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Review JN4-GD17, staged butanol and wetland causal graphs (batch 22) #1346

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realmarcin merged 1 commit into from
Oct 6, 2026
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Review JN4-GD17, staged butanol and wetland causal graphs (batch 22) #1346

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94 changes: 55 additions & 39 deletions .../communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.html
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Expand Up @@ -563,39 +563,37 @@ <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 Clostridium-Thermoanaerobacterium JN4-GD17 Cellulosic Biofuel Coculture</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 (cross-feeding, competition).</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="symbolDiamond"
data-color="#57c7ab"></svg> Cross-feeding
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTimes"
data-color="#a91919"></svg> Competition
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Cellulosic Biofuel Efficiency Enhancement</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>Enhanced Community Fermentation Products</h3>
</div>
<p class="prewrap interaction-description">Coculturing C. thermocellum JN4 with T. thermosaccharolyticum GD17 improves overall cellulosic biofuel production efficiency.</p>
<p class="prewrap interaction-description">The JN4-GD17 coculture produced more lactate, acetate and ethanol than JN4 alone in the reported cellulose experiments, without improved overall cellulose utilization. This is a community product outcome, not cellulose donation. Cellulose is the feedstock; soluble glucose and cellobiose are the proposed exchanged carbon.</p>


<p><strong>Source Taxon:</strong> Clostridium thermocellum JN4</p>


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

<p><strong>Target Taxon:</strong> Thermoanaerobacterium thermosaccharolyticum GD17</p>
Clostridium thermocellum JN4,

Thermoanaerobacterium thermosaccharolyticum GD17

</p>



Expand Down Expand Up @@ -653,9 +651,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>GD17 Competitive Conversion of Released Sugars</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">T. thermosaccharolyticum GD17 has a competitive metabolic advantage over C. thermocellum JN4 in converting glucose or cellobiose into final fermentation products.</p>
<p class="prewrap interaction-description">GD17 consumed glucose and cellobiose and produced fermentation products faster than JN4 in separate monoculture assays. Low soluble sugars and altered cellulolytic-gene transcription in coculture support a resource-competition model. PARTIAL - these measurements do not directly partition partner carbon flux or establish reciprocal harm required by the COMPETITION enum.</p>


<p><strong>Source Taxon:</strong> Thermoanaerobacterium thermosaccharolyticum GD17</p>
Expand Down Expand Up @@ -697,9 +694,8 @@ <h3>GD17 Competitive Conversion of Released Sugars</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Cellulosic Biofuel Efficiency Enhancement
<p class="prewrap causal-description">GD17 capture and conversion of cellobiose or glucose released from lignocellulose accounts for the increased formation of fermentation end products in the cellulosic biofuel coculture.
</p>
<span class="flow-arrow">→</span> Enhanced Community Fermentation Products
<p class="prewrap causal-description">PARTIAL - faster GD17 conversion of JN4-released soluble sugars can contribute to higher community fermentation output. Monoculture conversion assays and coculture product measurements support this model, but do not directly measure the partner-specific contribution.</p>
</div>

</div>
Expand All @@ -715,7 +711,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31551972/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31551972</a>

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

<div class="snippet">"strong competitive metabolic advantage of T. thermosaccharolyticum GD17 over C. thermocellum JN4"</div>
Expand All @@ -742,9 +738,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>GD17 Growth Inhibition of JN4</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Despite relieving carbon catabolite repression, T. thermosaccharolyticum GD17 hampers C. thermocellum JN4 growth in coculture.</p>
<p class="prewrap interaction-description">JN4 biomass estimated from total protein and genomic community proportions was lower in coculture; this is not a direct viable-cell count. Dextrin or sucrose addition favored GD17 and largely stopped cellulose use. PARTIAL - the positive perturbation supports community rebalancing, but also adds carbon and changes sampling time, so it does not selectively isolate growth suppression or prove reciprocal harm.</p>


<p><strong>Source Taxon:</strong> Thermoanaerobacterium thermosaccharolyticum GD17</p>
Expand Down Expand Up @@ -774,9 +769,8 @@ <h3>GD17 Growth Inhibition of JN4</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Cellulosic Biofuel Efficiency Enhancement
<p class="prewrap causal-description">GD17-driven suppression of the cellulolytic JN4 population can rebalance the coculture away from cellulose degradation, making that competition a negative regulator of net cellulosic biofuel formation.
</p>
<span class="flow-arrow">→</span> Enhanced Community Fermentation Products
<p class="prewrap causal-description">PARTIAL - reduced JN4 biomass and cellulose use can constrain the cellulose-derived contribution to community products. Stimulant-driven rebalancing supports this possibility, not a measured reduction of total fermentation products or a resolved carbon balance when extra substrate is supplied.</p>
</div>

</div>
Expand All @@ -792,7 +786,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31551972/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31551972</a>

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

<div class="snippet">"T. thermosaccharolyticum GD17 significantly hampers the growth of C. thermocellum JN4"</div>
Expand All @@ -805,7 +799,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31551972/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31551972</a>

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

<div class="snippet">"relieves the carbon catabolite repression of C. thermocellum JN4"</div>
Expand All @@ -818,7 +812,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31551972/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31551972</a>

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

<div class="snippet">"re-balanced cocultures largely stopped degrading cellulose"</div>
Expand All @@ -834,6 +828,25 @@ <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>
How do GD17 sugar conversion and JN4 suppression separately determine cellulose-derived product flux?
</h3>
<p class="prewrap">Monoculture rates, coculture products, sugar concentrations and transcription support the proposed model. Protein-based biomass estimates and added-substrate rebalancing are not selective viable-growth or flux measurements. Partner-resolved carbon tracing and matched-carbon perturbations would distinguish conversion benefit from suppression without assuming reciprocal harm.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Enhanced Community Fermentation Products</code>, <code>ecological_interactions#GD17 Competitive Conversion of Released Sugars</code>, <code>ecological_interactions#GD17 Growth Inhibition of JN4</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1250,7 +1263,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1269,7 +1282,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Cellulosic Biofuel Efficiency Enhancement",
label: "Enhanced Community Fermentation Products",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1278,23 +1291,26 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Clostridium thermocellum JN4";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Thermoanaerobacterium thermosaccharolyticum GD17";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Clostridium thermocellum JN4",

"Thermoanaerobacterium thermosaccharolyticum GD17"

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

})();

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


Expand Down Expand Up @@ -1338,7 +1354,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down
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