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Review cellobiose biofilm, yeast-cellulose and X514 causal graphs (batch 21) #1339

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realmarcin merged 1 commit into from
Oct 6, 2026
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Review cellobiose biofilm, yeast-cellulose and X514 causal graphs (batch 21) #1339

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125 changes: 56 additions & 69 deletions docs/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.html
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74 changes: 51 additions & 23 deletions docs/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -601,6 +601,11 @@ <h2>Ecological Interactions</h2>
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
</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>

Expand All @@ -610,7 +615,7 @@ <h2>Ecological Interactions</h2>
<h3>Cellulose Hydrolysis Feeds Yeast Fermentation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">C. phytofermentans hydrolyzes alpha-cellulose and releases soluble sugars that can be fermented by S. cerevisiae cdt-1.</p>
<p class="prewrap interaction-description">C. phytofermentans hydrolysis supplies soluble sugars, including cellodextrins and glucose, that support S. cerevisiae cdt-1. Cellulose is the upstream feedstock. The approximately 22 g/L ethanol result used added endoglucanase; unsupplemented coculture did not show the same productivity improvement. Under the low-oxygen ethanol-production regime, ethanol is an output rather than the proposed sugar-transfer currency.</p>


<p><strong>Source Taxon:</strong> Clostridium phytofermentans ISDg</p>
Expand Down Expand Up @@ -662,9 +667,8 @@ <h3>Cellulose Hydrolysis Feeds Yeast Fermentation</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Long-Term Symbiotic Population Maintenance
<p class="prewrap causal-description">C. phytofermentans cellulose hydrolysis supplies soluble sugars that support yeast fermentation during the maintained bacterium-yeast population pairing.
</p>
<span class="flow-arrow">→</span> Oxygen-Dependent Long-Term Population Maintenance
<p class="prewrap causal-description">Bacterial cellulose hydrolysis provides soluble carbon that can sustain yeast in the oxygen-controlled culture. PARTIAL - the long-term viable-count comparison supports this cooperation but does not directly partition carbon transfer or isolate every stabilizing mechanism.</p>
</div>

</div>
Expand Down Expand Up @@ -709,7 +713,7 @@ <h4>Evidence</h4>
<h3>Oxygen Protection of Anaerobic Cellulolytic Partner</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">S. cerevisiae cdt-1 removes introduced oxygen, protecting oxygen-sensitive C. phytofermentans and allowing the coculture to persist under controlled oxygen delivery.</p>
<p class="prewrap interaction-description">The oxygen-removal arm of a condition-dependent mutualism protects oxygen-sensitive C. phytofermentans, while bacterial sugar supply benefits the yeast. Semi-aerobic mono-/coculture comparisons support respiratory protection, and controlled low oxygen delivery supports yeast persistence. This is not a claim that either organism universally requires its partner under other culture conditions.</p>


<p><strong>Source Taxon:</strong> Saccharomyces cerevisiae cdt-1</p>
Expand Down Expand Up @@ -747,9 +751,8 @@ <h3>Oxygen Protection of Anaerobic Cellulolytic Partner</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Long-Term Symbiotic Population Maintenance
<p class="prewrap causal-description">Yeast oxygen removal protects the anaerobic cellulolytic partner under controlled oxygen transfer, allowing both populations to persist in the long-term symbiosis.
</p>
<span class="flow-arrow">→</span> Oxygen-Dependent Long-Term Population Maintenance
<p class="prewrap causal-description">PARTIAL - yeast respiratory protection together with oxygen-supported yeast growth and bacterial sugar supply can stabilize the pairing. Oxygen-positive versus oxygen-negative viable-count controls support the conditional cooperation, without selectively measuring every mediator.</p>
</div>

</div>
Expand Down Expand Up @@ -791,17 +794,20 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Long-Term Symbiotic Population Maintenance</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>Oxygen-Dependent Long-Term Population Maintenance</h3>
</div>
<p class="prewrap interaction-description">Controlled diffusive oxygen transfer supported maintenance of both C. phytofermentans and S. cerevisiae cdt-1 populations for 50 days.</p>
<p class="prewrap interaction-description">With controlled oxygen delivery, both partners remained culturable at the reported 30-, 40- and 50-day samples; without oxygen the yeast fell below detection before day 30. This long-term arm used 25 mL medium and 150 g/L alpha-cellulose. Population maintenance is a community outcome, distinct from the enzyme-assisted ethanol experiment and from an unconditional mutualism claim.</p>


<p><strong>Source Taxon:</strong> Saccharomyces cerevisiae cdt-1</p>


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

<p><strong>Target Taxon:</strong> Clostridium phytofermentans ISDg</p>
Clostridium phytofermentans ISDg,

Saccharomyces cerevisiae cdt-1

</p>



Expand Down Expand Up @@ -847,6 +853,25 @@ <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 oxygen delivery and hydrolytic capacity separately control persistence and ethanol productivity?
</h3>
<p class="prewrap">The oxygen controls support conditional cooperation and viable population maintenance, while additional endoglucanase improves conversion. These are different experimental arms. Mediator-specific or partner-resolved measurements would separate respiratory protection, sugar supply and enzyme effects without inferring universal obligacy or unsupplemented productivity gains.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Cellulose Hydrolysis Feeds Yeast Fermentation</code>, <code>ecological_interactions#Oxygen Protection of Anaerobic Cellulolytic Partner</code>, <code>ecological_interactions#Oxygen-Dependent Long-Term Population Maintenance</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1378,7 +1403,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1391,7 +1416,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Long-Term Symbiotic Population Maintenance",
label: "Oxygen-Dependent Long-Term Population Maintenance",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1400,17 +1425,20 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Saccharomyces cerevisiae cdt-1";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Clostridium phytofermentans ISDg";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Clostridium phytofermentans ISDg",

"Saccharomyces cerevisiae cdt-1"

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

})();

Expand Down
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