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Bound denitrification and pine graph claims; document sparse graphs (batch85) #1710

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259 changes: 54 additions & 205 deletions docs/communities/Phylogenetically_Diverse_Denitrifying_SynCom.html
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52 changes: 51 additions & 1 deletion docs/communities/Pichia_Lactiplantibacillus_CCMA_Plant_Beverage_Coculture.html
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Expand Up @@ -571,7 +571,7 @@ <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 @@ -586,6 +586,56 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which source-supported fermentation and host-response nodes belong in this currently absent graph?
</h3>
<p class="prewrap">Preserve the observed 24 h viable counts (9.32 and 7.05 log CFU/mL), carbohydrate utilization, acidification, increased bioactive compounds and simulated-digestion bioaccessibility. The fermented whole beverage promoted microbial recovery in vancomycin-treated BALB/c mice. These positives do not establish partner-resolved cross-feeding, reciprocal fitness, intestinal colonization, mediation by a specific compound, or benefit in humans. Primary access is abstract-only. New graph structure remains #1707; a one-community Edison dry run is not a reviewed paid report. No node or arrow is added in this discussion-only review.</p>

<p class="muted small">Attaches to: <code>engineering_design</code>, <code>growth_media#Oat-almond-sunflower plant-based beverage</code></p>



<details class="evidence-list">
<summary class="muted small">2 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/42637394/" rel="nofollow noreferrer">PMID:42637394</a>


</div>
<p class="snippet small prewrap">The process facilitated carbohydrate utilization, acidification, and the generation of bioactive metabolites.</p>
<p class="muted small prewrap">Supports fermentation-associated substrate use, acidification, and metabolite production by the defined co-culture.</p>
</div>

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



<a href="https://pubmed.ncbi.nlm.nih.gov/42637394/" rel="nofollow noreferrer">PMID:42637394</a>


</div>
<p class="snippet small prewrap">Administration of the fermented beverage promoted microbial recovery</p>
<p class="muted small prewrap">Supports testing the fermented co-culture beverage in a host dysbiosis recovery assay.</p>
</div>

</details>


</div>

</section>
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54 changes: 54 additions & 0 deletions docs/communities/Picocystis_Activated_Sludge_Refinery_SWW_Consortium.html
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Expand Up @@ -585,6 +585,60 @@ <h2>Ecological Interactions</h2>

<!-- 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 treatment-specific removal and biomass phenotypes can be represented without inventing exchange mechanisms?
</h3>
<p class="prewrap">Pico-Bac achieved 72% COD and 96.4% polyphenol removal in 10% SWW and 80.4% hydrocarbon removal in 25% SWW. Preserve these positives, while Pico monoculture had the greatest oil-and-grease removal (62.2%) in 25% SWW. The abstract does not resolve the Pico/Pico-Bac arm for the 55 mg/g lipid endpoint or treated-water seed response; the existing phytotoxicity qualification remains correct. Pollutant removal does not establish complete mineralization, an O2/CO2 exchange route, or species-resolved bacterial function. Bacteria remains a broad canonical domain grounding. Primary access is abstract-only. New graph structure remains #1708 pending a scoped Edison report; no node or arrow is added by this discussion-only review.</p>

<p class="muted small">Attaches to: <code>engineering_design</code>, <code>environmental_factors#COD and polyphenol removal</code>, <code>environmental_factors#Hydrocarbon removal</code></p>



<details class="evidence-list">
<summary class="muted small">2 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/42397522/" rel="nofollow noreferrer">PMID:42397522</a>


</div>
<p class="snippet small prewrap">Pico-Bac achieved maximum COD and polyphenol reductions of 72% and 96.4%</p>
<p class="muted small prewrap">Quantifies the maximum COD and polyphenol removal attributed to the Pico-Bac consortium.</p>
</div>

<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/42397522/" rel="nofollow noreferrer">PMID:42397522</a>


</div>
<p class="snippet small prewrap">hydrocarbon removal was highest (80.4%) at 25% SWW</p>
<p class="muted small prewrap">Quantifies the maximum hydrocarbon removal measured for the consortium.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

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