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Bound soy community graphs and record unresolved sfSynCom identity (batch104) #1822

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152 changes: 41 additions & 111 deletions docs/communities/Soy_Sauce_Temporal_SevenSpecies_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -856,17 +856,12 @@ <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 Soy Sauce Temporal Seven-Species SynCom</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).</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="symbolTriangle2"
Expand All @@ -878,81 +873,9 @@ <h2>Ecological Interactions</h2>

<div class="interaction-card">
<div class="interaction-header">
<h3>Four-phase temporal soy sauce inoculation</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The final seven-species community was assembled by separating dominant LAB, other LAB, and yeasts across the immediate-early, early/middle, and late moromi phases while A. oryzae made the koji substrate.</p>








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

<li>
fermentation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006113"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006113</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> W-&gt;L-&gt;P+T-&gt;Z+C soy-sauce flavor output
<p class="prewrap causal-description">The four-stage ordering led to the W-&gt;L-&gt;P+T-&gt;Z+C group that outperformed other temporal LAB orderings in the 40-day assay.</p>
</div>

</div>



<h4>Evidence</h4>
<ul class="evidence-list">

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42195939/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42195939</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Based on the identified core microbes, soy sauce fermentation conducted with different synthetic communities was performed to optimize the assembly of SynCom."</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42195939/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42195939</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"W → L → P+T → Z+C +W. paramesenteroides +L. plantarum +P. pentosaceus +T. halophilus"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>W-&gt;L-&gt;P+T-&gt;Z+C soy-sauce flavor output</h3>
<h3>Laboratory Soy-Sauce Flavor Outcomes</h3>
</div>
<p class="prewrap interaction-description">The W-&gt;L-&gt;P+T-&gt;Z+C SynCom increased 40-day glutamic acid, 4-ethylguaiacol, and total volatile output relative to the traditional fermentation control and had higher alcohol, ester, and phenolic compound levels than the other tested SynComs.</p>
<p class="prewrap interaction-description">The selected seven-species treatment had higher reported glutamic acid, 4-ethylguaiacol and total volatile endpoints than the traditional control in the laboratory comparison, with higher alcohol, ester and phenolic levels than the other tested SynCom treatments. These are measured fermentation outcomes, not proof of reduced competition, a universally optimal community or industrial efficacy. The source&#39;s ambiguous fold-change wording is not reinterpreted here.</p>



Expand Down Expand Up @@ -1040,7 +963,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -1077,6 +1000,41 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which ecological mechanisms account for the laboratory flavor differences, and do they transfer beyond the tested setting?
</h3>
<p class="prewrap">Temporal scheduling and endpoint differences do not by themselves demonstrate niche partitioning or identify a donor-recipient mechanism. The original workflow node and its arrow are removed; measured outcomes remain. The primary conclusion explicitly limits the study to laboratory proof-of-concept. No cultivation or optimization instructions are added. Non-graph abundance/timing metadata remains outside this repair under #1821.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Laboratory Soy-Sauce Flavor Outcomes</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">OTHER</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42195939/" rel="nofollow noreferrer">PMID:42195939</a>


</div>
<p class="snippet small prewrap">Thus, our results should be considered a laboratory-scale proof-of-concept, and pilot-scale validation is required before practical application.</p>
<p class="muted small prewrap">The authors explicitly limit practical transfer of the measured outcomes.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down Expand Up @@ -1422,34 +1380,6 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("fermentation");


var evidenceCount = 2;

nodes.push({
id: intId,
label: "Four-phase temporal soy sauce inoculation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
processes: processes,
evidenceCount: evidenceCount
});




})();

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

Expand All @@ -1469,7 +1399,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "W-\u003eL-\u003eP+T-\u003eZ+C soy-sauce flavor output",
label: "Laboratory Soy-Sauce Flavor Outcomes",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down Expand Up @@ -1501,7 +1431,7 @@ <h4 style="color: var(--text);">Evidence</h4>
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
var nodeCount = 9;
var nodeCount = 8;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);

Expand Down
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