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realmarcin merged 1 commit into from
Oct 6, 2026
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Review coculture and crucian carp causal graphs (batch 24) #1355

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94 changes: 55 additions & 39 deletions ...communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -560,34 +560,37 @@ <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 Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture</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).</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.</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
<span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Riboflavin-Mediated Redox Coupling</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>Riboflavin-Supplemented Coculture Response</h3>
</div>
<p class="prewrap interaction-description">S. oneidensis provides an electroactive coculture partner for C. glutamicum, and riboflavin is the most effective screened redox-active additive for further improving anaerobic succinic acid production.</p>
<p class="prewrap interaction-description">The complete abstract reports that externally supplied riboflavin was the most effective of five screened redox-active additives, with 0.1 mM supplementation further improving coculture production. This supports an additive response, not demonstrated Shewanella secretion, directed interspecies electron transfer or thermodynamic syntrophy. Parent-strain and K1 experiments must be distinguished; the abstract does not resolve every additive/transcript assay to K1.</p>


<p><strong>Source Taxon:</strong> Shewanella oneidensis</p>


<p><strong>Participating Taxa:</strong>

<p><strong>Target Taxon:</strong> Corynebacterium glutamicum (ldhA-deleted strain K1)</p>
Corynebacterium glutamicum (ldhA-deleted strain K1),

Shewanella oneidensis

</p>



Expand Down Expand Up @@ -618,8 +621,8 @@ <h3>Riboflavin-Mediated Redox Coupling</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Reprogrammed Corynebacterium Reductive TCA Flux
<p class="prewrap causal-description">Coculture redox coupling leads into the transcriptome-level reinforcement of the C. glutamicum electron transport system and reductive TCA flux.</p>
<span class="flow-arrow">→</span> Corynebacterium Coculture Transcript Response
<p class="prewrap causal-description">HYPOTHESIZED - altered coculture redox conditions could contribute to the Corynebacterium transcript response. Additive screening and the transcriptomic interpretation support this candidate link, but the accessible abstract does not selectively establish riboflavin-dependent electron transfer as its cause.</p>
</div>

</div>
Expand Down Expand Up @@ -648,17 +651,14 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Reprogrammed Corynebacterium Reductive TCA Flux</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>Corynebacterium Coculture Transcript Response</h3>
</div>
<p class="prewrap interaction-description">In coculture, C. glutamicum globally reprograms metabolism, reinforcing its electron transport system, redistributing carbon flux toward the reductive TCA pathway, and suppressing succinic-acid-consuming pathways.</p>

<p class="prewrap interaction-description">Coculture changed C. glutamicum transcript profiles, interpreted by the authors as enhanced electron transport, redistribution toward the reductive TCA pathway and suppression of succinic-acid-consuming pathways. This is transcript-based metabolic interpretation, not directly traced carbon or electron flux. The canonical entry includes K1; the abstract does not identify the strain used for every transcript comparison.</p>

<p><strong>Source Taxon:</strong> Shewanella oneidensis</p>

<p><strong>Source Taxon:</strong> Corynebacterium glutamicum (ldhA-deleted strain K1)</p>


<p><strong>Target Taxon:</strong> Corynebacterium glutamicum (ldhA-deleted strain K1)</p>



Expand Down Expand Up @@ -690,7 +690,7 @@ <h3>Reprogrammed Corynebacterium Reductive TCA Flux</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Enhanced Succinic Acid Production
<p class="prewrap causal-description">Redistribution toward the reductive TCA pathway and suppression of succinic-acid-consuming pathways provide the immediate metabolic basis for higher succinic acid yield.</p>
<p class="prewrap causal-description">PARTIAL - the transcript-based interpretation is consistent with metabolic changes contributing to increased succinic acid yield. Positive coculture, riboflavin and ldhA-deletion outcomes support the production strategy, but do not selectively establish this transcript response or inferred flux redistribution as the mediator of each yield comparison.</p>
</div>

</div>
Expand All @@ -706,7 +706,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42203120/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42203120</a>

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

<div class="snippet">"Transcriptomic analysis revealed that co-culture induced global metabolic reprogramming in C. glutamicum, including reinforcement of the electron transport system, redistribution of carbon flux toward the reductive TCA pathway"</div>
Expand All @@ -720,9 +720,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Enhanced Succinic Acid Production</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">The optimized coculture increases succinic acid yield over C. glutamicum monoculture without markedly altering glucose consumption, and the ldhA-deleted K1 strain maintains an enhanced succinic acid yield in the coculture system.</p>
<p class="prewrap interaction-description">The abstract reports an optimized parent-strain coculture yield of 0.169 g/g, 45.65% above monoculture without markedly changing glucose consumption. Separately, ldhA deletion abolished lactate formation in K1; its coculture reached 0.686 g/g and showed up to 23.4% higher yield during extended fermentation than monoculture. These positive interventions do not establish thermodynamic syntrophy or assign the parent-strain result to K1.</p>



Expand Down Expand Up @@ -776,6 +775,25 @@ <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 redox and metabolic changes mediate the strain-specific succinate yield improvements?
</h3>
<p class="prewrap">Only the complete primary abstract was accessible; publisher full-body access returned 403. Direct electron/carbon flux, mediator-specific perturbations and exact strain/condition assignments are needed to resolve the two proposed arrows. Riboflavin is externally supplied, not proven to be secreted by Shewanella. Preserve the positive parent-strain and K1 treatment outcomes without conflating them. Top-level description and donor-role metadata require separate followup #1354.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Riboflavin-Supplemented Coculture Response</code>, <code>ecological_interactions#Corynebacterium Coculture Transcript Response</code>, <code>ecological_interactions#Enhanced Succinic Acid Production</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -940,7 +958,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -957,7 +975,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Riboflavin-Mediated Redox Coupling",
label: "Riboflavin-Supplemented Coculture Response",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -966,23 +984,26 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Shewanella oneidensis";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Corynebacterium glutamicum (ldhA-deleted strain K1)";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Corynebacterium glutamicum (ldhA-deleted strain K1)",

"Shewanella oneidensis"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();

(function() {
var intId = "interaction:1";
var intType = "SYNTROPHY";
var intType = "UNKNOWN";
var metabolites = [];


Expand All @@ -999,7 +1020,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Reprogrammed Corynebacterium Reductive TCA Flux",
label: "Corynebacterium Coculture Transcript Response",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1008,23 +1029,18 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Shewanella oneidensis";
var srcKey = "Corynebacterium glutamicum (ldhA-deleted strain K1)";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}



var tgtKey = "Corynebacterium glutamicum (ldhA-deleted strain K1)";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}

})();

(function() {
var intId = "interaction:2";
var intType = "SYNTROPHY";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down
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