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Bound nitrifier, OMM12, ORNL trophic and PD10 causal claims (batch78) #1651

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43 changes: 37 additions & 6 deletions docs/communities/Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium.html
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Expand Up @@ -616,11 +616,10 @@ <h2>Ecological Interactions</h2>

<div class="interaction-card">
<div class="interaction-header">
<h3>Nitrifier Guild Metabolic Handoff</h3>
<h3>Putative Nitrifier Guild Metabolic Handoff</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The consortium contains ammonia-oxidizing and nitrite-oxidizing guilds whose sequential nitrogen transformations were monitored under aerobic and anoxic redox conditions; Nitrosospira represented the dominant AOB MAG and Nitrobacter represented an NOB MAG in the starting material.
</p>
<p class="prewrap interaction-description">PARTIAL - Starting-material Nitrosospira and Nitrobacter MAGs support ammonia- and nitrite-oxidizing guild potential, but do not resolve an active, exclusive donor-recipient flux. Aerobic cultures showed consistent net ammonia removal and nitrate accumulation only after about day 30; anoxic cultures accumulated ammonia. These measured consortium outcomes do not demonstrate nitrification under anoxia or assign the aerobic flux solely to the two starting dominant guilds.</p>



Expand Down Expand Up @@ -666,14 +665,27 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41457319/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41457319</a>

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

<div class="snippet">"ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) that rely on metabolic handoffs to carry out nitrification
"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41457319/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41457319</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"All cultures accumulated ammonia over 4 weeks, with only aerobic cultures reducing ammonia levels thereafter."</div>

</li>

</ul>

</div>
Expand Down Expand Up @@ -736,6 +748,25 @@ <h2>Associated Datasets</h2>
</div>
</section>

<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 exact-system measurements distinguish the observed outcome from the proposed mechanism?
</h3>
<p class="prewrap">Retain the observed aerobic ammonia-removal outcome after the lag, anoxic ammonia accumulation, and positive nitrogen-cycling gene potential. An initial aerobic ammonia decrease was followed by rebound before consistent net removal after day 30. Nitrosospira and Nitrobacter declined in aerobic abundance and mapped RNA; Nitrobacter nitrogen-gene RNA was not detected, and other populations could contribute. Gene presence and amoC transcription alone do not establish complete ammonia-monooxygenase activity. Periodic oxygen supply, pH change and alternative nitrogen sources are proposed contributors, not isolated mediators. The bulk ammonia assay does not distinguish NH3 from NH4+. Missing redox-dependent endpoint nodes require separate source-backed causal research; the existing one-node graph remains needs_research.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Putative Nitrifier Guild Metabolic Handoff</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1076,11 +1107,11 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "Nitrifier Guild Metabolic Handoff",
label: "Putative Nitrifier Guild Metabolic Handoff",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
59 changes: 30 additions & 29 deletions docs/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.html
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Expand Up @@ -521,21 +521,16 @@ <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 OMM12 Gnotobiotic Mouse Gut 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 (competition, colonization facilitation).</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="symbolTimes"
data-color="#a91919"></svg> Competition
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -544,9 +539,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Double-Dose OMM12 Engraftment</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">A standardized frozen mixture of the 12 OMM strains can be gavaged into germ-free mice, and repeating the application 72 h after the initial inoculation improves stable community composition and engraftment.</p>
<p class="prewrap interaction-description">A second frozen OMM12 inoculum application 72 h after the first improved establishment across the participating germ-free mouse facilities, including more reliable detection of the slow-colonizing Muribaculum intestinale YL27. This is a tested dosing-protocol improvement, not demonstrated biotic facilitation by one member. Some strains remained below fecal qPCR detection in some samples, and the facility cohorts were not a fully matched randomized comparison.</p>



Expand All @@ -573,7 +567,7 @@ <h3>Double-Dose OMM12 Engraftment</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Reproducible Multi-Strain Intestinal Colonization
<p class="prewrap causal-description">The optimized double-dose frozen inoculum protocol enables reproducible de novo association of germ-free mice with the full OMM12 synthetic community.</p>
<p class="prewrap causal-description">The repeat application after 72 h improved reproducibility of OMM12 establishment, particularly YL27 detection, relative to the single-dose protocol. This supports a protocol-to-colonization effect in the studied facility cohorts, not guaranteed detection of every strain or isolation of the effects of dose, timing and gut redox.</p>
</div>

</div>
Expand Down Expand Up @@ -603,9 +597,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Colonization Resistance Against Salmonella</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">OMM12 was designed to provide conventional-like colonization resistance against Salmonella enterica serovar Typhimurium in gnotobiotic mice, making it useful for dissecting microbe-microbe and host-microbe mechanisms that prevent pathogen expansion.</p>
<p class="prewrap interaction-description">The 12-member OMM12 community provided colonization resistance against Salmonella enterica serovar Typhimurium in gnotobiotic mice, but less than a conventional complex microbiota. Conventional-like resistance belongs to the expanded version with three added facultative anaerobic bacteria, not to this 12-member community. The phenotype is retained without assigning a uniquely established competition mechanism.</p>



Expand Down Expand Up @@ -641,7 +634,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"confers colonization resistance against Salmonella enterica serovar Typhimurium"</div>
<div class="snippet">"provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota."</div>

</li>

Expand All @@ -652,9 +645,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Reproducible Multi-Strain Intestinal Colonization</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">OMM12 can reproducibly colonize germ-free mice across different animal facilities, and individual strain abundances can be resolved by strain-specific qPCR. This makes the consortium a standardized model for comparing mouse microbiome experiments.</p>
<p class="prewrap interaction-description">OMM12 was established in multiple germ-free mouse facilities, with strain-resolved fecal 16S rRNA gene-copy qPCR monitoring. The repeat-dose protocol improved reproducibility and YL27 establishment, but some other strains were undetected in some samples and facility differences persisted. Gene-copy counts per volume of extracted DNA are not viable cell counts or uniformly fecal-mass-normalized abundance. Compositional reproducibility alone does not establish functional equivalence or increased pathogen resistance.</p>



Expand All @@ -676,16 +668,6 @@ <h3>Reproducible Multi-Strain Intestinal Colonization</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Colonization Resistance Against Salmonella
<p class="prewrap causal-description">Stable multi-strain Oligo-MM12 colonization supplies the defined community context in which the consortium resists expansion of Salmonella enterica serovar Typhimurium.</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -761,6 +743,25 @@ <h2>Associated Datasets</h2>
</div>
</section>

<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 exact-system measurements distinguish the observed outcome from the proposed mechanism?
</h3>
<p class="prewrap">Preserve the positive repeat-dose establishment and 12-member resistance results. The protocol study compared staged facility cohorts and did not isolate a member-mediated redox mechanism; early colonizers lowering gut redox is proposed. Double inoculation improved YL27 detection while four other strains remained variably undetected. Facility-associated variation persisted, and compositional similarity was not a functional challenge assay. The 2016 primary abstract distinguishes OMM12 resistance from conventional-like resistance of the version expanded by three facultative anaerobes; full infection Methods were not inspected because the publisher provides subscription preview only. Remove the context-only colonization-to-resistance arrow rather than treating the two separate studies as a mediation experiment.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Double-Dose OMM12 Engraftment</code>, <code>ecological_interactions#Colonization Resistance Against Salmonella</code>, <code>ecological_interactions#Reproducible Multi-Strain Intestinal Colonization</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -975,7 +976,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down Expand Up @@ -1003,7 +1004,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down Expand Up @@ -1031,7 +1032,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down
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