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Bound syntrophic feedback, energetic constraints and ES5 effects (batch112) #1879

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81 changes: 47 additions & 34 deletions docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html
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117 changes: 91 additions & 26 deletions docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html
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146 changes: 68 additions & 78 deletions docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html
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109 changes: 68 additions & 41 deletions docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html
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Original file line number Diff line number Diff line change
Expand Up @@ -572,6 +572,11 @@ <h2>Ecological Interactions</h2>
aria-hidden="true" data-symbol="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
</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 @@ -581,8 +586,7 @@ <h2>Ecological Interactions</h2>
<h3>Butyrate Oxidation and H2 Production</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Syntrophomonas wolfei β-oxidizes butyrate (C4) to acetate, using protons as the electron acceptor and producing H2 as the electron sink product. This fatty acid β-oxidation is thermodynamically unfavorable under standard conditions and only proceeds when H2 partial pressure is kept extremely low by a syntrophic partner. The organism cannot utilize common electron acceptors (nitrate, sulfate, etc.) and is therefore obligately dependent on syntrophic H2 removal.
</p>
<p class="prewrap interaction-description">S. wolfei oxidizes butyrate to acetate with hydrogen as an electron-sink product in the studied syntrophic cultures. Common electron acceptors did not support the tested butyrate metabolism. This is substrate- and assay-bounded dependence on a hydrogen-using partner, not a claim that every substrate requires coculture.</p>


<p><strong>Source Taxon:</strong> Syntrophomonas wolfei</p>
Expand Down Expand Up @@ -654,7 +658,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"The addition of H(2) to the medium stopped growth and butyrate degradation by S"</div>
<div class="snippet">"An anaerobic, nonphototrophic bacterium that beta-oxidizes saturated fatty acids (butyrate through octanoate) to acetate or acetate and propionate using protons as the electron acceptor"</div>

</li>

Expand All @@ -667,7 +671,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"An anaerobic, nonphototrophic bacterium that beta-oxidizes saturated fatty acids (butyrate through octanoate) to acetate or acetate and propionate using protons as the electron acceptor"</div>
<div class="snippet">"Common electron acceptors are not utilized with butyrate as the electron donor"</div>

</li>

Expand All @@ -680,8 +684,7 @@ <h4>Evidence</h4>
<h3>Interspecies Hydrogen Transfer and Methanogenesis</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Methanospirillum hungatei consumes the H2 produced by S. wolfei, combining it with CO2 to produce methane via hydrogenotrophic methanogenesis. This H2 removal maintains a low H2 partial pressure (&lt;10^-4 atm), making the thermodynamically unfavorable butyrate oxidation by S. wolfei energetically feasible. This interspecies hydrogen transfer (IHT) is the classic example of syntrophic metabolism in anaerobic environments.
</p>
<p class="prewrap interaction-description">M. hungatei is a documented hydrogen-using partner of S. wolfei. Hydrogen removal supports bacterial butyrate oxidation and methanogenesis. The abstract reports inhibition of growth and butyrate degradation by added hydrogen, but does not provide an exact permissive partial-pressure threshold or quantify competing carrier contributions.</p>


<p><strong>Source Taxon:</strong> Methanospirillum hungatei</p>
Expand Down Expand Up @@ -724,7 +727,7 @@ <h3>Interspecies Hydrogen Transfer and Methanogenesis</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Butyrate Oxidation and H2 Production
<p class="prewrap causal-description">H2 scavenging by M. hungatei keeps the H2 partial pressure low enough for butyrate β-oxidation to remain thermodynamically feasible; S. wolfei grows and degrades butyrate only in association with an H2-using partner, and adding H2 back to the medium stops both. Reciprocal (feedback) arm of the syntrophic loop.</p>
<p class="prewrap causal-description">DIRECTLY IMPLIED feedback: removal of hydrogen by the methanogenic partner relieves a constraint on S. wolfei butyrate oxidation. The 1981 abstract reports that added hydrogen stops growth and butyrate degradation; it does not specify a numerical permissive threshold or isolate hydrogen from all alternative carrier routes in this exact pairing.</p>
</div>

<div class="flow-item">
Expand All @@ -749,7 +752,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Growth and degradation of fatty acids occur only in syntrophic association with H(2)-using bacteria"</div>
<div class="snippet">"cocultures of S. wolfei with Desulfovibrio and Methanospirillum hungatei"</div>

</li>

Expand All @@ -762,33 +765,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"The addition of H(2) to the medium stopped growth and butyrate degradation by S"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/16345745/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:16345745</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Common electron acceptors are not utilized with butyrate as the electron donor"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/16345745/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:16345745</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Common electron acceptors are not utilized with butyrate as the electron donor"</div>
<div class="snippet">"The addition of H(2) to the medium stopped growth and butyrate degradation by S. wolfei."</div>

</li>

Expand All @@ -799,10 +776,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Syntrophic Butyrate-to-Methane Conversion</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">S. wolfei oxidizes butyrate only when a hydrogen-consuming partner such as M. hungatei removes the produced H2, coupling fatty-acid beta-oxidation to hydrogenotrophic methanogenesis in the two-member consortium.
</p>
<p class="prewrap interaction-description">S. wolfei butyrate oxidation is coupled to hydrogen-consuming M. hungatei methanogenesis in the documented coculture. This is a community conversion endpoint, not an additional pairwise exchange; acetate is retained as an organic product.</p>



Expand Down Expand Up @@ -859,6 +834,19 @@ <h3>Syntrophic Butyrate-to-Methane Conversion</h3>
<h4>Evidence</h4>
<ul class="evidence-list">

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

<a href="https://pubmed.ncbi.nlm.nih.gov/16345745/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:16345745</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"cocultures of S. wolfei with Desulfovibrio and Methanospirillum hungatei"</div>

</li>

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

Expand All @@ -881,6 +869,45 @@ <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>
What quantitative carrier constraints apply to this exact butyrate coculture?
</h3>
<p class="prewrap">The accessible primary abstract supports the named partner and hydrogen-addition inhibition, but not the former less-than-10^-4-atm threshold. The existing feedback remains directly implied; no carrier-exclusive mechanism or universal obligacy is asserted. The older full-text XML endpoint failed, so detailed perturbation conditions remain unverified here.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Butyrate Oxidation and H2 Production</code>, <code>ecological_interactions#Interspecies Hydrogen Transfer and Methanogenesis</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/16345745/" rel="nofollow noreferrer">PMID:16345745</a>


</div>
<p class="snippet small prewrap">The addition of H(2) to the medium stopped growth and butyrate degradation by S. wolfei.</p>
<p class="muted small prewrap">The reported hydrogen perturbation supports product-inhibition feedback; the abstract does not specify every assay condition or a numerical threshold.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1547,7 +1574,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("methanogenesis");


var evidenceCount = 4;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1576,7 +1603,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1595,7 +1622,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("methanogenesis");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
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