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Repair tailings, algal, milk and seed-biocontrol causal claims (batch82) #1684

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689 changes: 104 additions & 585 deletions docs/communities/Panzhihua_Vanadium_Titanium_Tailings.html
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130 changes: 77 additions & 53 deletions docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
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99 changes: 70 additions & 29 deletions docs/communities/Parmigiano_NWS_Set2_LAB_Triculture.html
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Expand Up @@ -616,7 +616,7 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>Set 2 milk acidification enhancement</h3>
</div>
<p class="prewrap interaction-description">The complete three-member LAB triculture increased maximum milk acidification rate and total lactic acid production relative to the monocultures and most pairwise co-cultures, supporting a positive mixed-culture effect during milk fermentation.</p>
<p class="prewrap interaction-description">The set 2 LBB04/C001.27/C5I3 triculture produced higher total lactic acid than the tested monocultures and pairwise cultures. Maximum acidification rate was high, but the exact set 2 C001.27/C5I3 pair was comparable to the triculture, so the triculture was not uniquely superior on this rate readout. Total inoculum was held constant across compositions. These positive community fermentation phenotypes do not establish per-strain growth, reciprocal benefit or a specific molecular exchange.</p>



Expand Down Expand Up @@ -652,16 +652,6 @@ <h3>Set 2 milk acidification enhancement</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> C5I3 activity enhancement in mixed culture
<p class="prewrap causal-description">Higher D-lactate in set 2 tricultures than in the corresponding C5I3 monoculture indicated that the Ld member remained viable and metabolically active in the mixed culture.</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -693,6 +683,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41859451/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41859451</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those observed under tri-culture conditions."</div>

</li>

</ul>

</div>
Expand All @@ -701,7 +704,7 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>C001.27-C5I3 acidification enhancement</h3>
</div>
<p class="prewrap interaction-description">In the set 2 pairwise subset, S. thermophilus C001.27 co-cultured with L. delbrueckii subsp. lactis C5I3 produced maximum acidification rates comparable with the complete triculture.</p>
<p class="prewrap interaction-description">The C001.27/C5I3 pair had a higher maximum acidification rate than either corresponding monoculture, and in set 2 its rate was comparable to that of the triculture. This is a positive two-member fermentation phenotype, not proof that adding LBB04 preserves a pair-specific causal mechanism or that both members benefit equally. The study interprets D-lactate predominance as preferential L. delbrueckii activity; exchanged formate, folate and peptides were not directly resolved in this assay.</p>



Expand Down Expand Up @@ -737,16 +740,6 @@ <h3>C001.27-C5I3 acidification enhancement</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Set 2 milk acidification enhancement
<p class="prewrap causal-description">The strong St + Ld pairwise response was retained within the complete LBB04/C001.27/C5I3 triculture.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -773,7 +766,7 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>LBB04-C5I3 reduced acidification subset</h3>
</div>
<p class="prewrap interaction-description">The L. helveticus LBB04 plus L. delbrueckii subsp. lactis C5I3 pairwise subset had weaker acidification than the matched C001.27/C5I3 co-culture and lower total lactic acid than tricultures and S. thermophilus-containing co-cultures in the set 2 lactate assay.</p>
<p class="prewrap interaction-description">The LBB04/C5I3 pair showed lower maximum acidification rates than the corresponding monocultures and the C001.27/C5I3 pair. Its total lactic acid was also lower than the triculture and St-containing pairs, with D-lactate comprising 75.95% of the pair’s total lactate. Preserve this negative fermentation response without converting bulk acidification to a strain-specific growth-inhibition assay or claiming a measured antimicrobial or nutrient-competition mechanism.</p>



Expand Down Expand Up @@ -840,15 +833,28 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41859451/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41859451</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"co-inoculation of milk with Lh and Ld resulted in reduced acidification rates compared with the corresponding monocultures"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>C5I3 activity enhancement in mixed culture</h3>
<h3>Set 2 Triculture D-Lactate Accumulation</h3>
</div>
<p class="prewrap interaction-description">D-lactate measurements showed that the set 2 triculture accumulated more D-lactate than the C5I3 monoculture, consistent with L. delbrueckii subsp. lactis remaining viable and metabolically active in mixed culture.</p>
<p class="prewrap interaction-description">At the end of fermentation, set 2 triculture D-lactate was significantly higher than in the C5I3 monoculture. This is a measured mixed-culture pool, consistent with L. delbrueckii metabolic activity but not exclusive C5I3 production or directly measured C5I3 cell growth. L. helveticus produces both enantiomers, and C001.27 monoculture was 83% L-lactate rather than exclusively L-lactate. Acidification and lactate are related readouts; an arrow from acidification to inferred member activity would reverse measurement and inference.</p>



Expand Down Expand Up @@ -906,7 +912,7 @@ <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 @@ -921,6 +927,41 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which member-resolved processes explain the positive and negative fermentation responses?
</h3>
<p class="prewrap">Four measured phenotypes remain. Pair and triculture comparisons do not form a causal sequence, and higher D-lactate is an observation used to infer activity, not an outcome caused by measuring acidification. No new mediator arrows are justified by the full main text. Preserve previous #1077-1079 removal of unsupported mutualism, taxon roles and exclusive C5I3 attribution; the existing molecular-mechanism gap remains open.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Set 2 milk acidification enhancement</code>, <code>ecological_interactions#C001.27-C5I3 acidification enhancement</code>, <code>ecological_interactions#LBB04-C5I3 reduced acidification subset</code>, <code>ecological_interactions#Set 2 Triculture D-Lactate Accumulation</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">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/41859451/" rel="nofollow noreferrer">PMID:41859451</a>


</div>
<p class="snippet small prewrap">co-cultivation of St strain C001.27 with Ld strain C5I3 resulted in μmax values comparable to those observed under tri-culture conditions.</p>
<p class="muted small prewrap">Exact set 2 exception to a uniquely highest triculture rate.</p>
</div>

</details>


</div>

</section>
Expand Down Expand Up @@ -1206,7 +1247,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("interspecies interaction between organisms");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1279,7 +1320,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("interspecies interaction between organisms");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1328,7 +1369,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "C5I3 activity enhancement in mixed culture",
label: "Set 2 Triculture D-Lactate Accumulation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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