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Qualify KZ and kombucha claims and record research gaps (batch60) #1544

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76 changes: 55 additions & 21 deletions docs/communities/Klebsiella_Arthrobacter_KZ_Phenanthrene_Cadmium_SynCom.html
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Expand Up @@ -602,34 +602,37 @@ <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 Klebsiella-Arthrobacter KZ Phenanthrene-Cadmium 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
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>SZ-3 to CW-D3T phenanthrene-mineralization division of labor</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Assay-Inferred Phenanthrene Catabolic Division Of Labor</h3>
</div>
<p class="prewrap interaction-description">Arthrobacter sp. SZ-3 supplied stronger upstream catalytic activity, measured as 50% higher 2H1N conversion, whereas Klebsiella sp. CW-D3T dominated downstream mineralization with more than 80% contribution in the biomass-normalized enzyme activity assays.</p>
<p class="prewrap interaction-description">Under 25 mg/L cadmium stress, the KZ pair showed better phenanthrene degradation and mineralization than the monocultures. Biomass-normalized enzyme assays assign stronger upstream 2H1N conversion to Arthrobacter sp. SZ-3 and a dominant downstream mineralization contribution to Klebsiella sp. CW-D3T. PARTIAL - these complementary activities support a division-of-labor model, not a resolved donor-to-recipient transfer or necessary mediation. The linked corrigendum and complete assay Methods remain unverified.</p>


<p><strong>Source Taxon:</strong> Arthrobacter sp. SZ-3</p>


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

<p><strong>Target Taxon:</strong> Klebsiella sp. CW-D3T</p>
Klebsiella sp. CW-D3T,

Arthrobacter sp. SZ-3

</p>



Expand All @@ -656,13 +659,26 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41365368/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41365368</a>

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

<div class="snippet">"Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (&gt;80 % contribution)."</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41365368/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41365368</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd2+), outperforming monocultures by 1.2-1.9-fold."</div>

</li>

</ul>

</div>
Expand All @@ -673,7 +689,7 @@ <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 All @@ -688,6 +704,21 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
What does the corrigendum change, and which transfers mediate KZ performance?
</h3>
<p class="prewrap">The complete abstract and public publisher preview support positive KZ outcomes and assay-inferred upstream/downstream roles. Full enzyme Methods, supplements and tracer or selective perturbation evidence were not read. PMID:41456976 / doi:10.1016/j.biortech.2025.133853 is a linked corrigendum; the official publisher API supplied metadata only, not its body. Do not assume the correction is biologically immaterial or infer expression from metagenomic gene content. #1541 tracks unresolved verification. Keep this record needs_research after the bounded #1540 repair. Existing medium/inoculation questions remain open; routine LB/MSM mentioned in the preview is not a verified co-contamination assay recipe.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Assay-Inferred Phenanthrene Catabolic Division Of Labor</code></p>




</div>

</section>
Expand Down Expand Up @@ -934,7 +965,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -943,11 +974,11 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "SZ-3 to CW-D3T phenanthrene-mineralization division of labor",
label: "Assay-Inferred Phenanthrene Catabolic Division Of Labor",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -956,17 +987,20 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Arthrobacter sp. SZ-3";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Klebsiella sp. CW-D3T";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Klebsiella sp. CW-D3T",

"Arthrobacter sp. SZ-3"

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

})();

Expand Down
17 changes: 16 additions & 1 deletion docs/communities/Komagataella_Ecoli_Coinducible_Biosynthesis_Coculture.html
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Expand Up @@ -549,7 +549,7 @@ <h2>Ecological Interactions</h2>
<!-- 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 All @@ -564,6 +564,21 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which strain-resolved relays and induction responses support a causal biosynthesis graph?
</h3>
<p class="prewrap">The abstract and public publisher Introduction/section previews report compatible co-growth, common-signal induction and relayed simvastatin/naringenin production. A design without engineered population-balancing interactions does not prove biological neutralism; sharing an induction signal is not metabolite cross-feeding. Monacolin J acid and an acyl donor are discussed, but exact chassis/construct assignments, transfer controls and full Methods remain unresolved. #1542 tracks the empty graph as needs_research, not absent biology. A reviewed one-community LITERATURE dry run contains 7,457 characters; zero provider submissions or credits. Specifically authorized research and primary verification are needed before adding new nodes/arrows. Preserve the existing intermediate-assignment discussion and canonical species IDs.</p>

<p class="muted small">Attaches to: <code>ecological_interactions</code>, <code>engineering_design</code></p>




</div>

</section>
Expand Down
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