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Review three syngas and minimal-medium coculture causal graphs #1323

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66 changes: 54 additions & 12 deletions docs/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -592,6 +592,11 @@ <h2>Ecological Interactions</h2>
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="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>

Expand All @@ -601,7 +606,7 @@ <h2>Ecological Interactions</h2>
<h3>Acetogenic CO and Syngas Fermentation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">C. autoethanogenum converts CO or syngas into acetate and ethanol, producing the substrates that support chain elongation by C. kluyveri.</p>
<p class="prewrap interaction-description">C. autoethanogenum converts CO or syngas to acetate and ethanol that support C. kluyveri chain elongation. Product profiles and pure-culture comparisons support this cross-feeding model. In the 2019 chemostat study, partner ethanol production and electron allocation in coculture were reverse-calculated from measured chain-elongated products and assumed stoichiometry, not directly measured partner-specific fluxes.</p>


<p><strong>Source Taxon:</strong> Clostridium autoethanogenum</p>
Expand Down Expand Up @@ -698,13 +703,15 @@ <h4>Evidence</h4>
<h3>Ethanol-Driven Chain Elongation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">C. kluyveri consumes ethanol and acetate produced by C. autoethanogenum, enabling formation of butyrate, caproate, butanol, and hexanol from CO or syngas.</p>
<p class="prewrap interaction-description">C. kluyveri uses ethanol and acetate for chain elongation to butyrate and caproate, which can supply C. autoethanogenum for reduction to butanol and hexanol. The 2016 study demonstrated acid formation by C. kluyveri and higher-alcohol formation by acid-supplemented C. autoethanogenum pure cultures. Higher alcohols are therefore coculture products, not products assigned to C. kluyveri alone; this attribution is bounded to the tested conditions.</p>


<p><strong>Source Taxon:</strong> Clostridium kluyveri</p>



<p><strong>Target Taxon:</strong> Clostridium autoethanogenum</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -788,10 +795,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Thermodynamic Ethanol Pull by C. kluyveri</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>Proposed thermodynamic ethanol pull by C. kluyveri</h3>
</div>
<p class="prewrap interaction-description">C. kluyveri removal of ethanol during co-cultivation shifts C. autoethanogenum metabolism toward solventogenesis, improving the electron flow into chain-elongated products.</p>
<p class="prewrap interaction-description">HYPOTHESIZED - ethanol consumption by C. kluyveri lowers its extracellular concentration and thermodynamically favors further ethanol formation by C. autoethanogenum. Chemostat products, reverse-calculated ethanol flux, hydrogen and acetate additions, and the absence of a major uniform central-metabolism transcript response support this interpretation. They do not exclude protein abundance or post-translational regulation. This node represents a proposed feedback effect of product removal, not ethanol donation from C. kluyveri to the acetogen.</p>


<p><strong>Source Taxon:</strong> Clostridium kluyveri</p>
Expand Down Expand Up @@ -830,8 +836,7 @@ <h3>Thermodynamic Ethanol Pull by C. kluyveri</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Acetogenic CO and Syngas Fermentation
<p class="prewrap causal-description">Continuous ethanol removal by C. kluyveri pulls C. autoethanogenum metabolism toward solventogenesis and improves electron flow from CO or syngas into chain-elongated products.
</p>
<p class="prewrap causal-description">HYPOTHESIZED - C. kluyveri consumption keeps ethanol low and could favor C. autoethanogenum solventogenesis, supplying further ethanol for chain elongation. Stoichiometric flux estimates and perturbations support this feedback model, but do not uniquely establish thermodynamics as its mediator.</p>
</div>

</div>
Expand All @@ -847,7 +852,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31792266/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31792266</a>

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

<div class="snippet">"shifted its metabolism significantly towards solventogenesis"</div>
Expand All @@ -860,13 +865,26 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31792266/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31792266</a>

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

<div class="snippet">"continuous removal of ethanol by C. kluyveri"</div>

</li>

<li class="evidence-item">
<div>

<a href="https://pubmed.ncbi.nlm.nih.gov/31792266/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31792266</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"protein levels or post-translational modifications cannot be ruled out"</div>

</li>

</ul>

</div>
Expand All @@ -876,6 +894,25 @@ <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>
Does ethanol removal directly mediate the solventogenic shift independently of protein-level regulation?
</h3>
<p class="prewrap">PMID:31792266 combines measured product pools, stoichiometric reverse-calculation, transcriptomics and hydrogen/acetate perturbations. The thermodynamic explanation is supported but not exclusive. Selective ethanol-removal perturbations with partner-resolved flux and protein-level measurements would distinguish it from alternative regulation. PMID:33240469 remains computational support, not a new experimentally demonstrated interaction.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Acetogenic CO and Syngas Fermentation</code>, <code>ecological_interactions#Ethanol-Driven Chain Elongation</code>, <code>ecological_interactions#Proposed thermodynamic ethanol pull by C. kluyveri</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1403,11 +1440,16 @@ <h4 style="color: var(--text);">Evidence</h4>



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

})();

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


Expand All @@ -1420,11 +1462,11 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("fermentation");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
label: "Thermodynamic Ethanol Pull by C. kluyveri",
label: "Proposed thermodynamic ethanol pull by C. kluyveri",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
101 changes: 31 additions & 70 deletions docs/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -585,21 +585,16 @@ <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-Caldicellulosiruptor Minimal Medium 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 (niche partitioning, colonization facilitation).</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="symbolSquare2"
data-color="#1212ed"></svg> Niche partitioning
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -608,10 +603,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Reduced-Nutrient Defined Cellulose-Xylan Medium</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">Nitrogen, sulfur, phosphate, and vitamin loads were reduced into a low-ionic-strength defined minimal medium that supported cellobiose, cellulose, acid-pretreated Populus, and the cellulose/xylan coculture condition used to maintain both thermophilic cellulolytic bacteria.
</p>
<p class="prewrap interaction-description">A low-ionic-strength defined medium with reduced nitrogen, sulfur, phosphate and vitamin supplements was developed after nutrient-response experiments. The primary abstract reports cellobiose, cellulose and acid-pretreated Populus fermentation and separately reports coculture maintenance on cellulose/xylan substrates. These statements do not establish that every substrate or nutrient-response experiment used the coculture. Medium development is cultivation context, not demonstrated partner-to-partner colonization facilitation.</p>



Expand Down Expand Up @@ -644,29 +637,7 @@ <h3>Reduced-Nutrient Defined Cellulose-Xylan Medium</h3>



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

<li>
cellulose catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0030245"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0030245</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Stable Co-Maintenance On Cellulose And Xylan
<p class="prewrap causal-description">The reduced defined medium was the chemical setting in which the C. thermocellum and C. bescii populations were maintained together.
</p>
</div>

</div>



Expand Down Expand Up @@ -706,10 +677,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Stable Co-Maintenance On Cellulose And Xylan</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
<h3>Observed Co-Maintenance On Cellulose And Xylan</h3>
</div>
<p class="prewrap interaction-description">The two bacterial populations were maintained together in the defined medium when the coculture was supplied with cellulose and xylan, showing compatible coexistence under mixed-polysaccharide conditions.</p>
<p class="prewrap interaction-description">Both populations were reported to be maintained in cocultures on substrates containing cellulose and xylan in defined medium with sulfate and basal vitamins. This is an observed co-maintenance endpoint. The accessible exact-system abstract does not resolve the duration, population trajectories or perturbations needed to establish long-term stability, reciprocal benefit, colonization facilitation or a unique maintenance mechanism.</p>



Expand Down Expand Up @@ -738,23 +708,6 @@ <h3>Stable Co-Maintenance On Cellulose And Xylan</h3>



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

<li>
biological process involved in interspecies interaction between organisms
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
</li>

<li>
cellulose catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0030245"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0030245</a>)
</li>

</ul>




Expand Down Expand Up @@ -795,9 +748,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Thermophilic Plant-Polysaccharide Conversion Capacity</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">C. thermocellum provides cellulolytic growth on crystalline cellulose, while C. bescii DSM 6725 has genome-supported capacity to use multiple plant polysaccharides, including cellulose- and xylan-associated responses that make it relevant to mixed lignocellulose substrates.</p>
<p class="prewrap interaction-description">Separate member-level evidence supports plant-polysaccharide conversion: C. thermocellum was grown on crystalline cellulose in the nutrient study, and C. bescii DSM 6725 was studied by genome analysis plus experimental transcriptomics and proteomics on polysaccharide substrates. Cellulose-responsive expression and cellulose/xylan-associated proteins are measured results, while functions of some hypothetical proteins remain inferred. These member assays do not demonstrate niche partitioning, interspecies substrate transfer or mediation of coculture maintenance.</p>



Expand Down Expand Up @@ -869,7 +821,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/21227922/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:21227922</a>

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

<div class="snippet">"overproduced on cellulose or xylan"</div>
Expand Down Expand Up @@ -932,6 +884,25 @@ <h2>Associated Datasets</h2>
</div>
</section>

<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 exact-system population measurements and nutrient or substrate perturbations explain co-maintenance?
</h3>
<p class="prewrap">PMID:23306120 is abstract-bounded in this review; its full body was not obtained through the attempted public routes. The abstract reports maintenance, not its duration or an isolated ecological mechanism. PMID:21227922 contains empirical C. bescii molecular responses as well as genomic inference, but does not test this coculture. Full-method access and partner-resolved time courses are needed before claiming nutrient-reduction causality, stability or niche partitioning. The earlier removed capacity-to-maintenance arrow remains absent.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Reduced-Nutrient Defined Cellulose-Xylan Medium</code>, <code>ecological_interactions#Observed Co-Maintenance On Cellulose And Xylan</code>, <code>ecological_interactions#Thermophilic Plant-Polysaccharide Conversion Capacity</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1401,7 +1372,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1414,10 +1385,6 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("cellulose catabolic process");


var evidenceCount = 2;

nodes.push({
Expand Down Expand Up @@ -1450,7 +1417,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1461,17 +1428,11 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("biological process involved in interspecies interaction between organisms");

processes.push("cellulose catabolic process");


var evidenceCount = 2;

nodes.push({
id: intId,
label: "Stable Co-Maintenance On Cellulose And Xylan",
label: "Observed Co-Maintenance On Cellulose And Xylan",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down Expand Up @@ -1499,7 +1460,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down
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