Skip to content

Bound field outcomes and model-derived ecological claims (batch96) #1771

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
realmarcin wants to merge 1 commit into from
Closed

Bound field outcomes and model-derived ecological claims (batch96) #1771

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
465 changes: 76 additions & 389 deletions docs/communities/Rifle_Uranium_Reducing_Community.html
View file
Open in desktop

Large diffs are not rendered by default.

60 changes: 46 additions & 14 deletions docs/communities/Rumen_Substrate_Adapted_Lignocellulose_Enrichment_Consortia.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1029,16 +1029,16 @@ <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 Rumen Substrate-Adapted Lignocellulose Enrichment Consortia</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>
Expand All @@ -1047,9 +1047,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Four-substrate rumen consortium specialization</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">Serial 72 h enrichment on alfalfa, barley straw, CMC, or xylan selected different late bacterial profiles from the same pooled rumen-fluid inoculum, with the CMC and xylan enrichments producing the strongest Bray-Curtis separation from the alfalfa and barley-straw lines.</p>
<p class="prewrap interaction-description">Serial 72 h enrichment on alfalfa, barley straw, CMC, or xylan selected different late bacterial profiles from the same pooled rumen-fluid inoculum, with the CMC and xylan enrichments producing the strongest Bray-Curtis separation from the alfalfa and barley-straw lines. Differences among separately enriched lines demonstrate substrate-dependent selection, not reduced competition through niche separation among coexisting members.</p>



Expand All @@ -1076,7 +1075,7 @@ <h3>Four-substrate rumen consortium specialization</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Xylan chain-elongation-associated phenotype
<p class="prewrap causal-description">The xylan enrichment diverged toward a distinct late community that accumulated caproate.</p>
<p class="prewrap causal-description">PARTIAL: repeated xylan selection generated the late consortium with caproate accumulation. Genus abundance and bulk end products are consistent with community mediation, but do not isolate the contribution of the compositional shift from substrate effects or demonstrate the proposed member-to-member flux.</p>
</div>

</div>
Expand Down Expand Up @@ -1119,9 +1118,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>CMC Bacteroides core selection</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The carboxymethyl-cellulose line reproducibly selected a Bacteroides-dominated core with Sporanaerobacter, Streptococcus, and Sphaerochaeta across G3, G6, and G10. The record treats this as substrate enrichment of a CMC-adapted guild, not as a resolved pairwise lactate-propionate exchange.</p>
<p class="prewrap interaction-description">The carboxymethyl-cellulose line reproducibly selected a Bacteroides-dominated core with Sporanaerobacter, Streptococcus, and Sphaerochaeta across G3, G6, and G10. The record treats this as substrate enrichment of a CMC-adapted guild, not as a resolved pairwise lactate-propionate exchange. Recurrent abundance does not itself establish complementary niches or competitive release.</p>



Expand Down Expand Up @@ -1181,9 +1179,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Xylan chain-elongation-associated phenotype</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The xylan line selected a Caproiciproducens-, Lactobacillus-, and Megasphaera-rich late community and developed caproate production by G10, a profile the paper interprets as consistent with reverse beta-oxidation but not yet supported by direct flux measurements.</p>
<p class="prewrap interaction-description">The xylan line selected a Caproiciproducens-, Lactobacillus-, and Megasphaera-rich late community and developed caproate production by G10, a profile the paper interprets as consistent with reverse beta-oxidation but not yet supported by direct flux measurements. These are culture-level endpoints and genus associations, not demonstrated hydrogen diversion, methane suppression or reduced competition.</p>



Expand Down Expand Up @@ -1281,7 +1278,7 @@ <h2>Associated Datasets</h2>
</section>

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(3)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -1364,6 +1361,41 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Does community composition mediate the substrate-specific endpoints?
</h3>
<p class="prewrap">All three positive observations and the existing direction remain. The complete primary main text supports substrate selection, CMC core composition and xylan caproate accumulation, while explicitly relying on inferred metabolic functions. The study does not isolate necessary member contributions or directly measure interspecies flux. Preserve the earlier hydrogen-flux and amplicon-scope discussions; no new pairwise mechanism or niche-partitioning classification is added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Four-substrate rumen consortium specialization</code>, <code>ecological_interactions#CMC Bacteroides core selection</code>, <code>ecological_interactions#Xylan chain-elongation-associated phenotype</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">COMPUTATIONAL</span>
<span class="badge small">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42197533/" rel="nofollow noreferrer">PMID:42197533</a>


</div>
<p class="snippet small prewrap">relies on inferred metabolic functions</p>
<p class="muted small prewrap">The primary limitations section bounds interpretation of metabolic networks.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down Expand Up @@ -1940,7 +1972,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down Expand Up @@ -1968,7 +2000,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down Expand Up @@ -1996,7 +2028,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down
92 changes: 66 additions & 26 deletions docs/communities/SF356_Cellulose_Degrader.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -685,7 +685,7 @@ <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 SF356 Thermophilic Cellulose-Degrading Community</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 (cross-feeding, mutualism, competition).</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 (cross-feeding, mutualism).</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
Expand All @@ -703,8 +703,8 @@ <h2>Ecological Interactions</h2>
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTimes"
data-color="#a91919"></svg> Competition
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand Down Expand Up @@ -791,7 +791,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"straminisolvens CSK1 supplied metabolites (acetate and glucose)"</div>
<div class="snippet">"C. straminisolvens CSK1 supplied metabolites (acetate and glucose)"</div>

</li>

Expand All @@ -804,8 +804,7 @@ <h4>Evidence</h4>
<h3>Oxygen Consumption and Anaerobiosis Creation</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Pseudoxanthomonas sp. M1-3 and Brevibacillus sp. M1-5 consume oxygen in the static, aerobic SF356 culture, introducing anaerobic conditions that allow the anaerobic cellulolytic CSK1 population to degrade cellulose.
</p>
<p class="prewrap interaction-description">Pseudoxanthomonas sp. M1-3 and Brevibacillus sp. M1-5 introduce anaerobic conditions that support cellulolytic CSK1 in the mixed culture. Together with CSK1 metabolite supply, this is a supported positive reciprocal relationship. It does not imply CSK1 cannot tolerate any oxygen.</p>



Expand Down Expand Up @@ -848,8 +847,7 @@ <h3>Oxygen Consumption and Anaerobiosis Creation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Thermophilic Cellulose Hydrolysis
<p class="prewrap causal-description">Aerobic oxygen consumption recreates the anaerobic microenvironment required for CSK1 cellulose fermentation in the mixed culture.
</p>
<p class="prewrap causal-description">Aerobic oxygen consumption lowers oxygen availability and supports CSK1 cellulose degradation in the mixed culture, completing the positive feedback with metabolite supply. This does not assert an absolute zero-oxygen requirement for the aerotolerant CSK1 isolate.</p>
</div>

</div>
Expand All @@ -868,7 +866,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"straminisolvens CSK1) and two strains of aerobic bacteria (Pseudoxanthomonas sp. strain M1-3 and Brevibacillus sp. strain M1-5) were observed; the aerobes introduced anaerobic conditions, and C"</div>
<div class="snippet">"the aerobes introduced anaerobic conditions"</div>

</li>

Expand All @@ -879,18 +877,14 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>FG4 Excess Acetate Inhibits Cellulose Degradation</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Clostridium sp. FG4 is a second cellulolytic member of SF356, but it can inhibit cellulose degradation by producing excess acetic acid, one of the negative interactions balanced in the stable mixed culture.
</p>
<p class="prewrap interaction-description">The primary abstract attributes inhibition of SF356 cellulose degradation to excess acetic acid produced by Clostridium sp. FG4. Retain this negative community-function link; it does not separately establish reciprocal harm between FG4 and CSK1 or isolated CSK1 toxicity.</p>


<p><strong>Source Taxon:</strong> Clostridium sp. FG4</p>



<p><strong>Target Taxon:</strong> Clostridium straminisolvens CSK1</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -921,8 +915,7 @@ <h3>FG4 Excess Acetate Inhibits Cellulose Degradation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Thermophilic Cellulose Hydrolysis
<p class="prewrap causal-description">Excess acetic acid made by FG4 inhibits the cellulose-degradation reaction driven by CSK1 in the SF356 consortium.
</p>
<p class="prewrap causal-description">Excess acetic acid attributed to FG4 inhibits cellulose degradation in the mixed culture, opposing the community hydrolysis/cross-feeding process. The accessible evidence does not isolate the effect on CSK1 from the rest of the consortium.</p>
</div>

</div>
Expand Down Expand Up @@ -952,10 +945,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Brevibacillus Suppression of Bordetella</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Brevibacillus sp. M1-5 suppresses growth of Bordetella sp. M1-6, providing a second negative interaction that is balanced with the positive CSK1-aerobe syntrophy during stable coexistence of all five SF356 members.
</p>
<p class="prewrap interaction-description">Brevibacillus sp. M1-5 suppresses growth of Bordetella sp. M1-6 in the relationships inferred from the SF356 knockout communities. Suppression is retained without asserting reciprocal harm or an identified inhibitory mechanism. The positive CSK1-aerobe relationship is separately retained.</p>


<p><strong>Source Taxon:</strong> Brevibacillus sp. M1-5</p>
Expand Down Expand Up @@ -1008,6 +999,60 @@ <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>
What causes the negative effects and which partners are harmed?
</h3>
<p class="prewrap">The fresh primary abstract supports the positive metabolite/oxygen feedback, FG4-associated excess-acid inhibition and Brevibacillus suppression of Bordetella. The available evidence does not establish reciprocal harm required by COMPETITION. The complete main text was not retrieved in this pass, so no further inhibitory mechanism is certified. Current SYNTROPHY does not require obligacy, but oxygen facilitation alone is not product-removal feedback. CSK1 aerotolerance also precludes an absolute zero-oxygen claim. Non-graph origin, physiological roles and whole-community cultivation claims remain issue1770.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Thermophilic Cellulose Hydrolysis</code>, <code>ecological_interactions#Oxygen Consumption and Anaerobiosis Creation</code>, <code>ecological_interactions#FG4 Excess Acetate Inhibits Cellulose Degradation</code>, <code>ecological_interactions#Brevibacillus Suppression of Bordetella</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/16269746/" rel="nofollow noreferrer">PMID:16269746</a>


</div>
<p class="snippet small prewrap">knockout communities</p>
<p class="muted small prewrap">The source investigated member removal, not merely coexistence.</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/15545431/" rel="nofollow noreferrer">PMID:15545431</a>


</div>
<p class="snippet small prewrap">grew under a gas phase containing up to 4 % O(2)</p>
<p class="muted small prewrap">The isolate abstract directly establishes CSK1 oxygen tolerance.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1427,7 +1472,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1460,16 +1505,11 @@ <h4 style="color: var(--text);">Evidence</h4>



var tgtKey = "Clostridium straminisolvens CSK1";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}

})();

(function() {
var intId = "interaction:3";
var intType = "COMPETITION";
var intType = "UNKNOWN";
var metabolites = [];

var processes = [];
Expand Down
Loading