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realmarcin merged 1 commit into from
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Review cinnamate and isoDCA causal graphs (batch 16) #1315

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67 changes: 29 additions & 38 deletions docs/communities/Cinnamate_Degradation_Consortium.html
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Expand Up @@ -601,7 +601,7 @@ <h2>Ecological Interactions</h2>
<div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
<svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
<title id="network-svg-title">Ecological interaction network for Cinnamate β-Oxidation Consortium</title>
<desc id="network-svg-desc">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, commensalism).</desc>
<desc id="network-svg-desc">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).</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
Expand All @@ -614,8 +614,8 @@ <h2>Ecological Interactions</h2>
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolWye"
data-color="#cf7830"></svg> Commensalism
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -624,9 +624,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Cinnamate β-Oxidation to Benzoate</h3>
<span class="interaction-type">COMMENSALISM</span>
</div>
<p class="prewrap interaction-description">Papillibacter cinnamivorans initiates anaerobic cinnamate degradation by producing benzoate through beta-oxidation.</p>
<p class="prewrap interaction-description">Papillibacter cinnamivorans converts cinnamate to benzoate, providing the intermediate for subsequent syntrophic degradation. Conversion still occurred with the methanogenesis inhibitor BESA. The authors propose beta-oxidation; the accessible abstract does not resolve its enzyme steps or establish a commensal fitness relationship.</p>


<p><strong>Source Taxon:</strong> Papillibacter cinnamivorans</p>
Expand All @@ -649,25 +648,14 @@ <h3>Cinnamate β-Oxidation to Benzoate</h3>



<p><strong>Biological Processes:</strong></p>
<ul>

<li>
fatty acid beta-oxidation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006635"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006635</a>)
</li>

</ul>



<div class="interaction-flow">
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Syntrophic Benzoate Degradation
<p class="prewrap causal-description">Benzoate produced from cinnamate becomes the substrate for downstream Syntrophus-methanogen degradation.</p>
<p class="prewrap causal-description">Benzoate formed by P. cinnamivorans supplies substrate for the Syntrophus-methanogen association. The reported stepwise conversion and BESA-associated arrest at benzoate support this substrate connection without resolving every enzyme step.</p>
</div>

</div>
Expand Down Expand Up @@ -699,7 +687,7 @@ <h4>Evidence</h4>
<h3>Syntrophic Benzoate Degradation</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Syntrophus sp. syntrophically degrades the benzoate intermediate to acetate, H2, and CO2 with the hydrogen-scavenging methanogen.</p>
<p class="prewrap interaction-description">Syntrophus sp. and the methanogen form the association reported to degrade benzoate to acetate, methane and carbon dioxide. Syntrophic interdependence is reported during growth on cinnamate. HYPOTHESIZED - H2 transfer is a candidate coupling mechanism, not an experimentally identified electron carrier in the accessible abstract.</p>


<p><strong>Source Taxon:</strong> Syntrophus sp.</p>
Expand All @@ -720,10 +708,6 @@ <h3>Syntrophic Benzoate Degradation</h3>
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30089"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30089</a>),

hydrogen
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18276"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18276</a>),

carbon dioxide
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>)
Expand All @@ -750,7 +734,7 @@ <h3>Syntrophic Benzoate Degradation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Methanogenesis
<p class="prewrap causal-description">H2 and CO2 from benzoate degradation feed Methanobacterium methanogenesis.</p>
<p class="prewrap causal-description">HYPOTHESIZED - benzoate oxidation could supply H2 as reducing equivalents for CO2-reducing methanogenesis. The observed association and methane product support metabolic coupling, but the accessible abstract does not discriminate electron carriers or trace carbon and electron flux between partners.</p>
</div>

</div>
Expand Down Expand Up @@ -782,7 +766,7 @@ <h4>Evidence</h4>
<h3>Methanogenesis</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Methanobacterium formicicum consumes syntrophy-derived H2 and CO2 to produce methane during complete cinnamate mineralization.</p>
<p class="prewrap interaction-description">PARTIAL - Methanobacterium formicicum replaced the original Methanobacterium isolate in the reconstituted consortium, and methane was reported among its degradation products. HYPOTHESIZED - consumption of partner-derived H2 with CO2 reduction explains a possible methanogenic route, but the accessible abstract does not resolve that transfer. Acetate remains among the reported products; complete mineralization of all cinnamate carbon is not established.</p>


<p><strong>Source Taxon:</strong> Methanobacterium formicicum</p>
Expand All @@ -793,10 +777,6 @@ <h3>Methanogenesis</h3>

<p><strong>Metabolites:</strong>

hydrogen
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18276"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18276</a>),

carbon dioxide
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>),
Expand Down Expand Up @@ -833,7 +813,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/12432464/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:12432464</a>

- SUPPORT (IN_VITRO)
- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"In the presence of bromoethanesulfonic acid (BESA), cinnamate was transformed to benzoate, whereas under methanogenic conditions without BESA, cinnamate was first transformed to benzoate via beta-oxidation and subsequently completely degraded into acetate, CH(4), and CO(2)"</div>
Expand All @@ -849,6 +829,25 @@ <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 interspecies electron carrier and carbon balance support methanogenesis during cinnamate degradation?
</h3>
<p class="prewrap">The primary abstract establishes benzoate formation, syntrophic benzoate degradation and acetate/methane/CO2 products, but not an experimentally resolved H2-versus-alternative carrier or full carbon mineralization. The subscription body was unavailable; exact-system gas/carrier measurements, partner perturbations and carbon balance are needed before promoting the proposed H2 route to demonstrated transfer. The supported benzoate substrate link remains intact.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Cinnamate β-Oxidation to Benzoate</code>, <code>ecological_interactions#Syntrophic Benzoate Degradation</code>, <code>ecological_interactions#Methanogenesis</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1059,7 +1058,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:0";
var intType = "COMMENSALISM";
var intType = "UNKNOWN";
var metabolites = [];


Expand All @@ -1070,10 +1069,6 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("fatty acid beta-oxidation");


var evidenceCount = 1;

nodes.push({
Expand Down Expand Up @@ -1106,8 +1101,6 @@ <h4 style="color: var(--text);">Evidence</h4>

metabolites.push("acetate");

metabolites.push("hydrogen");

metabolites.push("carbon dioxide");


Expand Down Expand Up @@ -1150,8 +1143,6 @@ <h4 style="color: var(--text);">Evidence</h4>
var metabolites = [];


metabolites.push("hydrogen");

metabolites.push("carbon dioxide");

metabolites.push("methane");
Expand Down
30 changes: 30 additions & 0 deletions history/records/Cinnamate_Degradation_Consortium/2026-10-05T222800Z-codex-cd0f4a.yaml
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@@ -0,0 +1,30 @@
history_version: 1
target:
kind: record
path: kb/communities/Cinnamate_Degradation_Consortium.yaml
slug: Cinnamate_Degradation_Consortium
session:
id: 2026-10-05T222800Z-codex-cd0f4a
timestamp: '2026-10-05T22:28:00Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1313
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain the supported benzoate substrate link and proposed beta-oxidation without
unsupported commensalism or fatty-acid process typing.; Retain measured syntrophic degradation
and mixed products; qualify the electron-carrier arrow and remove unqualified hydrogen
metabolite assertions.; Retain methane production with partial route evidence; distinguish
the reconstituted methanogen from the original isolate and avoid complete-mineralization
claims.
details: Source-based self-adversarial review, abstract-bounded mechanism repair, no new
structure. reports/causal_graph_review/decisions/20261005-two-records-batch16.yaml
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