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Separate process outcomes and molecular responses from causal mediation (batch108) #1848

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154 changes: 80 additions & 74 deletions docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html
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Original file line number Diff line number Diff line change
Expand Up @@ -558,32 +558,26 @@ <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 SynCom BsBv Cigar Tobacco Leaf Fermentation</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 (mutualism, 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="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
</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>


<div class="interaction-card">
<div class="interaction-header">
<h3>Cooperative macromolecule degradation by the BsBv SynCom</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>Macromolecule degradation after BsBv inoculation</h3>
</div>
<p class="prewrap interaction-description">Co-inoculation of the two cellulase/amylase/protease-producing Bacillus members on cigar tobacco leaves accelerated the degradation of key macromolecules, reducing cellulose, protein, and starch contents by 52.48 %, 56.36 %, and 68.47 % respectively, markedly greater than the uninoculated control (a community-level, emergent function of the consortium).</p>
<p class="prewrap interaction-description">BsBv inoculation accelerated cellulose, protein and starch loss during the tested leaf fermentation, with reductions of 52.48%, 56.36% and 68.47%, respectively, greater than the uninoculated control. This is a measured consortium-associated process outcome; it does not establish that both bacterial partners benefit or that the mixture exceeds each monoculture.</p>



Expand Down Expand Up @@ -621,9 +615,8 @@ <h3>Cooperative macromolecule degradation by the BsBv SynCom</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Volatile Flavor Profile Remodeling
<p class="prewrap causal-description">Faster cellulose, protein, and starch degradation is one SynCom-driven process associated with the volatile flavor-metabolite changes measured during cigar-tobacco leaf fermentation.
</p>
<span class="flow-arrow">→</span> Volatile flavor and sensory-quality outcomes
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: macromolecule conversion is proposed to contribute to the altered chemical and sensory outcomes under BsBv inoculation. The abstract reports chemical changes and a path-model interpretation, but does not isolate degradation of any one substrate as the mediator of a specific volatile or sensory change.</p>
</div>

</div>
Expand Down Expand Up @@ -653,9 +646,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>SynCom-driven bacterial community succession and Bacillus enrichment</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">Inoculation with the SynCom shifted the leaf bacterial community structure, increasing the relative abundance of Firmicutes and significantly enriching the genus Bacillus during fermentation (community-level restructuring driven by the introduced consortium).</p>
<p class="prewrap interaction-description">BsBv inoculation shifted bacterial community structure, including greater relative abundance of Firmicutes and enrichment of Bacillus. The authors also used PLS-PM to infer a microbiome-mediated contribution to sensory quality. Relative abundance and modeled mediation do not establish absolute population increases, niche separation or a Bacillus-specific causal mechanism.</p>



Expand All @@ -664,26 +656,14 @@ <h3>SynCom-driven bacterial community succession and Bacillus enrichment</h3>



<p><strong>Biological Processes:</strong></p>
<ul>

<li>
biological process involved in interspecies interaction between organisms
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Volatile Flavor Profile Remodeling
<p class="prewrap causal-description">BsBv-driven enrichment of Bacillus and Firmicutes is the community succession pattern associated with SynCom flavor metabolism during the 42-day leaf fermentation.
</p>
<span class="flow-arrow">→</span> Volatile flavor and sensory-quality outcomes
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: community restructuring is proposed to contribute to the sensory component of the BsBv-associated outcome, consistent with the authors beta-diversity path-model interpretation. This does not identify Bacillus enrichment as the necessary mediator of each volatile change, or equate relative-abundance shifts with the modeled beta-diversity variable.</p>
</div>

</div>
Expand All @@ -706,17 +686,28 @@ <h4>Evidence</h4>

</li>

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

<a href="https://doi.org/10.1016/j.indcrop.2025.122621"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122621</a>

- PARTIAL (COMPUTATIONAL)
</div>

<div class="snippet">"indirectly improved sensory quality by mediating shifts in microbial β-diversity"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Volatile Flavor Profile Remodeling</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>Volatile flavor and sensory-quality outcomes</h3>
</div>
<p class="prewrap interaction-description">BsBv inoculation remodeled volatile flavor metabolites during the 42-day cigar-tobacco fermentation, increasing honey, floral, and baked aroma contributions while reducing irritancy.
</p>
<p class="prewrap interaction-description">Metabolomics identified 31 differentially accumulated volatile compounds after BsBv inoculation. The source associates increased phenylacetic acid, phytol and farnesol with honey, floral and baked aromas and reduced irritancy. These chemical and sensory outcomes are distinct from reciprocal microbial fitness and from direct measurements of the upstream degradation processes.</p>



Expand All @@ -725,35 +716,25 @@ <h3>Volatile Flavor Profile Remodeling</h3>



<p><strong>Biological Processes:</strong></p>
<ul>

<li>
cellulose catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0030245"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0030245</a>)
</li>

<li>
starch catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0005983"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0005983</a>)
</li>

<li>
protein catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0030163"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0030163</a>)
</li>

</ul>
<h4>Evidence</h4>
<ul class="evidence-list">

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

<a href="https://doi.org/10.1016/j.indcrop.2025.122621"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122621</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Metabolomic profiling identified 31 differentially accumulated volatile flavor compounds"</div>

<h4>Evidence</h4>
<ul class="evidence-list">
</li>

<li class="evidence-item">
<div>
Expand All @@ -764,7 +745,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Metabolomic profiling identified 31 differentially accumulated volatile flavor compounds"</div>
<div class="snippet">"phenylacetic acid, phytol, and farnesol, which were upregulated in the BsBv group and contributed to enhanced honey, floral, and baked aromas, while reducing irritancy."</div>

</li>

Expand All @@ -777,6 +758,43 @@ <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>
Which components of the BsBv-associated fermentation response mediate the volatile and sensory outcomes?
</h3>
<p class="prewrap">Keep the positive degradation, community and flavor observations and the source path-model hypothesis. The reviewed abstract does not isolate substrate conversion or Bacillus enrichment as the causal mediator. Reciprocal bacterial benefit and spatial or temporal niche separation are not established.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Macromolecule degradation after BsBv inoculation</code>, <code>ecological_interactions#SynCom-driven bacterial community succession and Bacillus enrichment</code>, <code>ecological_interactions#Volatile flavor and sensory-quality outcomes</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://doi.org/10.1016/j.indcrop.2025.122621" rel="noreferrer">doi:10.1016/j.indcrop.2025.122621</a>

</div>
<p class="snippet small prewrap">indirectly improved sensory quality by mediating shifts in microbial β-diversity</p>
<p class="muted small prewrap">Reports the authors statistical mediation interpretation, not an experimentally isolated taxon effect.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -951,7 +969,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -968,7 +986,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Cooperative macromolecule degradation by the BsBv SynCom",
label: "Macromolecule degradation after BsBv inoculation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -983,16 +1001,12 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("biological process involved in interspecies interaction between organisms");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand All @@ -1011,24 +1025,16 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("cellulose catabolic process");

processes.push("starch catabolic process");

processes.push("protein catabolic process");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "Volatile Flavor Profile Remodeling",
label: "Volatile flavor and sensory-quality outcomes",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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