BioModels record MODEL2310020001 contains an integrated metabolic metaorganism model of aging mice that connects a merged mouse gut microbiome metabolic model to colon, liver, and brain host-tissue models through gut lumen and bloodstream exchange compartments.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
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| mouse gut Bacillota MAGs — ontology label: Bacillota | NCBITaxon:1239 · TaxonMech · TraitMech | N/A | |
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| mouse gut Bacteroidota MAGs — ontology label: Bacteroidota | NCBITaxon:976 · TaxonMech · TraitMech | 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-Predicted Beneficial Gut Interactions
COMPUTATIONAL - pairwise community FBA compares single and paired growth for mouse gut MAG reconstructions. Across age groups, inferred beneficial interactions decline. This collection is not uniformly commensal, and concurrent metabolite predictions do not establish that interaction loss causes reduced metabolic output. The aging comparison uses separate age cohorts, not a longitudinal competition intervention.
Biological Processes:
- growth (GO:0040007 · PathwayMech)
Evidence
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PMID:40140706 - SUPPORT (COMPUTATIONAL)"Growth was estimated by FBA for single growth and community FBA for combined growth."
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PMID:40140706 - SUPPORT (COMPUTATIONAL)"We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species."
Aging Shift Toward Competitive Gut Interactions
COMPETITIONCOMPUTATIONAL - normalized pairwise interaction frequencies shift toward the model's competition category with age, while amensal, commensal and neutral categories decline. COMPETITION refers to the paired-growth classification, not a cause of every aging-associated metabolite change. Reduced amensalism and neutralism are not themselves losses of beneficial commensalism.
Biological Processes:
- growth (GO:0040007 · PathwayMech)
Evidence
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PMID:40140706 - SUPPORT (COMPUTATIONAL)"We observed a significant decrease in amensal, commensal and neutral interactions at the expense of increased competitive interactions"
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PMID:40140706 - SUPPORT (COMPUTATIONAL)"Aging-related microbiome changes led to the accumulation of pro-aging metabolites (D-galactose, succinate) and a decline in beneficial metabolites (nucleotides, butyrate)."
Microbiota-Dependent Host Nucleotide Support
COMPUTATIONAL - a separate pooled microbiome/host metamodel links colon, liver and brain reconstructions and predicts age-associated nucleotide co-metabolism changes. Host-to-microbe and microbe-to-host routes are reciprocal, not established commensalism. PARTIAL - a contribution to barrier integrity is hypothesized; predicted flux ranges, gene associations and broad germ-free/colonization validation do not establish donor-traced exchange or route-specific causal rescue.
Metabolites: nucleotide (CHEBI:36976 · MediaIngredientMech · CMMMech)
Biological Processes:
- nucleotide metabolic process (GO:0009117 · PathwayMech)
Evidence
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PMID:40140706 - SUPPORT (COMPUTATIONAL)"In this metamodel, the host is represented by three different tissues (colon, liver and brain) connected through the bloodstream and interacting with the microbiome through the gut lumen"
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PMID:40140706 - PARTIAL (COMPUTATIONAL)"An aging-associated decline in nucleotide co-metabolism could underlie diminished intestinal barrier integrity"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
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BioModels metamodel SBML
Integrated metabolic metaorganism SBML model submitted to BioModels. |
OTHER | BIOMODELS | metamodel_20230510.xml |
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Peer-reviewed primary publication
Nature Microbiology article describing the mouse host-microbiome metabolic metamodel. |
OTHER | OTHER | PMID:40140706 |
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Fecal metagenomic reads and MAG assemblies
European Nucleotide Archive BioProject containing metagenomic reads and MAG assembly data. |
METAGENOMICS | ENA | PRJEB73981 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Do targeted partner and nucleotide interventions link ecological changes to host outcomes?
Species-level community FBA and the pooled host-microbiome model are separate analyses; their association is not a causal chain. The metamodel uses human Recon 2.2 reconstructions as a mouse-host proxy; FVA ranges are not measured fluxes. The 52-male aging cohort differs from the separate 24-female germ-free validation cohort. Main text and figure captions were read, but supplementary data, images and models were not inspected or rerun.
Attaches to: ecological_interactions#Model-Predicted Beneficial Gut Interactions, ecological_interactions#Aging Shift Toward Competitive Gut Interactions, ecological_interactions#Microbiota-Dependent Host Nucleotide Support
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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BioModels entry
Integrated metabolic metaorganism model of mice and their microbiome. |
BIOMODELS | MODEL2310020001 |
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