Public KBase narrative centered on metabolic model editing, merged community modeling, and flux analyses for the Zahmeeth Original PLOS model set.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Escherichia coli | NCBITaxon:562 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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| Pseudomonas fluorescens | NCBITaxon:294 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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| Bacteroides thetaiotaomicron | NCBITaxon:818 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
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N/A |
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| Klebsiella | NCBITaxon:570 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Model-Architecture-Dependent Information Flow
Mixed-bag models generally had higher mutual-information scores than compartmentalized models. The authors attribute this to pooling reactions without intermember transport constraints; this is a model-architecture interpretation, not observed niche partitioning or a selectively validated biological transport mechanism. Methods/Results identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.
Participating Taxa: Escherichia coli, Bacteroides thetaiotaomicron
Evidence
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doi:10.1101/2023.08.23.554558 - SUPPORT (COMPUTATIONAL)"mixed-bag framework conducts greater information flow than the compartmentalized framework"
Model-Conditional Growth Contrasts
Community models grew on dextrin where the E. coli isolate model did not. Aerobic isolated B. theta growth and information flow were manually set to zero, with that constraint lifted in community models; the contrast is not independently predicted partner rescue. Model growth does not establish actual strain growth, resolved cross-feeding, stable community formation or reciprocal benefit. Methods/Results identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.
Participating Taxa: Escherichia coli, Bacteroides thetaiotaomicron
Metabolites: dextrin (CHEBI:28675 · MediaIngredientMech · CMMMech)
Evidence
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doi:10.1101/2023.08.23.554558 - SUPPORT (COMPUTATIONAL)"despite that E. coli failed to grow as an isolate"
Greater Community Information Flow
RFMIA generally returned higher mutual-information scores for the community models than for isolated models under the tested nutrient combinations. These are computed information-theoretic outputs in bits, not measured molecular communication, a universal growth advantage or mutualism. Methods/Results identify E. coli iML1515 and B. theta iAH991; the abstract names different pairs. The two canonical participants delimit the modeled comparison, not a four-member consortium; the source/metadata discrepancy remains #1527.
Participating Taxa: Escherichia coli, Bacteroides thetaiotaomicron
Evidence
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doi:10.1101/2023.08.23.554558 - SUPPORT (COMPUTATIONAL)"information flow is greater through communities than isolated models"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
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Primary publication
bioRxiv preprint describing information flow through microbial community metabolic models. |
OTHER | OTHER | doi:10.1101/2023.08.23.554558 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which model-dependent findings persist with verified partners and experimentally tested constraints?
Remove adaptation/construction nodes and all five procedural or co-occurrence arrows. Keep three existing modeled observations without imposing a new causal chain. Primary full v1 PDF text/captions read and selected Methods, equations, table, architecture and charts visually inspected; no independent mathematical derivation, supplement/code/raw simulation audit or model rerun. Manually imposed aerobic constraints cannot validate partner rescue. #1527 tracks non-graph model/partner metadata and #1528 the mismatching cached abstract. Canonical identifiers and raw non-graph blocks are preserved; no new graph structure.
Attaches to: ecological_interactions#Model-Architecture-Dependent Information Flow, ecological_interactions#Model-Conditional Growth Contrasts, ecological_interactions#Greater Community Information Flow
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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KBase narrative
Models for Zahmeeth_Original_PLOS narrative page. |
KBASE | ws.40576.obj.330 |
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Cross-Mech Suite Links
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