
Attaches to: ecological_interactions#Interspecies Hydrogen Transfer, ecological_interactions#Spatially Proximate Methanogenic Coculture, ecological_interactions#Coculture-Associated Aggregation and Transcriptome Shift
+
+
+
+
+ 1 evidence item(s)
+
+
+
+
concomitant formation of exopolysaccharide (EPS)-based cell aggregates
+
Supports observed EPS-based aggregates accompanying the high-density coculture; specific mediation is not isolated by this quote.
+
+
+
+
@@ -1322,7 +1367,7 @@ Evidence
(function() {
var intId = "interaction:1";
- var intType = "COLONIZATION_FACILITATION";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1348,23 +1393,26 @@ Evidence
});
- var srcKey = "Methanocaldococcus jannaschii DSM 2661";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Thermotoga maritima MSB8";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Thermotoga maritima MSB8",
+
+ "Methanocaldococcus jannaschii DSM 2661"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
(function() {
var intId = "interaction:2";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
@@ -1386,17 +1434,20 @@ Evidence
});
- var srcKey = "Thermotoga maritima MSB8";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
- var tgtKey = "Methanocaldococcus jannaschii DSM 2661";
- if (taxonNodeIds[tgtKey]) {
- links.push({ source: intId, target: taxonNodeIds[tgtKey] });
- }
+ "Thermotoga maritima MSB8",
+
+ "Methanocaldococcus jannaschii DSM 2661"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml b/history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml
new file mode 100644
index 000000000..0c255c281
--- /dev/null
+++ b/history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml
+ slug: Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture
+session:
+ id: 2026-10-08T090644Z-codex-512c88
+ timestamp: '2026-10-08T09:06:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1888
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain acetate-linked syntrophy and the reversible pathway; distinguish extracellular
+ carriers from cofactors and avoid all-substrate obligacy.; Retain hydrogen-removing methanogenesis
+ with exact TM/PB expression and hydrogen-pressure context; do not exclude formate use
+ or import DeltaH/butyrate results.; Retain indirectly supported formate transfer as PARTIAL,
+ with the detailed ATP/proton-coupled mechanism HYPOTHESIZED rather than established.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
diff --git a/history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml b/history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml
new file mode 100644
index 000000000..d951acc9f
--- /dev/null
+++ b/history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml
+ slug: Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy
+session:
+ id: 2026-10-08T090644Z-codex-4fdbb0
+ timestamp: '2026-10-08T09:06:44Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1889
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain supported hydrogen syntrophy and separate study-specific density effects;
+ qualify the existing arrow as partial mediation through the higher-density context.; Recast
+ proximity as an explicit two-participant community observation; retain a PARTIAL transport
+ interpretation without colonization or mandatory-contact typing.; Recast growth-phase
+ aggregation/transcription as a community phenotype, with the exact within-culture 292-versus-24
+ contrast and no extra exchange claim.
+ details: Source-based self-adversarial graph review; reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
diff --git a/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml b/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml
index 6273921f6..77dfe3dbc 100644
--- a/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml
+++ b/kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml
@@ -124,9 +124,12 @@ taxonomy:
explanation: Supports strain TM as the thermophilic methanogenic member using the source spelling.
ecological_interactions:
- name: Syntrophic Acetate Oxidation by Thermacetogenium
- description: T. phaeum oxidizes acetate in coculture through the reversible CO dehydrogenase/
- acetyl-CoA pathway, producing reduced carriers that require removal by the methanogenic
- partner for favorable syntrophic growth.
+ description: T. phaeum PB oxidizes acetate in the studied syntrophic coculture with M. thermautotrophicus TM.
+ Enzyme activities and substrate-switch experiments support reversible use of the CO dehydrogenase/acetyl-CoA
+ (Wood-Ljungdahl) pathway. Removal of reduced products supports acetate oxidation; this does not assert obligate
+ partnership on other substrates, since T. phaeum also grows acetogenically in pure culture. Hydrogen and formate
+ are extracellular electron-carrier candidates, not a claim that intracellular cofactors are passed between cells.
+ The detailed formate-linked energy-conservation mechanism remains a model.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -163,10 +166,10 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Hydrogenotrophic Methanogenesis by Methanothermobacter
- description: >
- T. phaeum acetate oxidation produces low-concentration reduced carriers
- that M. thermautotrophicus consumes during hydrogenotrophic
- methanogenesis.
+ description: Acetate oxidation by T. phaeum supplies reduced products for the methanogenic partner, coupling
+ acetate conversion to methane formation. Hydrogen consumption is supported by the TM/PB coculture experiments;
+ PARTIAL for the partition of electron flow between hydrogen and formate and the specific formate-producing
+ energy-conservation model. This is not direct acetate utilization by the methanogen.
evidence:
- reference: PMID:15866934
supports: SUPPORT
@@ -179,13 +182,18 @@ ecological_interactions:
snippet: CO dehydrogenase/acetyl-CoA pathway reversibly
explanation: Supports the reversible biochemical pathway used during acetate oxidation.
- reference: PMID:31849917
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: yielding formate as reduced product
- explanation: Supports formate as a reduced product of the energy-conserving acetate-oxidation mechanism.
+ explanation: The authors infer formate production from enzyme/proteome results; the detailed proton-coupled
+ mechanism is not fully demonstrated.
- name: Hydrogenotrophic Methanogenesis by Methanothermobacter
- description: M. thermautotrophicus TM consumes low-concentration hydrogen and carbon dioxide
- during syntrophic growth and expresses methanogenesis machinery adapted to coculture conditions.
+ description: M. thermautotrophicus TM consumes hydrogen during acetate-fed coculture with T. phaeum PB, supporting
+ product removal and methane formation. The 2002 TM/PB experiment maintained 20 to 80 Pa hydrogen and detected
+ mcr/MRI rather than mrt/MRII expression in coculture; other assayed methanogenesis genes were expressed in both
+ culture modes. This is not a universal activation of all methanogenesis genes or evidence of obligate dependence
+ on PB. TM can also use formate; the hydrogenotrophic designation does not exclude formate-supported electron
+ transfer. The separate DeltaH/butyrate coculture is not the PB/TM system.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -230,11 +238,17 @@ ecological_interactions:
- reference: PMID:11872465
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: catalyzing the final step of methanogenesis
- explanation: Supports methanogenesis gene expression in the coculture.
-- name: Formate Transfer to the Methanogenic Partner
- description: Proteomic and enzyme evidence supports a reversed electron transport mechanism
- in T. phaeum that produces formate for transfer to the methanogenic partner.
+ snippet: only the mcr gene
+ explanation: Within the tested methyl-coenzyme-M reductase pair, mcr/MRI was detected in coculture, unlike mrt/MRII;
+ this does not mean mcr was the only expressed methanogenesis gene.
+- name: Formate-Linked Syntrophic Electron Transfer
+ description: 'PARTIAL: formate involvement in T. phaeum PB to M. thermautotrophicus TM electron transfer is supported
+ by the partner-comparison literature discussed in the 2019 study, not dismissed as a genomic conjecture. The
+ 2019 proteome and enzyme assays support a quinone-linked formate dehydrogenase and methyl-THF oxidation machinery.
+ HYPOTHESIZED: their coupling through reverse electron transport, an ATP-supported proton gradient and ATP-independent
+ acetate activation. Proton-gradient coupling and physiological acetate reduction were not demonstrated there.
+ Neither the exact in vivo formate flux nor its fraction of total transferred electrons is established by these
+ enzyme assays.'
interaction_type: CROSS_FEEDING
scope: PAIRWISE
source_taxon:
@@ -263,20 +277,23 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Hydrogenotrophic Methanogenesis by Methanothermobacter
- description: >
- Formate and reducing equivalents generated by T. phaeum are transferred
- to the methanogenic partner that completes syntrophic acetate oxidation.
+ description: 'PARTIAL: formate produced by T. phaeum can supply reducing equivalents to the formate-utilizing
+ TM partner for methanogenesis, while removal helps maintain favorable acetate oxidation. HYPOTHESIZED for
+ the specific proton-coupled production mechanism; this arrow does not establish its in vivo flux or convert
+ formate utilization into hydrogen-only metabolism.'
evidence:
- reference: PMID:31849917
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: transferred to the methanogenic partner
- explanation: Supports transfer of formate/reducing equivalents to the methanogenic partner.
+ explanation: Authors interpret formate as a transferred product; the quoted conclusion does not itself measure
+ interspecies flux or validate all proposed coupling steps.
- reference: PMID:31849917
supports: SUPPORT
evidence_source: IN_VITRO
snippet: quinone-dependent formate dehydrogenase
- explanation: Supports the formate-linked energy-conservation machinery in T. phaeum.
+ explanation: In vitro quinone-analogue assays support enzyme activity, not demonstration of the entire physiological
+ reverse-electron-transport mechanism.
environmental_factors:
- name: Thermophilic temperature
value: 55 to 58
@@ -512,3 +529,35 @@ cultivation_setup:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: whereas the syntrophic co-culture was grown with acetate as substrate
+discussions:
+- discussion_id: formate-coupling-and-flux-batch114
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ prompt: How much electron transfer uses formate, and which proton-coupled steps operate during PB/TM acetate oxidation?
+ rationale: 'The formate-transfer interpretation is supported, but enzyme/proteome results do not establish the
+ complete energy budget or in vivo electron partition. The 2019 study explicitly leaves proton coupling and physiological
+ acetate reduction unresolved. Preserve these distinctions when interpreting the two incoming methanogenesis
+ arrows. Non-graph assay-condition followup remains issue #1890.'
+ attaches_to:
+ - ecological_interactions#Syntrophic Acetate Oxidation by Thermacetogenium
+ - ecological_interactions#Hydrogenotrophic Methanogenesis by Methanothermobacter
+ - ecological_interactions#Formate-Linked Syntrophic Electron Transfer
+ evidence:
+ - reference: PMID:31849917
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: transferred to the methanogenic partner
+ explanation: Authors interpret formate as a transferred product; the quoted conclusion does not itself measure
+ interspecies flux or validate all proposed coupling steps.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T09:06:42Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain acetate-linked syntrophy and the reversible pathway; distinguish extracellular carriers from cofactors
+ and avoid all-substrate obligacy.; Retain hydrogen-removing methanogenesis with exact TM/PB expression and hydrogen-pressure
+ context; do not exclude formate use or import DeltaH/butyrate results.; Retain indirectly supported formate
+ transfer as PARTIAL, with the detailed ATP/proton-coupled mechanism HYPOTHESIZED rather than established. Issue#1888;
+ reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
+ llm_assisted: true
diff --git a/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml b/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml
index 7b0f8530c..e1b5c6566 100644
--- a/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml
+++ b/kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml
@@ -135,9 +135,11 @@ taxonomy:
explanation: Supports M. jannaschii as the archaeal partner in the exact coculture.
ecological_interactions:
- name: Interspecies Hydrogen Transfer
- description: T. maritima produces hydrogen during fermentative growth, and M. jannaschii
- consumes transferred hydrogen as a hydrogenotrophic methanogen, allowing the
- coculture to sustain higher T. maritima cell densities than monoculture.
+ description: T. maritima produces hydrogen during fermentation, and hydrogen consumption by M. jannaschii supports
+ methanogenesis while relieving bacterial product inhibition. The 1997 study reported a tenfold bacterial density
+ increase at 85 C and methanogen growth without external H2/CO2. The separate 2006 study reported a three- to
+ fivefold density increase under its own conditions. These are assay-specific effects, not a single universal
+ fold change or obligate mutual dependence under all conditions; T. maritima also grew in monoculture.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -174,8 +176,11 @@ ecological_interactions:
label: methanogenesis
downstream:
- target: Coculture-Associated Aggregation and Transcriptome Shift
- description: Sustained interspecies hydrogen transfer places T. maritima in the methanogenic
- coculture state that changes its transcriptome and promotes EPS-based aggregation.
+ description: 'PARTIAL: hydrogen removal relieves growth inhibition and enables the higher-density coculture
+ context in which aggregation and altered growth-phase transcription were observed. Hydrogen-removal comparisons
+ support a contribution to physiology, but do not selectively demonstrate mediation of every EPS or transcript
+ response by hydrogen transfer alone. Growth phase, population density and culture/gas-handling conditions
+ remain part of this causal interpretation.'
evidence:
- reference: PMID:18636642
supports: SUPPORT
@@ -193,21 +198,12 @@ ecological_interactions:
snippet: Interspecies H2 transfer resulted in three- to fivefold-higher T. maritima cell densities
explanation: Supports the syntrophic hydrogen-transfer mechanism and growth response.
- name: Spatially Proximate Methanogenic Coculture
- description: Physical separation prevented establishment of the coculture, indicating
- that close spatial proximity is important for hydrogen transfer between the
- fermentative bacterium and methanogenic archaeon.
- interaction_type: COLONIZATION_FACILITATION
- scope: PAIRWISE
- source_taxon:
- preferred_term: Methanocaldococcus jannaschii DSM 2661
- term:
- id: NCBITaxon:243232
- label: Methanocaldococcus jannaschii DSM 2661
- target_taxon:
- preferred_term: Thermotoga maritima MSB8
- term:
- id: NCBITaxon:243274
- label: Thermotoga maritima MSB8
+ description: 'PARTIAL: the 1997 coculture failed to establish when partners were separated by a dialysis membrane,
+ and the methanogen occurred in larger cell sorts. These observations support the importance of spatial proximity
+ in that assay. They do not demonstrate direct cell contact as obligatory, a specific molecular adhesion mechanism,
+ or directional colonization facilitation by the archaeon. Hydrogen transport and metabolic-rate effects were
+ also modeled, rather than all directly measured.'
+ scope: COMMUNITY_LEVEL
metabolites:
- preferred_term: dihydrogen
term:
@@ -220,8 +216,10 @@ ecological_interactions:
label: biological process involved in interspecies interaction between organisms
downstream:
- target: Interspecies Hydrogen Transfer
- description: Close spatial proximity allows transferred hydrogen to reach M. jannaschii and
- establish the methanogenic coculture.
+ description: 'PARTIAL: proximity can reduce the transport distance for hydrogen from the fermenter to the methanogen,
+ helping establish hydrogen-transfer syntrophy. Failure across a dialysis membrane and size-fraction association
+ support this interpretation, but do not uniquely identify diffusion distance, direct contact or a specific
+ attachment mechanism as the cause.'
evidence:
- reference: PMID:18636642
supports: SUPPORT
@@ -229,26 +227,28 @@ ecological_interactions:
snippet: could not be established if the two organisms were physically separated
explanation: Supports the importance of spatial proximity for establishing the coculture.
- reference: PMID:18636642
- supports: SUPPORT
+ supports: PARTIAL
evidence_source: IN_VITRO
snippet: suggesting the importance of spatial proximity
- explanation: Supports close-range interaction as a curated mechanism.
-- name: Coculture-Associated Aggregation and Transcriptome Shift
- description: Methanogenic coculture altered the T. maritima transcriptome and promoted
- exopolysaccharide-based cell aggregates, linking syntrophic interaction to
- community structure and bacterial physiology.
- interaction_type: SYNTROPHY
- scope: PAIRWISE
- source_taxon:
- preferred_term: Thermotoga maritima MSB8
+ explanation: The source explicitly interprets the separation result as suggesting spatial proximity, not proof
+ of direct-contact dependence or directional colonization.
+ participating_taxa:
+ - preferred_term: Thermotoga maritima MSB8
term:
id: NCBITaxon:243274
label: Thermotoga maritima MSB8
- target_taxon:
- preferred_term: Methanocaldococcus jannaschii DSM 2661
+ - preferred_term: Methanocaldococcus jannaschii DSM 2661
term:
id: NCBITaxon:243232
label: Methanocaldococcus jannaschii DSM 2661
+- name: Coculture-Associated Aggregation and Transcriptome Shift
+ description: T. maritima aggregation and transcription changed with growth phase in methanogenic coculture. In
+ the 2006 study, 292 genes changed at least twofold from mid-log to early stationary phase within coculture,
+ versus 24 for that transition within monoculture; these are not 292 genes in a direct coculture-versus-monoculture
+ contrast. EPS-based aggregates were prominent during mid-log growth and diminished during stationary phase.
+ Proposed sigma-factor, ppGpp and EPS-remodeling mechanisms are interpretations, not demonstrated regulatory
+ necessity. The phenotype is not an additional measured metabolite-transfer event from bacterium to archaeon.
+ scope: COMMUNITY_LEVEL
biological_processes:
- preferred_term: interspecies interaction between organisms
term:
@@ -259,17 +259,29 @@ ecological_interactions:
supports: SUPPORT
evidence_source: IN_VITRO
snippet: 292 genes differentially expressed in T. maritima
- explanation: Supports broad transcriptomic response in the coculture.
+ explanation: The 292 count describes a within-coculture growth-phase contrast, not a direct comparison against
+ monoculture.
- reference: PMID:16391122
supports: SUPPORT
evidence_source: IN_VITRO
snippet: concomitant formation of exopolysaccharide (EPS)-based cell aggregates
- explanation: Supports EPS-based aggregation as an observed coculture phenotype.
+ explanation: Supports observed EPS-based aggregates accompanying the high-density coculture; specific mediation
+ is not isolated by this quote.
- reference: PMID:16391122
supports: SUPPORT
evidence_source: IN_VITRO
snippet: syntrophic interactions can impact the transcriptome of heterotrophs
- explanation: Supports syntrophic regulation of the T. maritima phenotype.
+ explanation: Supports a coculture-associated bacterial phenotype; it does not establish a second directional
+ metabolic exchange.
+ participating_taxa:
+ - preferred_term: Thermotoga maritima MSB8
+ term:
+ id: NCBITaxon:243274
+ label: Thermotoga maritima MSB8
+ - preferred_term: Methanocaldococcus jannaschii DSM 2661
+ term:
+ id: NCBITaxon:243232
+ label: Methanocaldococcus jannaschii DSM 2661
environmental_factors:
- name: Hyperthermophilic temperature
value: 85
@@ -410,3 +422,36 @@ metal_relevance: NOT_APPLICABLE
metal_notes: >
No metal or rare earth element transformation role is curated for this
hyperthermophilic hydrogen-transfer coculture.
+discussions:
+- discussion_id: proximity-hydrogen-density-mediation-batch114
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ prompt: Which proximity and hydrogen-removal effects specifically mediate aggregation and the bacterial transcript
+ response?
+ rationale: 'Dialysis separation, hydrogen-removal comparisons and growth-phase observations support the existing
+ qualified links, but do not isolate every step. Density-matched and gas-handling-matched comparisons would help
+ distinguish hydrogen transfer from other coculture effects. The 1997 and 2006 assay conditions must remain separate;
+ non-graph metadata followup remains issue #1891.'
+ attaches_to:
+ - ecological_interactions#Interspecies Hydrogen Transfer
+ - ecological_interactions#Spatially Proximate Methanogenic Coculture
+ - ecological_interactions#Coculture-Associated Aggregation and Transcriptome Shift
+ evidence:
+ - reference: PMID:16391122
+ supports: PARTIAL
+ evidence_source: IN_VITRO
+ snippet: concomitant formation of exopolysaccharide (EPS)-based cell aggregates
+ explanation: Supports observed EPS-based aggregates accompanying the high-density coculture; specific mediation
+ is not isolated by this quote.
+ posed_by: codex
+ posed_date: '2026-10-08'
+curation_history:
+- timestamp: '2026-10-08T09:06:43Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Retain supported hydrogen syntrophy and separate study-specific density effects; qualify the existing
+ arrow as partial mediation through the higher-density context.; Recast proximity as an explicit two-participant
+ community observation; retain a PARTIAL transport interpretation without colonization or mandatory-contact typing.;
+ Recast growth-phase aggregation/transcription as a community phenotype, with the exact within-culture 292-versus-24
+ contrast and no extra exchange claim. Issue#1889; reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 8be3361ed..6879d2c17 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,32 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch114: Thermophilic Syntrophy And Mechanism Limits
+
+[Decisions](decisions/20261008-two-records-batch114.yaml),
+[provenance](cache-provenance-20261008-batch114.json),
+[validation](validation-20261008-batch114.json), and
+[self-adversarial review](adversarial-review-20261008-batch114.yaml) cover
+the Thermacetogenium-Methanothermobacter and Thermotoga-Methanocaldococcus records.
+All six existing nodes and four directions remain. Formate involvement retains
+experimental support while its detailed energy-conservation mechanism remains
+qualified. Proximity and aggregation are scoped community observations, not
+directional colonization or another measured exchange. The 292-versus-24 gene
+counts retain their within-culture growth-phase meaning.
+
+Six primary abstracts and one fresh full main-body extraction were read, along
+with three existing cached primary main bodies. Fresh retrieval of those older
+full texts failed; original figure pixels, supplements and raw data were not
+reviewed. All 18 graph/discussion quotations match fresh primary text and existing
+caches. No publication bodies or cache files were added. Two append-only histories
+preserve non-graph blocks, 458 other records and all 923 caches.
+Thermotoga adds one explicitly scoped mixed record; both members already have
+pairwise connectivity credit. Connectivity logic and the share guard are unchanged.
+
+Repairs #1888-#1889 await protected-main merge. Separate metadata followups
+#1890-#1891 remain open. No new topology or Edison spend is introduced.
+Self-review is not independent approval or completion of the corpus review.
+
## Batch113: Marine Assay And Causal Boundaries
[Decisions](decisions/20261008-three-records-batch113.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch114.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch114.yaml
new file mode 100644
index 000000000..efddff7ac
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch114.yaml
@@ -0,0 +1,288 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 553707b254ed6652b264bed8ab14101a1bcf9c8d
+scope:
+- kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml
+- kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch114.json
+findings:
+- issue: 1888
+ severity: P2
+ finding: Qualify the Thermacetogenium formate energy-conservation mechanism
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1889
+ severity: P2
+ finding: Bound Thermotoga proximity and aggregation causal claims to tested contrasts
+ status: addressed_in_this_change
+ disposition: Close only after protected-main merge.
+- issue: 1890
+ severity: P2
+ finding: Separate Thermacetogenium growth optimum from coculture assay conditions
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+- issue: 1891
+ severity: P2
+ finding: Separate 1997 and 2006 Thermotoga coculture media and gas conditions
+ status: open_non_graph_follow_up
+ disposition: Remain open until separately verified.
+adversarial_checks:
+- 'Every original node and direction has a disposition: six nodes and four directions retained, one node renamed.
+ No added topology; all targets and discussion anchors resolve.'
+- 'Overcorrection check: retain demonstrated acetate-linked methanogenesis, hydrogen-removal growth benefits and
+ formate involvement supported by the 2001 partner-comparison literature. Qualification of the detailed energy-conservation
+ model does not erase these results or imply universal obligacy.'
+- 'Acetate/formate: enzyme assays with artificial acceptors and proteomic abundance support component activities,
+ not the entire reverse-electron-transport pathway. Proton-gradient coupling and physiological acetate reduction
+ were not demonstrated in 2019. Both methanogenesis arrows distinguish overall coupling from carrier partition
+ and measured flux.'
+- 'Methanogenesis: preserve exact 2002 TM/PB hydrogen conditions and the mcr/MRI-versus-mrt/MRII result, not universal
+ activation of all genes. TM can use formate; hydrogenotrophic does not mean hydrogen-only. The separate DeltaH/butyrate
+ system is not silently imported.'
+- 'Thermotoga: the dialysis and size-fraction observations support proximity, not proven directional colonization,
+ mandatory contact or a specific adhesion mechanism. The original proximity-to-transfer direction remains PARTIAL.'
+- 'Phenotype: 292 versus 24 describes within-culture mid-log-to-early-stationary-phase contrasts, not 292 genes
+ in a coculture-versus-monoculture contrast. Aggregation declines in stationary phase. Hydrogen removal supports
+ physiology without isolating every EPS/transcript mediator; growth phase, density and gas handling remain relevant.'
+- 'Source scope: six fresh primary abstracts, 2019 full main-body XML, three complete existing cached primary main
+ bodies and the 2001 publisher abstract read. Fresh older full XML retrieval failed; no bypass. Original figure
+ pixels, supplements, raw data and incomplete cached table cells not audited. All 18 graph/discussion quotes match
+ fresh primary texts and existing caches; no new publication bodies or cache files.'
+- Two guarded records and append-only histories preserve 458 other records, 923 caches, all non-graph raw blocks
+ and prior history/decision artifacts. One explicit participant-list user added. Measured census is 413 community-level,
+ 137 mixed, 276 community-only, 1565 taxa and 1273 solely credited; the added pair already has pairwise credit.
+ Connectivity logic and share guards unchanged.
+- Five real in-memory control/mutation/restored-control probes reject formate SUPPORT inflation, colonization typing,
+ the wrong 292 contrast, unqualified hydrogen mediation and exclusion of TM formate use. Actual mutations and rejecting
+ assertions recorded; canonical hashes unchanged; not additional pytest tests.
+- 'Nine focused tests and 1033 combined regressions pass. Both records pass schema, strict, terms, full-record references,
+ snippets, history and rank. The 56 network warnings are unchanged, with zero structural defects. Deterministic
+ rendering and exact HTML-description coverage: 456 pages, 1366 nodes, 531 arrows, not UI screenshots. Local reference
+ passes do not certify Linux; full-corpus snippets remain informational.'
+- 'Graph repairs #1888/#1889 await protected-main merge; non-graph #1890/#1891 remain open. No Edison invocation
+ or new topology. Prior Ruegeria extension #1883 and other needs_research records remain incomplete. Self-review
+ is not independent approval; exact-head publication and postcommit docs-current are separate gates. Root CI blocker
+ #1836 is not bypassed; dependent branches are not deleted.'
+- 'Corpus: 366 reviewed, 40 pending, 54 needs_research across 460 records. The overall goal remains incomplete.'
+adversarial_regression_proof:
+ report:
+ cases:
+ - mutation: Formate transfer interpretation promoted to fully established coupling
+ test: test_formate_support_survives_without_proving_the_energy_coupling_model
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 52
+ assertion: assert node["evidence"][0]["supports"] == "PARTIAL"
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/2/evidence/0/supports
+ before: PARTIAL
+ after: SUPPORT
+ - mutation: Proximity retyped as directional colonization
+ test: test_proximity_is_not_colonization_or_obligatory_direct_contact
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 71
+ assertion: assert "interaction_type" not in node
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/1/interaction_type
+ before: null
+ after: COLONIZATION_FACILITATION
+ - mutation: 292 genes reassigned to the between-culture contrast
+ test: test_292_is_a_within_culture_growth_phase_contrast
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 82
+ assertion: assert "within coculture, versus 24" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/2/description
+ before: T. maritima aggregation and transcription changed with growth phase in methanogenic coculture. In
+ the 2006 study, 292 genes changed at least twofold from mid-log to early stationary phase within coculture,
+ versus 24 for that transition within monoculture; these are not 292 genes in a direct coculture-versus-monoculture
+ contrast. EPS-based aggregates were prominent during mid-log growth and diminished during stationary phase.
+ Proposed sigma-factor, ppGpp and EPS-remodeling mechanisms are interpretations, not demonstrated regulatory
+ necessity. The phenotype is not an additional measured metabolite-transfer event from bacterium to archaeon.
+ after: 292 genes differ directly between coculture and monoculture.
+ - mutation: Hydrogen transfer promoted to selective mediation of every phenotype
+ test: test_hydrogen_to_phenotype_mediation_is_partial
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 91
+ assertion: assert edge["description"].startswith("PARTIAL:")
+ restored_control: PASS
+ changed_values:
+ - path: records/1/ecological_interactions/0/downstream/0/description
+ before: 'PARTIAL: hydrogen removal relieves growth inhibition and enables the higher-density coculture context
+ in which aggregation and altered growth-phase transcription were observed. Hydrogen-removal comparisons
+ support a contribution to physiology, but do not selectively demonstrate mediation of every EPS or transcript
+ response by hydrogen transfer alone. Growth phase, population density and culture/gas-handling conditions
+ remain part of this causal interpretation.'
+ after: Hydrogen transfer alone demonstrably causes every EPS and transcript response.
+ - mutation: TM formate use excluded from methanogenesis interpretation
+ test: test_tm_expression_is_not_all_genes_or_the_deltah_system
+ control: PASS
+ mutation_applied: true
+ mutation_rejected: true
+ assertion_line: 37
+ assertion: assert "does not exclude formate-supported electron transfer" in node["description"]
+ restored_control: PASS
+ changed_values:
+ - path: records/0/ecological_interactions/1/description
+ before: M. thermautotrophicus TM consumes hydrogen during acetate-fed coculture with T. phaeum PB, supporting
+ product removal and methane formation. The 2002 TM/PB experiment maintained 20 to 80 Pa hydrogen and detected
+ mcr/MRI rather than mrt/MRII expression in coculture; other assayed methanogenesis genes were expressed
+ in both culture modes. This is not a universal activation of all methanogenesis genes or evidence of obligate
+ dependence on PB. TM can also use formate; the hydrogenotrophic designation does not exclude formate-supported
+ electron transfer. The separate DeltaH/butyrate coculture is not the PB/TM system.
+ after: M. thermautotrophicus TM consumes hydrogen during acetate-fed coculture with T. phaeum PB, supporting
+ product removal and methane formation. The 2002 TM/PB experiment maintained 20 to 80 Pa hydrogen and detected
+ mcr/MRI rather than mrt/MRII expression in coculture; other assayed methanogenesis genes were expressed
+ in both culture modes. This is not a universal activation of all methanogenesis genes or evidence of obligate
+ dependence on PB. TM can also use formate; the hydrogenotrophic designation excludes formate-supported
+ electron transfer. The separate DeltaH/butyrate coculture is not the PB/TM system.
+ canonical_files_unchanged: true
+ checked_file_sha256:
+ kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml: f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992
+ kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml: 05b09dc41d9f2e54eac83d1021d69d2ea733144e9e5386295dd99cc9cae6293c
+ tests/test_causal_review_batch114.py: 9c3fffeefa7091b002e1af8cc18d88b536f5d192e7511262364541ad13830522
+ probe_script_sha256: f819405f484f59de391a803046c8af7b5419d18cbef750a4e9a8eb3fc67d6a88
+ scope: In-memory control/mutation/restored-control; no canonical writes and not additional pytest tests.
+ artifact: /private/tmp/communitymech-batch114/adversarial-regression-proof.json
+ sha256: 003816ecccd77488eeb3f06dd4ceb941e753f7f36aab208d0a5a4b8dfbf437df
+verification:
+ combined_regressions: 1033 passed in 414.10s (0:06:54)
+ new_regression_tests: 9
+ total_recorded_gate_outputs: 27
+ primary_graph_snippet_proof:
+ graph_quotations: 16
+ discussion_quotations: 2
+ fresh_primary_literal_matches: 18
+ all_cached_literal_matches: 18
+ retained_nodes: 6
+ removed_nodes: 0
+ renamed_nodes: 1
+ retained_arrows: 4
+ removed_arrows: 0
+ new_nodes_or_directions: 0
+ references: Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment.
+ Total checks in the reference CLI counts issues, not examined snippets.
+ snippet_counts_by_record:
+ kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml:
+ MATCH: 36
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml:
+ MATCH: 27
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ full_corpus_snippet_audit:
+ counts:
+ records: 460
+ total: 9019
+ categories:
+ MATCH: 8874
+ RENDERING: 28
+ ASSEMBLED: 1
+ WEAK: 0
+ MISMATCH: 40
+ NOCONTENT: 76
+ caveat: Informational audit exit0 is not clean-corpus or entailment certification.
+ network:
+ existing_findings_preserved: 56
+ added_findings: {}
+ removed_findings: {}
+ structural_defects: 0
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml: 80fde422c660d0b4cdee61623b5aaaa381fa28f6fb04082407ae5ee702979bdf
+ tests/test_causal_review_batch114.py: 9c3fffeefa7091b002e1af8cc18d88b536f5d192e7511262364541ad13830522
+ tests/test_participating_taxa.py: 2abb167c84b237eac4d24e15590fb27efa3c4845e169bd2a3de1936ed1fd8efc
+ tests/test_community_level_connectivity_credit.py: 1af00518c5e73a612339531474000886eec61e21c438337d272b0b9a1e4ed18e
+ tests/test_causal_review_batch109.py: b5b99af9d142cfac972a3e08c09c25fbcdec4a4a2f015d33758998acaa16d203
+ reports/causal_graph_review/cache-provenance-20261008-batch114.json: 0a5b861834ef55c1ed2b0c441a573a1e3482867aa315374b21b3e15eaccb12d1
+ kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml: f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992
+ kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml: 05b09dc41d9f2e54eac83d1021d69d2ea733144e9e5386295dd99cc9cae6293c
+ history_sha256:
+ history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml: 8948eac9627a3d629a8b8461f7f2c8336cef9825fb88880deebff82b9eba570c
+ history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml: a603723e87c68bd2fe5c54c4575e32a9932191db0ea9c626b68f2cec6aae5a35
+ unchanged_records: 458
+ unchanged_caches: 923
+ immutable_prior_history_and_decision_files: 862
+ cache_changes: []
+ edison:
+ required_for_this_repair: false
+ provider_submissions: 0
+ credits_spent: 0
+ new_nodes_or_directions: 0
+ prior_extension_blocker: 'Ruegeria issue1883: configuredkey unavailable in prior approved invocation; not retried
+ without state change.'
+ post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+ current:
+ records: 460
+ with_community_level: 413
+ mixed: 137
+ community_level_only: 276
+ taxa: 1565
+ credited_solely_by_the_rule: 1273
+ delta_from_batch113:
+ records: 0
+ with_community_level: 1
+ mixed: 1
+ community_level_only: 0
+ taxa: 2
+ credited_solely_by_the_rule: 0
+ explanation: Thermotoga adds one explicit participant-list user and mixed-scope record; both taxa already have
+ pairwise credit. No connectivity rule or share-guard changes.
+corpus:
+ records: 460
+ nodes: 1380
+ edges: 539
+ review_status_counts:
+ needs_research: 54
+ pending: 40
+ reviewed: 366
+lint_environment:
+ path: /private/tmp/communitymech-batch100/lint-env
+ scope: Temporary established Python3.13 lint environment; project dependencies unchanged.
+limitations:
+- Fresh baseline across both roots before source research:460 records,923 caches,56 unchanged warnings,zero structural
+ defects. Six existing nodes/four directions reviewed and retained;one node renamed,no new topology.
+- Both whole canonical records and all existing graph snippets read. Six fresh primary abstracts and Crossref identities
+ retrieved. Complete 2019 main-body XML extraction read (folded lines1-650), including figure captions and serialized
+ tables; original pixels, supplements and raw data not reviewed.
+- Complete existing cached main bodies of2002expression,2005pathway and2006phenotype read in folded chunks, including
+ methods/results/discussion/captions. Fresh fullTextXML returned500 after retries; PMC browser requests for2005/2006
+ showed access challenges. No bypass. Cached tables are incomplete; no numerical table-cell claims based on those
+ caches.1997transfer and2000strain are abstract-bounded.
+- 2001formate partner-comparison publisher abstract read at https://www.sciencedirect.com/science/article/pii/S1389172301801377
+ ; supports involvement by fasterPB/TM versusPB/DeltaH conversion and lowformate. No full-paper access or new repository
+ quotation/cache claimed. This evidence prevents erasing measured support while qualifying the2019detailed mechanism.
+- 2019formate enzyme activity and proteomic support retained;proton-gradient coupling,physiological acetate reduction
+ and completeATPbudget remain proposed. No all-substrate obligacy.2002TM/PBexpression not generalized to allgenes
+ or confused withDeltaH/butyrate.
+- Thermotoga proximity is a two-participant community observation,not directional colonization or mandatorycontact.
+ Hydrogen removal supports growth physiology but does not isolate everyEPS/transcript mediator.292versus24 are
+ within-culture growth-phase contrasts;1997and2006density effects remain separate.
+- All1131existing issue titles/bodies searched initially and repeated pre-creation;matching#800read and unrelated.
+ Ignored/hidden-inclusive local path search found132files,excluding.git,docs,site,references_cache,.env;not allhistorical
+ file bodies orPRcomments reviewed.
+- No Edison invocation for this existing-graph repair,no newnodes/directions. Prior authorized Ruegeria extension
+ remains blocked in configuredkey loader; no credential search or retry performed. Overallgoal andotherneeds_researchrecords
+ remain incomplete.
+- Non-graphblocks,458otherrecords,923caches and priorhistories/decisions preserved. Separate metadata followups1890/1891remainopen.
+ No runtime/schema/validator/connectivity-rule changes. Self-review is not independentapproval;requiredCI andprotectedmerge
+ mustbeverified independently.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch114.json b/reports/causal_graph_review/cache-provenance-20261008-batch114.json
new file mode 100644
index 000000000..134bf96f3
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch114.json
@@ -0,0 +1,281 @@
+{
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+ "doi": "10.3389/fmicb.2019.02785",
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+ "title": "Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum .",
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+ {
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+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch114/formate-abstract.txt",
+ "abstract_sha256": "4bbdba87b3a796a579b9711068aade1802c83cf8ac9f59eb26ede5d37c91d088",
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+ "primary_text_sha256": "5c5d1150fbd133e6dbd44da8647809b1021816ac2e3574bb4fea79c2048b4692",
+ "license": [
+ "https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms."
+ ],
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+ },
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+ "URL": "https://creativecommons.org/licenses/by/4.0/"
+ }
+ ]
+ },
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+ "doi": "10.1099/00207713-50-4-1601",
+ "pmcid": null,
+ "title": "Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium.",
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+ "status": "retrieved"
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+ ],
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+ "doi": "10.1002/(sici)1097-0290(19971105)56:3<268::aid-bit4>3.0.co;2-h",
+ "pmcid": null,
+ "title": "Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures.",
+ "metadata": "/private/tmp/communitymech-batch114/transfer-metadata.json",
+ "metadata_sha256": "8e22443802d74ea471a21ac690036dba341d42da08c98757c7fed1f7073813f5",
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+ "phenotype": {
+ "pmid": "16391122",
+ "doi": "10.1128/aem.72.1.811-818.2006",
+ "pmcid": "PMC1352257",
+ "title": "The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture.",
+ "metadata": "/private/tmp/communitymech-batch114/phenotype-metadata.json",
+ "metadata_sha256": "9a44dd04e4dcac94321ac13236edd00635c341ec502b5536e0b54363e8aa5dc3",
+ "retrievals": [
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+ "status": "retrieved"
+ },
+ {
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+ "status": "retrieval_failed",
+ "error": "HTTP Error 500: "
+ }
+ ],
+ "abstract": "/private/tmp/communitymech-batch114/phenotype-abstract.txt",
+ "abstract_sha256": "898df821189eec684b541d0956c1df32237cd8d877fb47ef34cb103dbebf084f",
+ "crossref": "/private/tmp/communitymech-batch114/phenotype-crossref.json",
+ "crossref_sha256": "4558b8ce8eef74e970bbf55180e6828c918e15834ad0da19ed4c87c100d3d72b",
+ "crossref_license": [
+ {
+ "start": {
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+ "timestamp": 1136073600000
+ },
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+ "delay-in-days": 0,
+ "URL": "https://journals.asm.org/non-commercial-tdm-license"
+ }
+ ]
+ }
+ },
+ "actual_read_scope": [
+ "Both whole canonical records and all existing graph snippets read. Six fresh primary abstracts and Crossref identities retrieved. Complete 2019 main-body XML extraction read (folded lines1-650), including figure captions and serialized tables; original pixels, supplements and raw data not reviewed.",
+ "Complete existing cached main bodies of2002expression,2005pathway and2006phenotype read in folded chunks, including methods/results/discussion/captions. Fresh fullTextXML returned500 after retries; PMC browser requests for2005/2006 showed access challenges. No bypass. Cached tables are incomplete; no numerical table-cell claims based on those caches.1997transfer and2000strain are abstract-bounded.",
+ "2001formate partner-comparison publisher abstract read at https://www.sciencedirect.com/science/article/pii/S1389172301801377 ; supports involvement by fasterPB/TM versusPB/DeltaH conversion and lowformate. No full-paper access or new repository quotation/cache claimed. This evidence prevents erasing measured support while qualifying the2019detailed mechanism."
+ ]
+ },
+ "limitations": [
+ "Fresh baseline across both roots before source research:460 records,923 caches,56 unchanged warnings,zero structural defects. Six existing nodes/four directions reviewed and retained;one node renamed,no new topology.",
+ "Both whole canonical records and all existing graph snippets read. Six fresh primary abstracts and Crossref identities retrieved. Complete 2019 main-body XML extraction read (folded lines1-650), including figure captions and serialized tables; original pixels, supplements and raw data not reviewed.",
+ "Complete existing cached main bodies of2002expression,2005pathway and2006phenotype read in folded chunks, including methods/results/discussion/captions. Fresh fullTextXML returned500 after retries; PMC browser requests for2005/2006 showed access challenges. No bypass. Cached tables are incomplete; no numerical table-cell claims based on those caches.1997transfer and2000strain are abstract-bounded.",
+ "2001formate partner-comparison publisher abstract read at https://www.sciencedirect.com/science/article/pii/S1389172301801377 ; supports involvement by fasterPB/TM versusPB/DeltaH conversion and lowformate. No full-paper access or new repository quotation/cache claimed. This evidence prevents erasing measured support while qualifying the2019detailed mechanism.",
+ "2019formate enzyme activity and proteomic support retained;proton-gradient coupling,physiological acetate reduction and completeATPbudget remain proposed. No all-substrate obligacy.2002TM/PBexpression not generalized to allgenes or confused withDeltaH/butyrate.",
+ "Thermotoga proximity is a two-participant community observation,not directional colonization or mandatorycontact. Hydrogen removal supports growth physiology but does not isolate everyEPS/transcript mediator.292versus24 are within-culture growth-phase contrasts;1997and2006density effects remain separate.",
+ "All1131existing issue titles/bodies searched initially and repeated pre-creation;matching#800read and unrelated. Ignored/hidden-inclusive local path search found132files,excluding.git,docs,site,references_cache,.env;not allhistorical file bodies orPRcomments reviewed.",
+ "No Edison invocation for this existing-graph repair,no newnodes/directions. Prior authorized Ruegeria extension remains blocked in configuredkey loader; no credential search or retry performed. Overallgoal andotherneeds_researchrecords remain incomplete.",
+ "Non-graphblocks,458otherrecords,923caches and priorhistories/decisions preserved. Separate metadata followups1890/1891remainopen. No runtime/schema/validator/connectivity-rule changes. Self-review is not independentapproval;requiredCI andprotectedmerge mustbeverified independently."
+ ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml b/reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
new file mode 100644
index 000000000..d7b8c03dc
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
@@ -0,0 +1,601 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 553707b254ed6652b264bed8ab14101a1bcf9c8d
+baseline_commit: 553707b254ed6652b264bed8ab14101a1bcf9c8d
+base_tree: 8e5f24d3fabb78756dfd6875385b1f3cbc2489f8
+pre_source_baseline_sha256: 82e9866979d7e5d4550afb26b47a3e22deaaa938b9401836639d03b766f2a56c
+issues:
+- 1888
+- 1889
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1890
+- 1891
+source_access:
+ retrieval_manifest:
+ pathway:
+ pmid: '15866934'
+ doi: 10.1128/jb.187.10.3471-3476.2005
+ pmcid: PMC1111993
+ title: Operation of the CO dehydrogenase/acetyl coenzyme A pathway in both acetate oxidation and acetate formation
+ by the syntrophically acetate-oxidizing bacterium Thermacetogenium phaeum.
+ metadata: /private/tmp/communitymech-batch114/pathway-metadata.json
+ metadata_sha256: 62ea22fc4c307f9b3c78e1517d483ceabc176d8534361f577290ae73d4a46962
+ retrievals:
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A15866934+AND+SRC%3AMED&format=json&resultType=core
+ status: retrieved
+ - url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC1111993/fullTextXML
+ status: retrieval_failed
+ error: 'HTTP Error 500: '
+ abstract: /private/tmp/communitymech-batch114/pathway-abstract.txt
+ abstract_sha256: e38fbc1b3be1ed20ce0b127d550e38cc004347b96253794cca0b14b36bdf96cd
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+ - 2001formate partner-comparison publisher abstract read at https://www.sciencedirect.com/science/article/pii/S1389172301801377
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+ reference: PMID:18636642
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+ scope: Normalized contiguous literal match, not entailment proof.
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+- record: Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy
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+ independent_primary_match: true
+ matched_artifact: /private/tmp/communitymech-batch114/phenotype-abstract.txt
+ cache_artifact: references_cache/PMID_16391122.md
+ scope: Normalized contiguous literal match, not entailment proof.
+- record: Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy
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+ provider_submissions: 0
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+ prior_extension_blocker: 'Ruegeria issue1883: configuredkey unavailable in prior approved invocation; not retried
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+limitations:
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+- Both whole canonical records and all existing graph snippets read. Six fresh primary abstracts and Crossref identities
+ retrieved. Complete 2019 main-body XML extraction read (folded lines1-650), including figure captions and serialized
+ tables; original pixels, supplements and raw data not reviewed.
+- Complete existing cached main bodies of2002expression,2005pathway and2006phenotype read in folded chunks, including
+ methods/results/discussion/captions. Fresh fullTextXML returned500 after retries; PMC browser requests for2005/2006
+ showed access challenges. No bypass. Cached tables are incomplete; no numerical table-cell claims based on those
+ caches.1997transfer and2000strain are abstract-bounded.
+- 2001formate partner-comparison publisher abstract read at https://www.sciencedirect.com/science/article/pii/S1389172301801377
+ ; supports involvement by fasterPB/TM versusPB/DeltaH conversion and lowformate. No full-paper access or new repository
+ quotation/cache claimed. This evidence prevents erasing measured support while qualifying the2019detailed mechanism.
+- 2019formate enzyme activity and proteomic support retained;proton-gradient coupling,physiological acetate reduction
+ and completeATPbudget remain proposed. No all-substrate obligacy.2002TM/PBexpression not generalized to allgenes
+ or confused withDeltaH/butyrate.
+- Thermotoga proximity is a two-participant community observation,not directional colonization or mandatorycontact.
+ Hydrogen removal supports growth physiology but does not isolate everyEPS/transcript mediator.292versus24 are
+ within-culture growth-phase contrasts;1997and2006density effects remain separate.
+- All1131existing issue titles/bodies searched initially and repeated pre-creation;matching#800read and unrelated.
+ Ignored/hidden-inclusive local path search found132files,excluding.git,docs,site,references_cache,.env;not allhistorical
+ file bodies orPRcomments reviewed.
+- No Edison invocation for this existing-graph repair,no newnodes/directions. Prior authorized Ruegeria extension
+ remains blocked in configuredkey loader; no credential search or retry performed. Overallgoal andotherneeds_researchrecords
+ remain incomplete.
+- Non-graphblocks,458otherrecords,923caches and priorhistories/decisions preserved. Separate metadata followups1890/1891remainopen.
+ No runtime/schema/validator/connectivity-rule changes. Self-review is not independentapproval;requiredCI andprotectedmerge
+ mustbeverified independently.
+records:
+- path: kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml
+ id: CommunityMech:000182
+ original_sha256: e06917ad89ca7d9c8b51c924bd8cf0ef18aed4feb86d4795f3b000bad0398639
+ record_sha256: f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain acetate-linked syntrophy and the reversible pathway; distinguish extracellular carriers from cofactors
+ and avoid all-substrate obligacy.; Retain hydrogen-removing methanogenesis with exact TM/PB expression and hydrogen-pressure
+ context; do not exclude formate use or import DeltaH/butyrate results.; Retain indirectly supported formate
+ transfer as PARTIAL, with the detailed ATP/proton-coupled mechanism HYPOTHESIZED rather than established.
+ node_decisions:
+ - node: Syntrophic Acetate Oxidation by Thermacetogenium
+ rationale: Retain acetate-linked syntrophy and the reversible pathway; distinguish extracellular carriers from
+ cofactors and avoid all-substrate obligacy.
+ - node: Hydrogenotrophic Methanogenesis by Methanothermobacter
+ rationale: Retain hydrogen-removing methanogenesis with exact TM/PB expression and hydrogen-pressure context;
+ do not exclude formate use or import DeltaH/butyrate results.
+ - node: Formate-Linked Syntrophic Electron Transfer
+ rationale: Retain indirectly supported formate transfer as PARTIAL, with the detailed ATP/proton-coupled mechanism
+ HYPOTHESIZED rather than established.
+ removed_node_decisions: []
+ renamed_nodes:
+ Formate Transfer to the Methanogenic Partner: Formate-Linked Syntrophic Electron Transfer
+ edges_before:
+ - &id001
+ source: Syntrophic Acetate Oxidation by Thermacetogenium
+ target: Hydrogenotrophic Methanogenesis by Methanothermobacter
+ description: 'T. phaeum acetate oxidation produces low-concentration reduced carriers that M. thermautotrophicus
+ consumes during hydrogenotrophic methanogenesis.
+
+ '
+ - &id003
+ source: Formate Transfer to the Methanogenic Partner
+ target: Hydrogenotrophic Methanogenesis by Methanothermobacter
+ description: 'Formate and reducing equivalents generated by T. phaeum are transferred to the methanogenic partner
+ that completes syntrophic acetate oxidation.
+
+ '
+ edges_after:
+ - &id002
+ source: Syntrophic Acetate Oxidation by Thermacetogenium
+ target: Hydrogenotrophic Methanogenesis by Methanothermobacter
+ description: Acetate oxidation by T. phaeum supplies reduced products for the methanogenic partner, coupling
+ acetate conversion to methane formation. Hydrogen consumption is supported by the TM/PB coculture experiments;
+ PARTIAL for the partition of electron flow between hydrogen and formate and the specific formate-producing
+ energy-conservation model. This is not direct acetate utilization by the methanogen.
+ - &id004
+ source: Formate-Linked Syntrophic Electron Transfer
+ target: Hydrogenotrophic Methanogenesis by Methanothermobacter
+ description: 'PARTIAL: formate produced by T. phaeum can supply reducing equivalents to the formate-utilizing
+ TM partner for methanogenesis, while removal helps maintain favorable acetate oxidation. HYPOTHESIZED for
+ the specific proton-coupled production mechanism; this arrow does not establish its in vivo flux or convert
+ formate utilization into hydrogen-only metabolism.'
+ retained_edge_decisions:
+ - before: *id001
+ after: *id002
+ rationale: Acetate oxidation by T. phaeum supplies reduced products for the methanogenic partner, coupling acetate
+ conversion to methane formation. Hydrogen consumption is supported by the TM/PB coculture experiments; PARTIAL
+ for the partition of electron flow between hydrogen and formate and the specific formate-producing energy-conservation
+ model. This is not direct acetate utilization by the methanogen.
+ - before: *id003
+ after: *id004
+ rationale: 'PARTIAL: formate produced by T. phaeum can supply reducing equivalents to the formate-utilizing
+ TM partner for methanogenesis, while removal helps maintain favorable acetate oxidation. HYPOTHESIZED for
+ the specific proton-coupled production mechanism; this arrow does not establish its in vivo flux or convert
+ formate utilization into hydrogen-only metabolism.'
+ removed_edge_decisions: []
+ references:
+ - PMID:11872465
+ - PMID:15866934
+ - PMID:31849917
+ issues:
+ - 1888
+ - 1890
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml
+- path: kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml
+ id: CommunityMech:000186
+ original_sha256: d095e9932a413f4245883e31e174605d1a246e821a10945d4009c99517e99b89
+ record_sha256: 05b09dc41d9f2e54eac83d1021d69d2ea733144e9e5386295dd99cc9cae6293c
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml
+ scope: Whole record and all existing nodes/arrows reviewed; existing-graph repair, not whole-record certification.
+ summary: Retain supported hydrogen syntrophy and separate study-specific density effects; qualify the existing
+ arrow as partial mediation through the higher-density context.; Recast proximity as an explicit two-participant
+ community observation; retain a PARTIAL transport interpretation without colonization or mandatory-contact typing.;
+ Recast growth-phase aggregation/transcription as a community phenotype, with the exact within-culture 292-versus-24
+ contrast and no extra exchange claim.
+ node_decisions:
+ - node: Interspecies Hydrogen Transfer
+ rationale: Retain supported hydrogen syntrophy and separate study-specific density effects; qualify the existing
+ arrow as partial mediation through the higher-density context.
+ - node: Spatially Proximate Methanogenic Coculture
+ rationale: Recast proximity as an explicit two-participant community observation; retain a PARTIAL transport
+ interpretation without colonization or mandatory-contact typing.
+ - node: Coculture-Associated Aggregation and Transcriptome Shift
+ rationale: Recast growth-phase aggregation/transcription as a community phenotype, with the exact within-culture
+ 292-versus-24 contrast and no extra exchange claim.
+ removed_node_decisions: []
+ renamed_nodes: {}
+ edges_before:
+ - &id005
+ source: Interspecies Hydrogen Transfer
+ target: Coculture-Associated Aggregation and Transcriptome Shift
+ description: Sustained interspecies hydrogen transfer places T. maritima in the methanogenic coculture state
+ that changes its transcriptome and promotes EPS-based aggregation.
+ - &id007
+ source: Spatially Proximate Methanogenic Coculture
+ target: Interspecies Hydrogen Transfer
+ description: Close spatial proximity allows transferred hydrogen to reach M. jannaschii and establish the methanogenic
+ coculture.
+ edges_after:
+ - &id006
+ source: Interspecies Hydrogen Transfer
+ target: Coculture-Associated Aggregation and Transcriptome Shift
+ description: 'PARTIAL: hydrogen removal relieves growth inhibition and enables the higher-density coculture
+ context in which aggregation and altered growth-phase transcription were observed. Hydrogen-removal comparisons
+ support a contribution to physiology, but do not selectively demonstrate mediation of every EPS or transcript
+ response by hydrogen transfer alone. Growth phase, population density and culture/gas-handling conditions
+ remain part of this causal interpretation.'
+ - &id008
+ source: Spatially Proximate Methanogenic Coculture
+ target: Interspecies Hydrogen Transfer
+ description: 'PARTIAL: proximity can reduce the transport distance for hydrogen from the fermenter to the methanogen,
+ helping establish hydrogen-transfer syntrophy. Failure across a dialysis membrane and size-fraction association
+ support this interpretation, but do not uniquely identify diffusion distance, direct contact or a specific
+ attachment mechanism as the cause.'
+ retained_edge_decisions:
+ - before: *id005
+ after: *id006
+ rationale: 'PARTIAL: hydrogen removal relieves growth inhibition and enables the higher-density coculture context
+ in which aggregation and altered growth-phase transcription were observed. Hydrogen-removal comparisons support
+ a contribution to physiology, but do not selectively demonstrate mediation of every EPS or transcript response
+ by hydrogen transfer alone. Growth phase, population density and culture/gas-handling conditions remain part
+ of this causal interpretation.'
+ - before: *id007
+ after: *id008
+ rationale: 'PARTIAL: proximity can reduce the transport distance for hydrogen from the fermenter to the methanogen,
+ helping establish hydrogen-transfer syntrophy. Failure across a dialysis membrane and size-fraction association
+ support this interpretation, but do not uniquely identify diffusion distance, direct contact or a specific
+ attachment mechanism as the cause.'
+ removed_edge_decisions: []
+ references:
+ - PMID:16391122
+ - PMID:18636642
+ issues:
+ - 1889
+ - 1891
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 3b9424b15..ce58ae102 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -420,12 +420,12 @@ kb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml CommunityMech:000072 01cbb69
kb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml CommunityMech:000100 1c99ca183a340680a90fcfa14327288bb8dac56f57733c219bc19902dbb5abac 6 2 100.0 pending
kb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml CommunityMech:000259 8b79efb0b04a43548b3c73ac280ac987b83c4e97f2531b55da5c940f29485eae 4 2 90.0 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml reviewed
kb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml CommunityMech:000162 f1e51614a8c4a7856a2669afe12574d1c982f12dcebf9f53f49c65d470f747d6 3 0 68.3 reports/causal_graph_review/decisions/20261008-three-records-batch113.yaml needs_research
-kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml CommunityMech:000182 e06917ad89ca7d9c8b51c924bd8cf0ef18aed4feb86d4795f3b000bad0398639 3 2 100.0 pending
+kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml CommunityMech:000182 f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992 3 2 100.0 reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml reviewed
kb/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml CommunityMech:000454 ab97378f5f2ca6160bdceebee4eb24276dbc2ffddc1b49051355ba4609dfae35 2 0 70.0 pending
kb/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml CommunityMech:000416 07c4856308831b4b7bdf1fc50d2442584f1a4c2e5c8431a334e81557eec66727 2 0 70.0 pending
kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml CommunityMech:000282 ec822e47b495189805f5dc2fc9c555e7f987de9d9e3a4986dd7f89920b4def28 3 2 100.0 pending
kb/communities/Thermophilic_Pyrite_QS_Consortium.yaml CommunityMech:000073 249f408c2d6a0d7c7fae5958952d0ceb6b0d5941b4e54a9ce527e5a1caf609a7 6 2 100.0 pending
-kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml CommunityMech:000186 d095e9932a413f4245883e31e174605d1a246e821a10945d4009c99517e99b89 3 2 100.0 pending
+kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml CommunityMech:000186 05b09dc41d9f2e54eac83d1021d69d2ea733144e9e5386295dd99cc9cae6293c 3 2 93.3 reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml reviewed
kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml CommunityMech:000239 309f75cc1846fbba278180170375585824019f86a2f8cae2b00768b3f9257e84 3 2 100.0 pending
kb/communities/Tinto_River_Iron_Cycling_Community.yaml CommunityMech:000074 84f2c22b3f585fe76a992fe664dfad82668a753d637d5c1af53d93031171409d 5 3 100.0 pending
kb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml CommunityMech:000106 b4d7702d9c87b2b55cb2b3c74598aed2bfded7afd454faed5628c817b2fdfa35 3 2 100.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 5a24bf12d..4035e049a 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -8,8 +8,8 @@
"records_without_edges": 187,
"review_status_counts": {
"needs_research": 54,
- "pending": 42,
- "reviewed": 364
+ "pending": 40,
+ "reviewed": 366
},
"structural_defects": [],
"network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch114.json b/reports/causal_graph_review/validation-20261008-batch114.json
new file mode 100644
index 000000000..33f3a9d08
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch114.json
@@ -0,0 +1,807 @@
+{
+ "base_commit": "553707b254ed6652b264bed8ab14101a1bcf9c8d",
+ "scope": [
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml"
+ ],
+ "results": [
+ {
+ "check": "focused",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch114.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/focused.log",
+ "log_sha256": "ca9d17054c9f382b16c5f44a43934beba9e3053c74282a44364694555d2de34f",
+ "output_tail": "......... [100%]\n9 passed in 1.31s\n"
+ },
+ {
+ "check": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch114/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-strict.tsv",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-strict.log",
+ "log_sha256": "6f0077561798546ef1f078d2835626a68c9dc4f2ecee855844d8957956542800",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch114/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-batch114/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-strict.tsv\n"
+ },
+ {
+ "check": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-references.log",
+ "log_sha256": "1e63b70aa7a5d1e6abe3459e37b89c29d8d3f58eb2f236c09186ac0b98cf8e86",
+ "output_tail": "Validating kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-snippets.log",
+ "log_sha256": "4ace74e3aebe07e44b4cf10e59c84ae43d648a819bd2fe1af316a6210582476a",
+ "output_tail": "# 36 evidence snippets scanned across 1 files\n MATCH 36\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": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-rank.log",
+ "log_sha256": "f80293966e75401265ae71d51fbabb14d23424bc4f668b3147745dab81f602c3",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000182\",\n \"name\": \"Thermacetogenium-Methanothermobacter Acetate Oxidation Coculture\",\n \"score\": 100.0,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [],\n \"path\": \"kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture/2026-10-08T090644Z-codex-512c88.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch114/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-strict.tsv",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-strict.log",
+ "log_sha256": "f5e6ba479e5aa2fa6b0597c77b9e5f98b6ee7a3b213edcc3cf094b8935f9a0f9",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch114/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-batch114/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-strict.tsv\n"
+ },
+ {
+ "check": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-references.log",
+ "log_sha256": "78b7981634175713d4dc960a264cb8c4f34a2091470406bf2baccc52e2e21a1b",
+ "output_tail": "Validating kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-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": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-rank.log",
+ "log_sha256": "d884d0df1bd60bcefcccf9f0405c1514d13b3f3d64daf33a46442e21dc180a56",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000186\",\n \"name\": \"Thermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\",\n \"score\": 93.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy/2026-10-08T090644Z-codex-4fdbb0.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy-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-batch114/verification/inventory.log",
+ "log_sha256": "cb00f7153342da4670bb79d8e31021d256b6032d83e61ebf0b020dd1c0d35797",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1380,\n \"edges\": 539,\n \"records_without_nodes\": 10,\n \"records_without_edges\": 187,\n \"review_status_counts\": {\n \"needs_research\": 54,\n \"pending\": 40,\n \"reviewed\": 366\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-batch114/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-batch114/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-batch114/verification/rank-all.log",
+ "log_sha256": "49dfd98f434fa477ce3d67d6d31aad28085a9dc091f2d9fa414738f14411b544",
+ "output_tail": "\t0\t4\t3\t5\tinteraction_type\t0\t0\n402\t97.5\tkb/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.yaml\tCommunityMech:000176\tORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community\t3\t3\t0\t4\t2\t8\tinteraction_type\t0\t0\n403\t97.5\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t8\tinteraction_type\t0\t0\n404\t97.5\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t8\tinteraction_type\t0\t0\n405\t97.9\tkb/communities/Maize_Drought_Response_SynCom.yaml\tCommunityMech:000103\tMaize Drought Response SynCom\t1\t1\t0\t7\t7\t8\tmetabolites_or_biological_processes\t0\t0\n406\t98.3\tkb/communities/Populus_Salt_Tolerant_SynComs.yaml\tCommunityMech:000090\tPopulus Salt-Tolerant Rhizosphere SynComs\t1\t1\t0\t3\t2\t3\tmetabolites_or_biological_processes\t0\t0\n407\t98.3\tkb/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml\tCommunityMech:000404\tWollastonite Ramichloridium-Talaromyces Fungal Consortium\t2\t2\t0\t3\t2\t5\tmetabolites_or_biological_processes\t0\t0\n408\t98.8\tdata/isolates/Chromobacterium_Gold_Biocyanidation.yaml\tCommunityMech:000273\tChromobacterium Gold Biocyanidation Platform\t1\t1\t0\t4\t2\t7\tmetabolites_or_biological_processes\t0\t0\n409\t100.0\tdata/isolates/Aspergillus_Indium_LED_Recovery.yaml\tCommunityMech:000320\tAspergillus Indium LCD Recovery Platform\t1\t1\t0\t5\t4\t6\t\t0\t0\n410\t100.0\tdata/isolates/Methylobacterium_REE_Ewaste_Platform.yaml\tCommunityMech:000322\tMethylobacterium REE E-waste Platform\t1\t1\t0\t4\t2\t6\t\t0\t0\n411\t100.0\tkb/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.yaml\tCommunityMech:000276\tANME/SRB Anaerobic Methanotrophic Syntrophic 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Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
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/private/tmp/communitymech-causal-batch114/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch114/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch114/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch114/docs/index.html\n"
+ },
+ {
+ "check": "render-repeat",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
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+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/render-repeat.log",
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+ "output_tail": "unitymech-causal-batch114/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch114/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-batch114/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch114/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 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/private/tmp/communitymech-causal-batch114/docs/index.html\n"
+ },
+ {
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+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json,runpy; print(json.dumps(runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']()))"
+ ],
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+ },
+ {
+ "check": "just-lint",
+ "command": [
+ "just",
+ "lint"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/just-lint.log",
+ "log_sha256": "24840a52b18ffe9882843149e28f5fc197379bb142f44d5df6001d95a1b83158",
+ "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\n367 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-batch114/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-batch114/verification/audit-snippets-all.log",
+ "log_sha256": "91c80bf284671493680f496c441561105cae96a4b26986ec572e92f1d646094b",
+ "output_tail": "# 9019 evidence snippets scanned across 460 files\n MATCH 8874\n RENDERING 28\n ASSEMBLED 1\n WEAK 0\n MISMATCH 40\n NOCONTENT 76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n 19 (19 hard) kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n 15 (15 hard) kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n 3 (3 hard) kb/communities/Coscinodiscus_Synthetic_Community.yaml\n 1 (1 hard) kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n 1 (1 hard) kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\n 1 (1 hard) kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch114/verification/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Fresh baseline across both roots before source research:460 records,923 caches,56 unchanged warnings,zero structural defects. Six existing nodes/four directions reviewed and retained;one node renamed,no new topology.",
+ "Both whole canonical records and all existing graph snippets read. Six fresh primary abstracts and Crossref identities retrieved. Complete 2019 main-body XML extraction read (folded lines1-650), including figure captions and serialized tables; original pixels, supplements and raw data not reviewed.",
+ "Complete existing cached main bodies of2002expression,2005pathway and2006phenotype read in folded chunks, including methods/results/discussion/captions. Fresh fullTextXML returned500 after retries; PMC browser requests for2005/2006 showed access challenges. No bypass. Cached tables are incomplete; no numerical table-cell claims based on those caches.1997transfer and2000strain are abstract-bounded.",
+ "2001formate partner-comparison publisher abstract read at https://www.sciencedirect.com/science/article/pii/S1389172301801377 ; supports involvement by fasterPB/TM versusPB/DeltaH conversion and lowformate. No full-paper access or new repository quotation/cache claimed. This evidence prevents erasing measured support while qualifying the2019detailed mechanism.",
+ "2019formate enzyme activity and proteomic support retained;proton-gradient coupling,physiological acetate reduction and completeATPbudget remain proposed. No all-substrate obligacy.2002TM/PBexpression not generalized to allgenes or confused withDeltaH/butyrate.",
+ "Thermotoga proximity is a two-participant community observation,not directional colonization or mandatorycontact. Hydrogen removal supports growth physiology but does not isolate everyEPS/transcript mediator.292versus24 are within-culture growth-phase contrasts;1997and2006density effects remain separate.",
+ "All1131existing issue titles/bodies searched initially and repeated pre-creation;matching#800read and unrelated. Ignored/hidden-inclusive local path search found132files,excluding.git,docs,site,references_cache,.env;not allhistorical file bodies orPRcomments reviewed.",
+ "No Edison invocation for this existing-graph repair,no newnodes/directions. Prior authorized Ruegeria extension remains blocked in configuredkey loader; no credential search or retry performed. Overallgoal andotherneeds_researchrecords remain incomplete.",
+ "Non-graphblocks,458otherrecords,923caches and priorhistories/decisions preserved. Separate metadata followups1890/1891remainopen. No runtime/schema/validator/connectivity-rule changes. Self-review is not independentapproval;requiredCI andprotectedmerge mustbeverified independently."
+ ],
+ "reference_validator_version": "0.1.7",
+ "snippet_counts_by_record": {
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml": {
+ "MATCH": 36,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml": {
+ "MATCH": 27,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_record_files": 458,
+ "unchanged_cache_files": 923,
+ "unchanged_raw_blocks": 37,
+ "cache_changes": [],
+ "edison": {
+ "required_for_this_repair": false,
+ "provider_submissions": 0,
+ "credits_spent": 0,
+ "new_nodes_or_directions": 0,
+ "prior_extension_blocker": "Ruegeria issue1883: configuredkey unavailable in prior approved invocation; not retried without state change."
+ },
+ "primary_artifacts": {
+ "/private/tmp/communitymech-batch114/baseline.json": "82e9866979d7e5d4550afb26b47a3e22deaaa938b9401836639d03b766f2a56c",
+ "/private/tmp/communitymech-batch114/expression-abstract.txt": "1215cbd0eb647cfe4e79649629b6fdb17c28572a6bde97546c5268cfba08b367",
+ "/private/tmp/communitymech-batch114/expression-crossref.json": "7e8c8b4c7af23e07c5e53f5925800f051cd821daec6d4a5eae074c584b3b03f3",
+ "/private/tmp/communitymech-batch114/expression-metadata.json": "7e303ad46252c3c85348d30a719cc3681a0d7b2cac26a53030dc23c3633f3ab8",
+ "/private/tmp/communitymech-batch114/formate-abstract.txt": "4bbdba87b3a796a579b9711068aade1802c83cf8ac9f59eb26ede5d37c91d088",
+ "/private/tmp/communitymech-batch114/formate-crossref.json": "791c91ef44ead67c223c91a810618826c4131b732f17074eafbdfa7420b7599f",
+ "/private/tmp/communitymech-batch114/formate-metadata.json": "35c17ac6eb8c615ce3a53652414cd23d10ca55bc0494290ecad8e4c42a1bf727",
+ "/private/tmp/communitymech-batch114/formate-primary.txt": "5c5d1150fbd133e6dbd44da8647809b1021816ac2e3574bb4fea79c2048b4692",
+ "/private/tmp/communitymech-batch114/formate-primary.xml": "c6cb62679c833197ae335967aee7be60b93be7433256a88ae4d560ad648735e5",
+ "/private/tmp/communitymech-batch114/issue-dedup-current.json": "4e8b1d9d78b4c94d468baf9cf8375b139a34e654879998d04cf316ad4ca51116",
+ "/private/tmp/communitymech-batch114/local-matches.txt": "73fc6f7e7caf36d4a3c9ad98afad72dfead18e0abcb4ad02bf3ddca48afe9c0c",
+ "/private/tmp/communitymech-batch114/pathway-abstract.txt": "e38fbc1b3be1ed20ce0b127d550e38cc004347b96253794cca0b14b36bdf96cd",
+ "/private/tmp/communitymech-batch114/pathway-crossref.json": "c1ab52604b4af64fc3814073c06bcc7dad5658353eb203aca8792631c5c9fb07",
+ "/private/tmp/communitymech-batch114/pathway-metadata.json": "62ea22fc4c307f9b3c78e1517d483ceabc176d8534361f577290ae73d4a46962",
+ "/private/tmp/communitymech-batch114/phenotype-abstract.txt": "898df821189eec684b541d0956c1df32237cd8d877fb47ef34cb103dbebf084f",
+ "/private/tmp/communitymech-batch114/phenotype-crossref.json": "4558b8ce8eef74e970bbf55180e6828c918e15834ad0da19ed4c87c100d3d72b",
+ "/private/tmp/communitymech-batch114/phenotype-metadata.json": "9a44dd04e4dcac94321ac13236edd00635c341ec502b5536e0b54363e8aa5dc3",
+ "/private/tmp/communitymech-batch114/primary-manifest.json": "9766cf3b76df94a21752b56e77ccd0d09e60d5bef6f03813c1c252554a2e89ca",
+ "/private/tmp/communitymech-batch114/strain-abstract.txt": "b37f7418c60af6e6dd1665ef445217d93a7df0881cc6f5bbbf79ca155b54ab6b",
+ "/private/tmp/communitymech-batch114/strain-crossref.json": "3391f1b3f258c9db182e4603446f987ebe8af8ccfd548a4df2fb08d74277acc0",
+ "/private/tmp/communitymech-batch114/strain-metadata.json": "3fab43b5405fed706cd3ab5dc33e9d0766136ae622cc20bc1fd7670a343bd1dc",
+ "/private/tmp/communitymech-batch114/transfer-abstract.txt": "a6e945c465f9701a6ba0b2ae41acefcffc72b526546951d3e90468cd3cdd0e17",
+ "/private/tmp/communitymech-batch114/transfer-crossref.json": "0f02bc7bb12f8d41a4a095dd7c9b085e5541c2a9f3f3cc231dc1bc8dc6fb771c",
+ "/private/tmp/communitymech-batch114/transfer-metadata.json": "8e22443802d74ea471a21ac690036dba341d42da08c98757c7fed1f7073813f5",
+ "references_cache/PMID_10939667.md": "0afab422ef8e6aacd1ff9e9575ebe37fce1126670c7d2141c5dda3564243aec7",
+ "references_cache/PMID_11872465.md": "52331fdc381b23122406cf000d731b578ce6a4bf7132da4c0f6622014c2ac2ea",
+ "references_cache/PMID_15866934.md": "baeceabc57844f78965ee975ce487e72e8eb2ecab66bf2470ae0786fb7a875b4",
+ "references_cache/PMID_16391122.md": "0e97692ff58f1f4a373cc0eb363939dd0ad35473c161ec8fc7802a04a12ff38e",
+ "references_cache/PMID_18636642.md": "5d63d135ab8d9f33c699751a33110327451b7a9645861b07aa2b4e6b4b34228c",
+ "references_cache/PMID_31849917.md": "892aa351daf3d1e745664252a922b6ecccc19c4fece123f5d95becb4b4bbff41"
+ },
+ "immutable_prior_history_and_decision_files": 862,
+ "primary_graph_snippet_proof": {
+ "graph_quotations": 16,
+ "discussion_quotations": 2,
+ "fresh_primary_literal_matches": 18,
+ "all_cached_literal_matches": 18,
+ "retained_nodes": 6,
+ "removed_nodes": 0,
+ "renamed_nodes": 1,
+ "retained_arrows": 4,
+ "removed_arrows": 0,
+ "new_nodes_or_directions": 0
+ },
+ "network_delta": {
+ "existing_findings_preserved": 56,
+ "added_findings": {},
+ "removed_findings": {},
+ "structural_defects": 0
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1366,
+ "arrows": 531
+ },
+ "render_scope": "Deterministic rendering and exact HTML description parsing, not screenshots; postcommit docs-current still required.",
+ "participant_census": {
+ "current": {
+ "records": 460,
+ "with_community_level": 413,
+ "mixed": 137,
+ "community_level_only": 276,
+ "taxa": 1565,
+ "credited_solely_by_the_rule": 1273
+ },
+ "delta_from_batch113": {
+ "records": 0,
+ "with_community_level": 1,
+ "mixed": 1,
+ "community_level_only": 0,
+ "taxa": 2,
+ "credited_solely_by_the_rule": 0
+ },
+ "explanation": "Thermotoga adds one explicit participant-list user and mixed-scope record; both taxa already have pairwise credit. No connectivity rule or share-guard changes."
+ },
+ "lint_environment": {
+ "path": "/private/tmp/communitymech-batch100/lint-env",
+ "scope": "Temporary established Python3.13 lint environment; project dependencies unchanged."
+ },
+ "full_corpus_snippet_counts": {
+ "records": 460,
+ "total": 9019,
+ "categories": {
+ "MATCH": 8874,
+ "RENDERING": 28,
+ "ASSEMBLED": 1,
+ "WEAK": 0,
+ "MISMATCH": 40,
+ "NOCONTENT": 76
+ }
+ },
+ "full_corpus_snippet_audit_caveat": "Informational audit exit0 is not clean-corpus or entailment certification.",
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1380,
+ "edges": 539,
+ "records_without_nodes": 10,
+ "records_without_edges": 187,
+ "review_status_counts": {
+ "needs_research": 54,
+ "pending": 40,
+ "reviewed": 366
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml": "80fde422c660d0b4cdee61623b5aaaa381fa28f6fb04082407ae5ee702979bdf",
+ "tests/test_causal_review_batch114.py": "9c3fffeefa7091b002e1af8cc18d88b536f5d192e7511262364541ad13830522",
+ "tests/test_participating_taxa.py": "2abb167c84b237eac4d24e15590fb27efa3c4845e169bd2a3de1936ed1fd8efc",
+ "tests/test_community_level_connectivity_credit.py": "1af00518c5e73a612339531474000886eec61e21c438337d272b0b9a1e4ed18e",
+ "tests/test_causal_review_batch109.py": "b5b99af9d142cfac972a3e08c09c25fbcdec4a4a2f015d33758998acaa16d203",
+ "reports/causal_graph_review/cache-provenance-20261008-batch114.json": "0a5b861834ef55c1ed2b0c441a573a1e3482867aa315374b21b3e15eaccb12d1",
+ "kb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml": "f45e52ffbf76a2c295b73efb10bf183a01ecc03056cc11f018afe3c6e3723992",
+ "kb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml": "05b09dc41d9f2e54eac83d1021d69d2ea733144e9e5386295dd99cc9cae6293c"
+ },
+ "pre_research_baseline": {
+ "base_commit": "553707b254ed6652b264bed8ab14101a1bcf9c8d",
+ "base_tree": "8e5f24d3fabb78756dfd6875385b1f3cbc2489f8",
+ "research_worktree": "/private/tmp/communitymech-causal-batch114",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch114/baseline-rank.log",
+ "sha256": "d749a76e6f0ef826166673cf1e4f31cb7562d44f970826fd691c5dc3296b4961"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch114/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-batch114/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-batch114/baseline-downstream.log",
+ "sha256": "996c07a9129a5c696d396231a1d202a01b565ee316f7400fdb41be187b8dce3f"
+ }
+ ],
+ "baseline_sha256": "82e9866979d7e5d4550afb26b47a3e22deaaa938b9401836639d03b766f2a56c"
+ },
+ "reference_validator_caveat": "Full-record local passes are macOS, not Linux certification. Literal matching does not establish entailment. Total checks in the reference CLI counts issues, not examined snippets.",
+ "status": "verified_existing_graph_repairs",
+ "total_recorded_gate_outputs": 27
+}
diff --git a/tests/test_causal_review_batch109.py b/tests/test_causal_review_batch109.py
index 455491086..edcd8dde5 100644
--- a/tests/test_causal_review_batch109.py
+++ b/tests/test_causal_review_batch109.py
@@ -176,15 +176,15 @@ def test_hashes_histories_and_canonical_identity_only_scope_are_explicit():
def test_current_scope_census_tracks_later_source_bounded_repairs():
- # Batch112 adds seven denominator taxa; the three ES5 members become solely credited.
+ # Batch114 adds two denominator taxa, both already connected by hydrogen syntrophy.
survey = runpy.run_path(str(ROOT / "tests/test_community_level_connectivity_credit.py"))[
"_survey"
]()
assert survey == {
"records": 460,
- "with_community_level": 412,
- "mixed": 136,
+ "with_community_level": 413,
+ "mixed": 137,
"community_level_only": 276,
- "taxa": 1563,
+ "taxa": 1565,
"credited_solely_by_the_rule": 1273,
}
diff --git a/tests/test_causal_review_batch114.py b/tests/test_causal_review_batch114.py
new file mode 100644
index 000000000..f22e3d6c5
--- /dev/null
+++ b/tests/test_causal_review_batch114.py
@@ -0,0 +1,131 @@
+"""Keep thermophilic syntrophy distinct from proposed mechanisms and assay contrasts."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-two-records-batch114.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ rows = ledger["records"]
+ return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_acetate_syntrophy_does_not_assert_all_substrate_obligacy():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][0]
+ assert node["interaction_type"] == "SYNTROPHY"
+ assert "grows acetogenically in pure culture" in node["description"]
+ assert "not a claim that intracellular cofactors" in node["description"]
+ assert (
+ "not direct acetate utilization by the methanogen" in node["downstream"][0]["description"]
+ )
+ assert node["evidence"][2]["supports"] == "PARTIAL"
+
+
+def test_tm_expression_is_not_all_genes_or_the_deltah_system():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][1]
+ assert "20 to 80 Pa" in node["description"]
+ assert "mcr/MRI rather than mrt/MRII" in node["description"]
+ assert "other assayed methanogenesis genes" in node["description"]
+ assert "separate DeltaH/butyrate" in node["description"]
+ assert "does not exclude formate-supported electron transfer" in node["description"]
+
+
+def test_formate_support_survives_without_proving_the_energy_coupling_model():
+ _, _, docs = records()
+ node = docs[0]["ecological_interactions"][2]
+ assert node["name"] == "Formate-Linked Syntrophic Electron Transfer"
+ assert node["interaction_type"] == "CROSS_FEEDING"
+ assert node["description"].startswith("PARTIAL:")
+ assert "not dismissed as a genomic conjecture" in node["description"]
+ assert "HYPOTHESIZED:" in node["description"]
+ assert (
+ "Proton-gradient coupling and physiological acetate reduction were not demonstrated"
+ in node["description"]
+ )
+ assert node["evidence"][0]["supports"] == "PARTIAL"
+ assert node["evidence"][1]["supports"] == "SUPPORT"
+ assert node["downstream"][0]["description"].startswith("PARTIAL:")
+
+
+def test_hydrogen_transfer_retains_separate_study_effect_sizes():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][0]
+ assert node["interaction_type"] == "SYNTROPHY"
+ assert "tenfold bacterial density increase at 85 C" in node["description"]
+ assert "separate 2006 study" in node["description"]
+ assert "three- to fivefold" in node["description"]
+ assert "also grew in monoculture" in node["description"]
+
+
+def test_proximity_is_not_colonization_or_obligatory_direct_contact():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][1]
+ assert node["scope"] == "COMMUNITY_LEVEL"
+ assert "interaction_type" not in node
+ assert "source_taxon" not in node and "target_taxon" not in node
+ assert "do not demonstrate direct cell contact as obligatory" in node["description"]
+ assert node["evidence"][1]["supports"] == "PARTIAL"
+ assert node["downstream"][0]["description"].startswith("PARTIAL:")
+
+
+def test_292_is_a_within_culture_growth_phase_contrast():
+ _, _, docs = records()
+ node = docs[1]["ecological_interactions"][2]
+ assert node["scope"] == "COMMUNITY_LEVEL" and "interaction_type" not in node
+ assert "within coculture, versus 24" in node["description"]
+ assert "not 292 genes in a direct coculture-versus-monoculture contrast" in node["description"]
+ assert "diminished during stationary phase" in node["description"]
+ assert "not demonstrated regulatory necessity" in node["description"]
+
+
+def test_hydrogen_to_phenotype_mediation_is_partial():
+ _, _, docs = records()
+ edge = docs[1]["ecological_interactions"][0]["downstream"][0]
+ assert edge["description"].startswith("PARTIAL:")
+ assert (
+ "do not selectively demonstrate mediation of every EPS or transcript response"
+ in edge["description"]
+ )
+ assert "culture/gas-handling conditions" in edge["description"]
+
+
+def test_original_topology_and_evidence_dispositions_are_accounted_for():
+ ledger, rows, _ = records()
+ counts = ledger["reviewed_counts"]
+ assert counts["original_nodes"] == counts["retained_nodes"] == 6
+ assert counts["original_arrows"] == counts["retained_arrows"] == 4
+ assert counts["removed_arrows"] == counts["removed_nodes"] == 0
+ assert counts["renamed_nodes"] == 1
+ assert counts["graph_quotations"] == 16 and counts["discussion_quotations"] == 2
+ assert [r["status"] for r in rows] == ["reviewed", "reviewed"]
+ assert ledger["issues"] == [1888, 1889]
+ assert ledger["unresolved_non_graph_issues"] == [1890, 1891]
+ assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+ assert all(p["independent_primary_match"] for p in ledger["snippet_checks"])
+
+
+def test_hashes_history_and_canonical_participants_are_guarded():
+ ledger, rows, docs = records()
+ assert ledger["independent_approval"] is False
+ for row, doc in zip(rows, docs, strict=True):
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert row["curation_events_added"] == len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).exists()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ canonical = [
+ {k: t["taxon_term"][k] for k in ["preferred_term", "term"]} for t in doc["taxonomy"]
+ ]
+ for node in doc["ecological_interactions"]:
+ assert all(e["target"] in names for e in node.get("downstream", []))
+ if node["scope"] == "COMMUNITY_LEVEL":
+ assert node["participating_taxa"] == canonical
+ for d in doc["discussions"]:
+ assert all(a.split("#", 1)[1] in names for a in d["attaches_to"])
diff --git a/tests/test_community_level_connectivity_credit.py b/tests/test_community_level_connectivity_credit.py
index 27167a35a..108482a71 100644
--- a/tests/test_community_level_connectivity_credit.py
+++ b/tests/test_community_level_connectivity_credit.py
@@ -109,7 +109,8 @@ def test_most_records_carry_a_community_level_interaction(survey):
# #1859 adds a scoped electrode process (407 -> 408); no new solely-credited taxa.
# #1865 separates the scoped butanol endpoint (408 -> 409), with no new sole credit.
# #1872/#1875/#1876 add three scoped outcomes; the ES5 triculture is community-only.
- assert 130 <= survey["with_community_level"] <= 412, survey
+ # #1889 scopes Thermotoga proximity/phenotype; both members retain pairwise credit.
+ assert 130 <= survey["with_community_level"] <= 413, survey
def test_the_mixed_records_are_where_the_coarseness_bites(survey):
@@ -128,7 +129,8 @@ def test_the_mixed_records_are_where_the_coarseness_bites(survey):
# #1851-#1854 add four mixed-scope records; batch109 pins the exact measured census.
# #1865 adds one mixed-scope record (133 -> 134); the share guard is unchanged.
# Batch112 adds two mixed-scope records and one community-only record.
- assert 35 <= survey["mixed"] <= 136, survey
+ # Batch114 adds one mixed record; no additional solely-credited taxa.
+ assert 35 <= survey["mixed"] <= 137, survey
assert survey["mixed"] + survey["community_level_only"] == survey["with_community_level"]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 405bb3afb..447f2c988 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -439,6 +439,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
"TCP_NonDehalogenimonas_Groundwater_Consortium.yaml",
"Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml",
"Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml",
+ "Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml",
"Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml",
"Trichodesmium_Alteromonas_Marine_Consortium.yaml",
"Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml",