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Bound dental and East River causal graphs to measured evidence (batch 35) #1423

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136 changes: 65 additions & 71 deletions docs/communities/Early_Dental_Biofilm_FiveSpecies.html
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Expand Up @@ -654,32 +654,26 @@ <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 Early Dental Biofilm Five-Species Model</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>


<div class="interaction-card">
<div class="interaction-header">
<h3>Actinomyces and S. mitis coaggregation during early biofilm assembly</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
<h3>A. naeslundii and S. mitis Planktonic Coaggregation</h3>
</div>
<p class="prewrap interaction-description">Actinomyces naeslundii AK6 and Streptococcus mitis SK24 formed visible coaggregates in diluted Todd-Hewitt broth within 15 min, indicating a direct cell-cell association that can contribute to mixed-species early dental biofilm assembly.</p>
<p class="prewrap interaction-description">A. naeslundii AK6 and S. mitis SK24 formed visible coaggregates within 15 min in a separate planktonic assay in 1/10 Todd-Hewitt broth. This is direct physical association, not a demonstrated directional benefit, colonization-facilitation effect or cause of acidification in the five-species biofilm. The authors propose an adhesion contribution but did not selectively perturb coaggregation in the pH assay.</p>


<p><strong>Source Taxon:</strong> Actinomyces naeslundii</p>
Expand All @@ -692,28 +686,7 @@ <h3>Actinomyces and S. mitis coaggregation during early biofilm assembly</h3>



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

<li>
biofilm formation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0042710"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0042710</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Five-species glucose acidification of the biofilm interface
<p class="prewrap causal-description">Direct A. naeslundii-S. mitis coaggregation contributes to assembly of the reproducible five-species biofilm that was challenged with glucose for microscale pH imaging.</p>
</div>

</div>



Expand All @@ -739,10 +712,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Actinomyces and S. sanguinis coaggregation during early biofilm assembly</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
<h3>A. naeslundii and S. sanguinis Planktonic Coaggregation</h3>
</div>
<p class="prewrap interaction-description">Actinomyces naeslundii AK6 also coaggregated with Streptococcus sanguinis SK150, forming small suspended aggregates within 2 h and providing a second direct pairwise attachment interaction in the five-member biofilm.</p>
<p class="prewrap interaction-description">A. naeslundii AK6 and S. sanguinis SK150 formed small suspended aggregates within 2 h in the separate planktonic assay, weaker than the A. naeslundii-S. mitis association. The source/target fields identify the measured pair, not a direction of facilitation. This does not establish an attachment route or acidification mechanism in the five-species flow biofilm.</p>


<p><strong>Source Taxon:</strong> Actinomyces naeslundii</p>
Expand All @@ -755,29 +727,8 @@ <h3>Actinomyces and S. sanguinis coaggregation during early biofilm assembly</h3



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

<li>
biofilm formation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0042710"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0042710</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Five-species glucose acidification of the biofilm interface
<p class="prewrap causal-description">Direct A. naeslundii-S. sanguinis coaggregation provides a second attachment route into the five-species biofilm whose glucose metabolism generated stable acidic microenvironments.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -803,12 +754,25 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Five-species glucose acidification of the biofilm interface</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">After the five species were established as a reproducible flow-channel biofilm, glucose addition immediately triggered biofilm acid production and generated stable extracellular pH microenvironments at the biofilm-substrate interface.</p>
<p class="prewrap interaction-description">Sequentially assembled five-species plastic flow-channel biofilms showed extracellular acidification after 0.4% or 10% glucose in sterile saliva, while the no-glucose control remained above pH 7. Spatial pH differences persisted for hours. This is a collective glucose-response endpoint, not demonstrated niche partitioning, metabolite exchange, species-specific acid flux or enamel demineralization. Growth in flowing diluted Todd-Hewitt broth and the later salivary glucose challenge are distinct stages.</p>




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

Streptococcus oralis,

Streptococcus sanguinis,

Streptococcus mitis,

Streptococcus downei,

Actinomyces naeslundii

</p>



Expand Down Expand Up @@ -862,6 +826,25 @@ <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 either pairwise coaggregation mechanism mediate biofilm acidification?
</h3>
<p class="prewrap">Planktonic coaggregation and glucose-responsive biofilm pH were measured in different assays. Neither pair was selectively disrupted or rescued in the biofilm; physical association does not establish colonization benefit or mediation of the pH response. Resolve species-specific acid flux and the origin of persistent pH heterogeneity experimentally. The two workflow-to-outcome arrows are removed. Flow rate, growth feed, substrate and temperature-stage metadata remain under #1420.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#A. naeslundii and S. mitis Planktonic Coaggregation</code>, <code>ecological_interactions#A. naeslundii and S. sanguinis Planktonic Coaggregation</code>, <code>ecological_interactions#Five-species glucose acidification of the biofilm interface</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1122,20 +1105,16 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("biofilm formation");


var evidenceCount = 1;

nodes.push({
id: intId,
label: "Actinomyces and S. mitis coaggregation during early biofilm assembly",
label: "A. naeslundii and S. mitis Planktonic Coaggregation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1160,20 +1139,16 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("biofilm formation");


var evidenceCount = 1;

nodes.push({
id: intId,
label: "Actinomyces and S. sanguinis coaggregation during early biofilm assembly",
label: "A. naeslundii and S. sanguinis Planktonic Coaggregation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1198,7 +1173,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1226,6 +1201,25 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Streptococcus oralis",

"Streptococcus sanguinis",

"Streptococcus mitis",

"Streptococcus downei",

"Actinomyces naeslundii"

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

})();


Expand Down
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