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Infant-gut Prebiotic-response SynCom

Community ID CommunityMech:000281
Ecological State ENGINEERED
Environment early-life (infant) gut; donor-derived faecal fermentations
ENVO:2100002

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. NCBITaxon:1678
PRIMARY_DEGRADER CROSS_FEEDER
N/A
  • doi:10.64898/2026.05.29.728681 - SUPPORT (IN_VITRO)
    "both human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promoted bifidobacterial expansion"
Bacteroides/Phocaeicola spp. NCBITaxon:816
PRIMARY_DEGRADER CROSS_FEEDER
N/A
Phocaeicola vulgatus NCBITaxon:821
CROSS_FEEDER
N/A
  • doi:10.64898/2026.05.29.728681 - SUPPORT (IN_VITRO)
    "Phocaeicola vulgatus as a context-dependent ecological hub that disproportionately shaped succinate and propionate production"
Escherichia coli NCBITaxon:562
SECONDARY_FERMENTER
N/A

Ecological Interactions

Ecological interaction network for Infant-gut Prebiotic-response SynCom Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation

Substrate-dependent cross-feeding network

CROSS_FEEDING

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 vulgatus hub modulates Escherichia coli metabolism

CROSS_FEEDING

Source Taxon: Phocaeicola vulgatus

Target Taxon: Escherichia coli

Metabolites: succinate (CHEBI:26806), propionate (CHEBI:17272)

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"

Lactate-mediated species-specific inhibition

COMPETITION

Metabolites: lactate (CHEBI:24996)

Evidence

Growth Media

eGAM (enhanced Gifu Anaerobic Medium); adjusted M9 minimal medium for metabolic labelling

Temperature 37 °C
Atmosphere ANAEROBIC

Preparation notes: Enhanced GAM (eGAM) was used for all routine culturing (adjusted M9 minimal medium for metabolic labelling and secondary-metabolite production); exact medium composition is given in the paper's supplementary Excel sheet. For SynCom assembly, baseline growth rates were measured in eGAM+glucose (1:100 dilution from a two-day culture); strains were abundance-equalised to reach OD 0.2 at 5 h, and each 48 h culture was centrifuged (3000 x g, 10 min, RT) and resuspended in fresh medium before pooling.

Evidence

doi:10.64898/2026.05.29.728681

"All bacteria were grown under anaerobic conditions (5% CO2, 5% H2, balanced with N2) using an anaerobic vinyl chamber (Coy Laboratory Products) at 37°C."

doi:10.64898/2026.05.29.728681

"As medium either eGAM (enhanced GAM; for all culturing if not indicated differently) or adjusted M9 minimal medium (for metabolic labelling and secondary metabolite production) was used"

doi:10.64898/2026.05.29.728681

"we constructed a six-member simplified defined microbial community (referred to as SynCom; see Methods) comprising Phocaeicola vulgatus"