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Bound LBNL plant gut and soil graph claims (batch61) #1549

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316 changes: 137 additions & 179 deletions docs/communities/LBNL_Brachypodium_Drought_SynCom15.html
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151 changes: 89 additions & 62 deletions docs/communities/LBNL_Human_Gut_Interaction_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -516,45 +516,37 @@ <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 LBNL Human Gut Interaction 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 (cross-feeding, 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="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="symbolSquare2"
data-color="#1212ed"></svg> Niche partitioning
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Pairwise Interaction-Dominated Community Dynamics</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>Pairwise Model Prediction Of Community Dynamics</h3>
</div>
<p class="prewrap interaction-description">Time-resolved measurements of lower-order assemblages showed that pairwise interactions, rather than higher-order interactions, are major drivers of the synthetic gut community dynamics.</p>
<p class="prewrap interaction-description">A generalized Lotka-Volterra model trained on monospecies and pairwise time series predicted much of the tested 11- and 12-member community dynamics; additional full-community training improved predictions. PARTIAL - model success supports important pairwise effects in these conditions, not absence of higher-order effects, perfect prediction or universal acetate cross-feeding. Abundance inputs combined 16S proportions with OD600, not direct viable-cell counts.</p>




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

human gut bacterial SynCom members

<p><strong>Metabolites:</strong>
</p>

acetate
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30089"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30089</a>)

</p>



Expand All @@ -571,16 +563,6 @@ <h3>Pairwise Interaction-Dominated Community Dynamics</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Positive-Negative Ecological Network Topology
<p class="prewrap causal-description">Pairwise inference resolved both negative and positive interactions that together define the ecological network topology of the synthetic gut community.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -605,23 +587,10 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/29930200/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:29930200</a>

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

<div class="snippet">"pairwise interactions are major drivers of multi-species community dynamics"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/29930200/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:29930200</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"cross‐feeding of metabolic by‐products such as acetate in the gut microbiota is a prevalent mechanism that could alter environmental pH"</div>
<div class="snippet">"pairwise interactions are major drivers of multi‐species community dynamics"</div>

</li>

Expand All @@ -631,13 +600,18 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Positive-Negative Ecological Network Topology</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Inferred Positive-Negative Ecological Network Topology</h3>
</div>
<p class="prewrap interaction-description">The inferred human-gut SynCom network contains many negative interactions and frequent positive interactions that form the interaction topology of the community.</p>
<p class="prewrap interaction-description">The fitted 12-species gut network contains frequent negative and positive interaction coefficients, including coupled positive/negative pairwise motifs. These are effective ecological effects inferred from abundance dynamics. Their signs do not uniquely identify nutrient competition, cross-feeding, niche partitioning or molecular mechanisms; conditioned-medium and metabolomics results provide complementary but imperfect support.</p>




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

human gut bacterial SynCom members

</p>



Expand All @@ -660,8 +634,8 @@ <h3>Positive-Negative Ecological Network Topology</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Robust Coexistence Feedback
<p class="prewrap causal-description">The mixed positive and negative topology enables feedback that balances differences in monospecies fitness and supports robust coexistence.</p>
<span class="flow-arrow">→</span> Modeled Pairwise Coexistence Feedback
<p class="prewrap causal-description">PARTIAL - in the fitted pairwise gLV models, coupled positive and negative effects create negative feedback that limits the higher-fitness partner and permits coexistence with the lower-fitness partner across a broader tested growth-rate range than mutual inhibition. This preserves the source-supported model mechanism, not proof of a universal or molecularly resolved feedback in the entire gut community.</p>
</div>

</div>
Expand All @@ -677,7 +651,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/29930200/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:29930200</a>

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

<div class="snippet">"The inferred ecological network exhibits a high proportion of negative and frequent positive interactions."</div>
Expand All @@ -690,14 +664,19 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Robust Coexistence Feedback</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Modeled Pairwise Coexistence Feedback</h3>
</div>
<p class="prewrap interaction-description">Positive and negative interactions implement a stabilizing negative feedback loop that balances monospecies fitness differences and enables robust coexistence.</p>
<p class="prewrap interaction-description">Within the inferred pairwise gLV models, a positive/negative motif implements negative feedback that balances monospecies fitness differences and supports coexistence over a broader tested parameter range than mutual inhibition. The CH-ER pair provides an experimentally coexisting example. PARTIAL - the mathematical mechanism is model-bounded; neither its molecular mediator nor universal stability of the full 12-member system follows from this analysis.</p>




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

human gut bacterial SynCom members

</p>




Expand Down Expand Up @@ -726,7 +705,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/29930200/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:29930200</a>

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

<div class="snippet">"positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop"</div>
Expand All @@ -742,6 +721,25 @@ <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>
Which molecular mechanisms realize the inferred signed interactions and feedback?
</h3>
<p class="prewrap">Remove the analytical inference-to-topology arrow, but retain topology-to-coexistence as a model-bounded causal mechanism. Acetate in the cited passage is a prior-literature example; separate metabolomics cultures supplemented ER and FP with acetate, which does not prove cross-feeding throughout this graph. Co-consumption/secretion only yields an ecological effect when relevant substrates limit growth, and conditioned-medium signs do not always match inferred coefficients. Higher-order effects, parameter uncertainty and OD-scaled abundance remain limitations. Canonical NCBITaxon:2 is only an aggregate placeholder for the 12-species experimental roster; #1548 tracks its grounding and non-graph metadata. No original figure pixels, separate supplements, raw data or executable model reproduction was performed.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Pairwise Model Prediction Of Community Dynamics</code>, <code>ecological_interactions#Inferred Positive-Negative Ecological Network Topology</code>, <code>ecological_interactions#Modeled Pairwise Coexistence Feedback</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -948,24 +946,20 @@ <h4 style="color: var(--text);">Evidence</h4>

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


metabolites.push("acetate");


var processes = [];


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


var evidenceCount = 3;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "Pairwise Interaction-Dominated Community Dynamics",
label: "Pairwise Model Prediction Of Community Dynamics",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -976,11 +970,22 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"human gut bacterial SynCom members"

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

})();

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

var processes = [];
Expand All @@ -993,7 +998,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Positive-Negative Ecological Network Topology",
label: "Inferred Positive-Negative Ecological Network Topology",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1004,11 +1009,22 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"human gut bacterial SynCom members"

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

})();

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

var processes = [];
Expand All @@ -1021,7 +1037,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Robust Coexistence Feedback",
label: "Modeled Pairwise Coexistence Feedback",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1032,6 +1048,17 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"human gut bacterial SynCom members"

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

})();


Expand Down
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