Bound Ferroplasma and Fomitopsis claims; record lung graph gap (batch 41)

docs/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.html

@@ -557,16 +557,21 @@ <h2>Ecological Interactions</h2>
                              aria-hidden="true" data-symbol="symbolTimes"
                              data-color="#a91919"></svg> Competition
                     </div>
+                    <div class="legend-item">
+                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
+                    </div>
                 </div>
             </div>
 
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>E. coli glucose competition imposes F. betulina carbon stress</h3>
+                    <h3>E. coli-Associated Glucose Depletion and F. betulina Stress</h3>
                     <span class="interaction-type">COMPETITION</span>
                 </div>
-                <p class="prewrap interaction-description">When E. coli ATCC 25922 was added to 3-day F. betulina liquid MEB cultures, glucose fell to zero within 1 day after bacterial addition, F. betulina dry biomass dropped from about 60 mg in monoculture to 34 mg in coculture, and RNA-seq after 3 days of coculture showed broad F. betulina differential expression consistent with carbon depletion and metabolic stress.</p>
+                <p class="prewrap interaction-description">PARTIAL: E. coli addition to established F. betulina liquid MEB cultures was followed by glucose depletion within one day, fungal biomass of 34 mg (reported as 44% lower), and stress-related fungal transcription after three days of coculture. These observations support nutrient competition as an interpretation, but the inspected selected primary excerpts do not describe selective glucose rescue establishing mediation. BGC expression indicates transcriptional response, not production or identification of an active secreted metabolite. Endpoint bacterial counts were not reduced in this liquid assay.</p>
 
 
                 <p><strong>Source Taxon:</strong> Escherichia coli ATCC 25922</p>
@@ -620,16 +625,28 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://doi.org/10.64898/2026.09.14.751415"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.09.14.751415</a>
+
+                            - SUPPORT (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"The bacterial count on agar medium at the end of the experiment did not reveal any impact of the coculture on the bacterial growth."</div>
+
+                    </li>
+
                 </ul>
 
             </div>
 
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>F. betulina distal inhibition of E. coli on malt extract agar</h3>
-                    <span class="interaction-type">COMPETITION</span>
                 </div>
-                <p class="prewrap interaction-description">In malt extract agar confrontation plates, F. betulina CIRM-BRFM 860 formed a visible zone that inhibited E. coli ATCC 25922 growth at a distance from the fungal mycelium. LC-MS metabolomics of media plugs from the inhibition zone detected enriched Sumiki&#39;s-acid-derivative, calcium-diformate, and sulfuric-acid features, and the authors linked the zone to local medium acidification rather than to detectable piptamine production.</p>
+                <p class="prewrap interaction-description">F. betulina inhibited distal E. coli growth on malt extract agar. Inhibition-zone UHPLC-HRMS features were putatively identified as a Sumiki&#39;s acid derivative, calcium diformate and sulfuric acid; these are not confirmed active compounds. HYPOTHESIZED: acid-associated local pH changes mediate inhibition. The inspected selected excerpts describe a pH gradient but no selective neutralization or defined-compound rescue establishing necessity. Piptamine was not detected under these conditions, not shown to be universally absent. This agar phenotype is distinct from liquid-culture stress transcription and unchanged endpoint bacterial counts.</p>
 
 
                 <p><strong>Source Taxon:</strong> Fomitopsis betulina CIRM-BRFM 860</p>
@@ -662,6 +679,19 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://doi.org/10.64898/2026.09.14.751415"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.09.14.751415</a>
+
+                            - PARTIAL (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"The features detected in the inhibition zone were putatively identified as a Sumiki&#39;s acid derivative, calcium diformate, and sulfuric acid."</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -671,6 +701,25 @@ <h4>Evidence</h4>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which mediators cause liquid fungal stress and separate agar bacterial inhibition?
+                </h3>
+                <p class="prewrap">Selected primary preprint excerpts support measured glucose depletion, fungal biomass loss and transcription in liquid, versus distal bacterial inhibition and putative acid features on agar. No selective glucose rescue or pH neutralization is described in those excerpts; the full paper was not re-read because the public PDF request returned HTTP 429, so this is not a claim of universal experimental absence. Piptamine nondetection is condition-specific; BGC induction is not active-product identification. Preserve two nodes and zero arrows rather than connect different assay regimes. Prior cache-support fixes #1169/#1170/#1171 and the natural-partner caveat removal #1173 remain intact.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#E. coli-Associated Glucose Depletion and F. betulina Stress</code>, <code>ecological_interactions#F. betulina distal inhibition of E. coli on malt extract agar</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -934,11 +983,11 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-            var evidenceCount = 2;
+            var evidenceCount = 3;
 
             nodes.push({
                 id: intId,
-                label: "E. coli glucose competition imposes F. betulina carbon stress",
+                label: "E. coli-Associated Glucose Depletion and F. betulina Stress",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -963,12 +1012,12 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "COMPETITION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,

docs/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.html

@@ -620,6 +620,23 @@ <h2>Ecological Interactions</h2>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which observed phenotypes and proposed mechanisms belong in the four-species causal graph?
+                </h3>
+                <p class="prewrap">The openly available primary main body (PMID:42545019; PMC13595950) now supports source review beyond the abstract. The record still has no interaction nodes and remains needs_research under #1461. Day-10 vPCR persistence, total CFU, DNA-qPCR and protein fractions are distinct readouts. P. koreensis-containing bicultures alkalinize, and community pH recovers after acid perturbation, but total CFU does not resolve member-specific compositional resilience. Siderophore uptake, partner-resolved acid/pyruvate exchange, ammonia mediation and AI-2 coordination require hypothesis-qualified treatment, not inferred flux or selective causality from proteins alone. Predicted antimicrobial pathways produced no inhibition zones in the tested agar assay, not proof of universal absence. Nutrient-rich BHI and pH 9-10 are not physiological healthy-airway conditions. Challenge organisms are not members of the canonical four-species record. One-community Edison dry run completed; specific credit authorization requested and no provider job or spend made. Add no speculative nodes or arrows while research is pending. Source body, tables and captions read; figure images, supplements and raw data not inspected. Strain and model metadata remain #1463.</p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 

history/records/Ferroplasma_Leptospirillum_Syntrophy/2026-10-06T104340Z-codex-37b7f6.yaml

@@ -0,0 +1,29 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml
+  slug: Ferroplasma_Leptospirillum_Syntrophy
+session:
+  id: 2026-10-06T104340Z-codex-37b7f6
+  timestamp: '2026-10-06T10:43:40Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1459
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain proposed organic supply as intrinsic source context without an unsupported
+    carbon-fixation route.; Retain proposed consumption with hypothesis-qualified evidence,
+    without measured detoxification or the reciprocal-response arrow.; Retain iron-metabolism
+    context with explicit strain and isolated-protein limits, not niche partitioning.; Retain
+    reciprocal filtered-medium growth without assigned mediator or obligate mutualism.
+  details: Existing-graph repair or explicit unresolved expansion; no new causal structure.
+    reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml

history/records/Fomitopsis_Ecoli_Nutritional_Stress_Coculture/2026-10-06T104341Z-codex-a2b56f.yaml

@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Fomitopsis_Ecoli_Nutritional_Stress_Coculture.yaml
+  slug: Fomitopsis_Ecoli_Nutritional_Stress_Coculture
+session:
+  id: 2026-10-06T104341Z-codex-a2b56f
+  timestamp: '2026-10-06T10:43:41Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1460
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain liquid glucose depletion and fungal stress with PARTIAL nutrient-competition
+    mediation.; Retain observed distal agar inhibition with putative identities and HYPOTHESIZED
+    acid mediation; no cross-regime arrow.
+  details: Existing-graph repair or explicit unresolved expansion; no new causal structure.
+    reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml

history/records/FourSpecies_Aerobic_Lung_Microbiome_Model/2026-10-06T104341Z-codex-319aac.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/FourSpecies_Aerobic_Lung_Microbiome_Model.yaml
+  slug: FourSpecies_Aerobic_Lung_Microbiome_Model
+session:
+  id: 2026-10-06T104341Z-codex-319aac
+  timestamp: '2026-10-06T10:43:41Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1461
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - discussions
+  summary: Record full-text graph-expansion candidates and retain needs_research; no new nodes
+    or arrows pending the one-community research workflow
+  details: Existing-graph repair or explicit unresolved expansion; no new causal structure.
+    reports/causal_graph_review/decisions/20261006-three-records-batch41.yaml