A defined synthetic microbial community (SynCom) modeling the early-life (infant) gut, studied alongside donor-derived infant faecal fermentations to dissect how prebiotic substrates reshape microbial and metabolic responses. Human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promote bifidobacterial expansion, while Bacteroides/Phocaeicola species are modulated in a feeding-mode- and substrate-dependent manner. The SynCom reveals extensive cross-feeding networks and substrate-dependent interaction rewiring, with Phocaeicola vulgatus acting as a context-dependent ecological hub that disproportionately shapes succinate and propionate production and alters Escherichia coli metabolic activity. Competitive outcomes are driven not only by acidification but by the chemical identity of fermentation products, with lactate exerting species-specific inhibition independent of bulk pH.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Bifidobacterium spp. — ontology label: Bifidobacterium | NCBITaxon:1678 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
|
N/A |
|
|||
| Bacteroides/Phocaeicola spp. — ontology label: Bacteroides | NCBITaxon:816 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
|
N/A |
|
|||
| Phocaeicola vulgatus | NCBITaxon:821 · TaxonMech · TraitMech |
CROSS_FEEDER
|
N/A |
|
|||
| Escherichia coli | NCBITaxon:562 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
|
N/A |
|
|||
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.
Substrate-Dependent Infant Community Interaction Responses
The primary preprint compares donor-derived infant fermentations with a separate six-species SynCom containing B. breve, B. infantis, P. vulgatus, E. coli, L. gasseri and R. gnavus. Substrate perturbations and semipermeable binary cultures show growth responses and substrate-dependent interactions, including relief of P. vulgatus inhibition with 2FL. Donor communities instead contain P. dorei and L. rhamnosus in the corresponding comparisons; abundance correlations there are not the same intervention. The four canonical entries are a cross-experiment subset, not a four-member assayed SynCom or a complete roster. Exact strains and missing members remain unresolved under #1514.
Participating Taxa: Bifidobacterium spp., Bacteroides/Phocaeicola spp., Phocaeicola vulgatus, Escherichia coli
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
PARTIAL - substrate-dependent fermentation can supply lactate whose accumulation may suppress susceptible members. Community metabolite profiles, binary growth responses and separate acid challenges support this route, but selective lactate depletion/rescue was not demonstrated in the inspected complete-community experiments; pH and other products can also contribute.
Evidence
-
doi:10.64898/2026.05.29.728681 - SUPPORT (IN_VITRO)"Mechanistic dissection using SynCom revealed extensive cross-feeding networks and substrate-dependent interaction rewiring"
Phocaeicola Omission Alters Community Metabolism and Ecoli Activity
Omitting P. vulgatus from the defined community changes succinate/propionate output and E. coli metabolic activity. Heavy-water Raman-FISH measurements under GOS found higher E. coli activity with P. vulgatus present, without an abundance change in that assay. This is positive community-context intervention evidence, not proof of direct two-member succinate or propionate transfer to E. coli. Growth in P. vulgatus-conditioned supernatants did not differ between GOS and glucose, leaving timing and other partners relevant. The listed taxa identify the omitted member and measured responder, not the whole tested community or universal abundance invariance.
Participating Taxa: Phocaeicola vulgatus, Escherichia coli
Metabolites: succinate (CHEBI:26806 · MediaIngredientMech · CMMMech), propionate (CHEBI:17272 · MediaIngredientMech · CMMMech)
Evidence
-
doi:10.64898/2026.05.29.728681 - SUPPORT (IN_VITRO)"disproportionately shaped succinate and propionate production and altered Escherichia coli metabolic activity without affecting its abundance"
-
doi:10.64898/2026.05.29.728681 - SUPPORT (IN_VITRO)"significantly higher activity when P. vulgatus was present"
Species-Specific Lactate and Acetate Inhibition
The preprint reports stronger inhibition of P. vulgatus and R. gnavus by lactate than acetate at comparable concentrations, with E. coli less affected. P. vulgatus was also inhibited at pH 5, and the authors discuss additive effects of pH and acid identity. Preserve these positive challenge results without claiming a universally pH-independent mechanism or an inspected pH-clamped protocol: the exact acid-challenge protocol is not in the main Methods and the external supplement was not obtained. The canonical P. vulgatus and E. coli entries are the represented comparison subset; R. gnavus remains missing under #1514.
Participating Taxa: Phocaeicola vulgatus, Escherichia coli
Metabolites: lactate (CHEBI:24996 · MediaIngredientMech · CMMMech)
Evidence
-
doi:10.64898/2026.05.29.728681 - SUPPORT (IN_VITRO)"stronger by lactate than acetate at comparable concentrations"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which exact members and metabolites mediate the substrate-dependent responses?
Remove the network-overview-to-hub arrow, which describes identification of a component rather than a causal mechanism. Preserve the positive P. vulgatus omission result, with higher E. coli activity when present under GOS, and the separate acid challenge. Retain fermentation-to-inhibition only as PARTIAL. #1514 tracks the exact six-member roster, R. gnavus-dependent 2FL availability and missing ex-vivo mouse-colon outcome representation. Full/P. vulgatus-omitted supernatants both suppress motility; matched SCFAs do not reproduce it and PEA was below detection in SynCom. These do not prove infant in-vivo physiology or endogenous PEA mediation. Full version-1 primary main text, Methods and embedded figure captions read; external supplement, exact strain sheet, raw data, code and figure pixels not inspected. One-community Edison dry run only; no paid report or new graph structure. Non-graph pH/roster claims remain outside this repair.
Attaches to: ecological_interactions#Substrate-Dependent Infant Community Interaction Responses, ecological_interactions#Phocaeicola Omission Alters Community Metabolism and Ecoli Activity, ecological_interactions#Species-Specific Lactate and Acetate Inhibition
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