A diverse synthetic human gut microbiome community used with model-guided time-series experiments to infer pairwise ecological interactions and metabolic drivers of coexistence.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| human gut bacterial SynCom members — ontology label: Bacteria | NCBITaxon:2 · 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.
Pairwise Model Prediction Of Community Dynamics
A generalized Lotka-Volterra model trained on monospecies and pairwise time series predicted much of the tested 11- and 12-member community dynamics; additional full-community training improved predictions. PARTIAL - model success supports important pairwise effects in these conditions, not absence of higher-order effects, perfect prediction or universal acetate cross-feeding. Abundance inputs combined 16S proportions with OD600, not direct viable-cell counts.
Participating Taxa: human gut bacterial SynCom members
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:29930200 - SUPPORT (IN_VITRO)"This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community."
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PMID:29930200 - SUPPORT (COMPUTATIONAL)"pairwise interactions are major drivers of multi‐species community dynamics"
Inferred Positive-Negative Ecological Network Topology
The fitted 12-species gut network contains frequent negative and positive interaction coefficients, including coupled positive/negative pairwise motifs. These are effective ecological effects inferred from abundance dynamics. Their signs do not uniquely identify nutrient competition, cross-feeding, niche partitioning or molecular mechanisms; conditioned-medium and metabolomics results provide complementary but imperfect support.
Participating Taxa: human gut bacterial SynCom members
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
PARTIAL - in the fitted pairwise gLV models, coupled positive and negative effects create negative feedback that limits the higher-fitness partner and permits coexistence with the lower-fitness partner across a broader tested growth-rate range than mutual inhibition. This preserves the source-supported model mechanism, not proof of a universal or molecularly resolved feedback in the entire gut community.
Evidence
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PMID:29930200 - SUPPORT (COMPUTATIONAL)"The inferred ecological network exhibits a high proportion of negative and frequent positive interactions."
Modeled Pairwise Coexistence Feedback
Within the inferred pairwise gLV models, a positive/negative motif implements negative feedback that balances monospecies fitness differences and supports coexistence over a broader tested parameter range than mutual inhibition. The CH-ER pair provides an experimentally coexisting example. PARTIAL - the mathematical mechanism is model-bounded; neither its molecular mediator nor universal stability of the full 12-member system follows from this analysis.
Participating Taxa: human gut bacterial SynCom members
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:29930200 - SUPPORT (COMPUTATIONAL)"positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which molecular mechanisms realize the inferred signed interactions and feedback?
Remove the analytical inference-to-topology arrow, but retain topology-to-coexistence as a model-bounded causal mechanism. Acetate in the cited passage is a prior-literature example; separate metabolomics cultures supplemented ER and FP with acetate, which does not prove cross-feeding throughout this graph. Co-consumption/secretion only yields an ecological effect when relevant substrates limit growth, and conditioned-medium signs do not always match inferred coefficients. Higher-order effects, parameter uncertainty and OD-scaled abundance remain limitations. Canonical NCBITaxon:2 is only an aggregate placeholder for the 12-species experimental roster; #1548 tracks its grounding and non-graph metadata. No original figure pixels, separate supplements, raw data or executable model reproduction was performed.
Attaches to: ecological_interactions#Pairwise Model Prediction Of Community Dynamics, ecological_interactions#Inferred Positive-Negative Ecological Network Topology, ecological_interactions#Modeled Pairwise Coexistence Feedback
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| model-guided synthetic community design | Lower-order assemblages were used to predict higher-dimensional human gut SynCom dynamics. | N/A |
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Growth Media
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