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Bound EcoFAB and E. coli causal graphs to tested mechanisms (batch 36) #1430

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484 changes: 311 additions & 173 deletions docs/communities/EcoFAB_Ring_Trial_SynCom17.html
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81 changes: 65 additions & 16 deletions docs/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.html
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Expand Up @@ -587,7 +587,7 @@ <h2>Ecological Interactions</h2>
<h3>Cysteine provision enabling cooperative 2&#39;-fucosyllactose degradation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">E. coli supplies cysteine to the auxotrophic B. bifidum, facilitating cooperative degradation of 2&#39;-fucosyllactose, the predominant human milk oligosaccharide.</p>
<p class="prewrap interaction-description">In the nutrient-limited in vitro model, E. coli K12 supplies the cysteine requirement of an infant-stool B. bifidum isolate, enabling growth and 2-fucosyllactose degradation without added cysteine or casamino acids. The delta-cysE donor control impaired coculture growth and ethanol-killed partner controls failed to support it. This supports cysteine-dependent cooperation, not a measured cysteine export rate or proof of active secretion rather than overflow or lysis.</p>


<p><strong>Source Taxon:</strong> Escherichia coli</p>
Expand Down Expand Up @@ -619,8 +619,7 @@ <h3>Cysteine provision enabling cooperative 2&#39;-fucosyllactose degradation</h

<div class="flow-item">
<span class="flow-arrow">→</span> Monosaccharide return sustaining E. coli growth
<p class="prewrap causal-description">Cysteine supplied by E. coli enables B. bifidum to cooperatively degrade 2&#39;-fucosyllactose, liberating monosaccharides that return carbon to E. coli.
</p>
<p class="prewrap causal-description">Cysteine-dependent support from E. coli permits the auxotrophic B. bifidum partner to grow and degrade 2-fucosyllactose under the tested nutrient limitation, releasing sugar substrates usable by E. coli. The mutant and killed-partner controls support the dependency; the sugar-consumption assay separately required spent-medium pH adjustment to 6.3.</p>
</div>

</div>
Expand All @@ -643,6 +642,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"observing a significant impairment of growth"</div>

</li>

</ul>

</div>
Expand All @@ -652,7 +664,7 @@ <h4>Evidence</h4>
<h3>Monosaccharide return sustaining E. coli growth</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Monosaccharides liberated from cooperative 2&#39;-fucosyllactose degradation sustain E. coli growth, completing a cooperative cross-feeding loop that may help regulate E. coli abundance in the infant gut.</p>
<p class="prewrap interaction-description">B. bifidum degraded 2-fucosyllactose and left fucose and galactose that E. coli K12 subsequently consumed, measured by chromatography. E. coli grew in this spent medium only after pH readjustment from 4.3 to 6.3. This measured in vitro return of carbon does not establish that the same exchange controls E. coli abundance in infants or quantify sugar-to-cysteine flux in coculture.</p>


<p><strong>Source Taxon:</strong> Bifidobacterium bifidum</p>
Expand Down Expand Up @@ -680,14 +692,7 @@ <h3>Monosaccharide return sustaining E. coli growth</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Cysteine provision enabling cooperative 2&#39;-fucosyllactose degradation
<p class="prewrap causal-description">Monosaccharides returned from B. bifidum sustain E. coli growth and close the cooperative loop that maintains cysteine provisioning to the auxotroph.
</p>
</div>

<div class="flow-item">
<span class="flow-arrow">→</span> Cooperative Infant-Gut HMO Mutualism
<p class="prewrap causal-description">Reciprocal cysteine and monosaccharide exchange completes the cooperative HMO-fed loop between E. coli and B. bifidum.
</p>
<p class="prewrap causal-description">PARTIAL - accessible HMO-derived sugars sustain E. coli growth and can maintain the donor population supporting the cysteine-dependent partner. Reciprocal nutrient dependence is experimentally supported, but a time-resolved sugar-to-cysteine feedback gain or isotope-resolved flux was not measured; the separate spent-medium assay required pH 6.3.</p>
</div>

</div>
Expand All @@ -710,6 +715,32 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"B. bifidum efficiently degraded 2’FL, but left galactose and fucose unconsumed"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"growth only when the pH was adjusted to its initial value of 6.3"</div>

</li>

</ul>

</div>
Expand All @@ -719,8 +750,7 @@ <h4>Evidence</h4>
<h3>Cooperative Infant-Gut HMO Mutualism</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">E. coli cysteine provision to B. bifidum and B. bifidum monosaccharide liberation from 2&#39;-fucosyllactose form a reciprocal, cooperative cross-feeding loop that sustains both partners in the infant-gut two-member model.
</p>
<p class="prewrap interaction-description">E. coli K12 and the infant-stool B. bifidum isolate co-grew in modified M9 with 0.5% 2-fucosyllactose and without added cysteine or casamino acids. Cysteine dependence, viable-partner controls and measured sugar utilization support reciprocal benefit in this restricted laboratory model. This node summarizes that exchange rather than adding a separate downstream outcome. Its prevalence, strength and effect on E. coli abundance in living infants remain untested.</p>



Expand Down Expand Up @@ -793,6 +823,25 @@ <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>
How strongly does the measured laboratory exchange operate in the infant gut?
</h3>
<p class="prewrap">The K12 donor and infant B. bifidum isolate support nutrient-limited reciprocal cooperation, not a universal species-level interaction or demonstrated regulation of E. coli abundance in vivo. Chromatographic sugar data and a delta-cysE control do not resolve cysteine release route, export rate or isotope-resolved feedback. The pH-adjusted spent-medium assay is distinct from the live coculture. The sugar-to-mutualism summary arrow is removed as a part/whole restatement, not an independently supported causal consequence. Experimental-strain and 0.1% screening versus 0.5% coculture metadata remain under #1428.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Cysteine provision enabling cooperative 2&#39;-fucosyllactose degradation</code>, <code>ecological_interactions#Monosaccharide return sustaining E. coli growth</code>, <code>ecological_interactions#Cooperative Infant-Gut HMO Mutualism</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -991,7 +1040,7 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1029,7 +1078,7 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down
49 changes: 45 additions & 4 deletions docs/communities/Ecoli_GL10_XL12_D_Lactate_Mixed_Sugar_SynCom.html
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Expand Up @@ -566,7 +566,7 @@ <h2>Ecological Interactions</h2>
<h3>GL10-XL12 glucose-xylose niche partitioning</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">GL10 and XL12 partition mixed glucose and xylose utilization as two E. coli metabolic specialists, enabling simultaneous hexose and pentose consumption and D-lactate accumulation in the synthetic consortium.</p>
<p class="prewrap interaction-description">GL10 and XL12 show partial, overlapping carbon-source specialization in the tested mixed-glucose/xylose fermentation. GL10 retains xylose metabolism in single-sugar medium, while XL12 still consumes glucose; these are not exclusive substrate users. The 1:1 consortium produced 3.76 g/L D-lactate at 36 h under the baseline conditions. NICHE_PARTITIONING denotes this engineered division of labor, not strain-resolved coculture flux, direct interstrain cross-feeding, partner-dependent growth or universal superiority across shaking speeds and inoculum ratios.</p>



Expand Down Expand Up @@ -636,7 +636,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42038008/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42038008</a>

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

<div class="snippet">"Microbial consortium using GL10 and XL12 with the inoculation ratio of 1:1 achieved complete glucose depletion and 53.21% xylose utilization simultaneously."</div>
Expand All @@ -656,6 +656,32 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42038008/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42038008</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"GL10 was not modified to block xylose metabolism"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42038008/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42038008</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"XL12 co-utilized glucose and xylose simultaneously"</div>

</li>

</ul>

</div>
Expand All @@ -666,7 +692,7 @@ <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 @@ -681,6 +707,21 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which strain-specific fluxes account for consortium output under each condition?
</h3>
<p class="prewrap">The two preferred strain labels must remain distinct despite shared NCBITaxon:562. Individual-strain phenotypes and consortium-level HPLC do not resolve each strain&#39;s flux during coculture or establish an exchanged metabolite. Keep the existing direct-cross-feeding gap and zero arrows; do not restore the dangling endpoint arrows removed under #826. The abstract and 36 h xylose quantities require reconciliation against unread original supplementary data under #1429, without merging supplement text back into the article cache (#827).</p>

<p class="muted small">Attaches to: <code>ecological_interactions#GL10-XL12 glucose-xylose niche partitioning</code></p>




</div>

</section>
Expand Down Expand Up @@ -1345,7 +1386,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("fermentation");


var evidenceCount = 3;
var evidenceCount = 5;

nodes.push({
id: intId,
Expand Down
29 changes: 29 additions & 0 deletions history/records/EcoFAB_Ring_Trial_SynCom17/2026-10-06T082610Z-codex-00f1fc.yaml
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@@ -0,0 +1,29 @@
history_version: 1
target:
kind: record
path: kb/communities/EcoFAB_Ring_Trial_SynCom17.yaml
slug: EcoFAB_Ring_Trial_SynCom17
session:
id: 2026-10-06T082610Z-codex-00f1fc
timestamp: '2026-10-06T08:26:10Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1424
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain three whole-treatment effects without colonization facilitation or symbiotic-process
claims.; Retain intrinsic OAS925 traits with only a hypothesized contribution to dominance.;
Retain relative community composition without competition or metabolome mediation.; Retain
net spent-medium profiles without assigning direct cross-feeding.; Retain measured whole-treatment
plant growth effects without a competition mechanism.
details: Nine existing nodes retained; one out-of-system node and two arrows removed; six
arrows retained with explicit limits. reports/causal_graph_review/decisions/20261006-three-records-batch36.yaml
28 changes: 28 additions & 0 deletions ...bacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture/2026-10-06T082611Z-codex-5468bc.yaml
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@@ -0,0 +1,28 @@
history_version: 1
target:
kind: record
path: kb/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.yaml
slug: Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture
session:
id: 2026-10-06T082611Z-codex-5468bc
timestamp: '2026-10-06T08:26:11Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1425
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain cysteine-dependent support with mutant and viability controls and unresolved
release route.; Retain measured fucose/galactose return with its pH constraint and partial
donor-maintenance feedback.; Retain reciprocal mutualism as an in vitro summary, not an
independently measured host endpoint.
details: Nine existing nodes retained; one out-of-system node and two arrows removed; six
arrows retained with explicit limits. reports/causal_graph_review/decisions/20261006-three-records-batch36.yaml
26 changes: 26 additions & 0 deletions ...records/Ecoli_GL10_XL12_D_Lactate_Mixed_Sugar_SynCom/2026-10-06T082611Z-codex-a5ce14.yaml
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@@ -0,0 +1,26 @@
history_version: 1
target:
kind: record
path: kb/communities/Ecoli_GL10_XL12_D_Lactate_Mixed_Sugar_SynCom.yaml
slug: Ecoli_GL10_XL12_D_Lactate_Mixed_Sugar_SynCom
session:
id: 2026-10-06T082611Z-codex-a5ce14
timestamp: '2026-10-06T08:26:11Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1426
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain the single division-of-labor node with overlapping substrate capacities,
zero unsupported arrows and an explicit quantitative evidence limitation.
details: Nine existing nodes retained; one out-of-system node and two arrows removed; six
arrows retained with explicit limits. reports/causal_graph_review/decisions/20261006-three-records-batch36.yaml
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