Feeding Type Shapes Infant Gut Microbiota and Metabolite Profiles in a Simulated Colonic Model

TL;DR

This study shows that the type of infant feeding strongly influences gut bacteria and metabolites in a simulated gut model.

Contribution

The study demonstrates that feeding type, more than time, shapes infant gut microbiota and SCFA profiles using an in vitro model.

Findings

Past-HM and GIF promoted Bifidobacterium dominance and higher SCFA levels compared to HM.

Feeding type had a stronger influence on microbiota and metabolite profiles than incubation time.

Bifidobacterium correlated with acetic acid, while Escherichia-Shigella correlated with propionic acid.

Abstract

The establishment of the infant gut microbiota is strongly influenced by feeding type, with human milk (HM) and infant formula (IF) driving distinct microbial profiles. This study compared the effects of donated raw human milk (HM) and Holder-pasteurised HM (Past-HM) on microbial composition using a 4-stage in vitro gut model inoculated with pooled faecal samples from five healthy 3–6-month-old infants. Colonic digesta were sampled over a 48-h period following introduction of raw HM, Past-HM and IFs for microbial diversity by quantitative polymerase chain reaction (qPCR) and 16S rRNA gene sequencing, and short-chain fatty acid (SCFA) analysis by gas chromatography. Microbial profiling revealed 2026 operational taxonomic units (OTUs) across eight phyla and 165 genera. Past-HM and goat milk-based IF (GIF) promoted Bifidobacterium dominance and produced higher levels of total SCFA, especially acetic acid, compared to HM. Spearman correlation linked Bifidobacterium with acetic acid and Escherichia-Shigella with propionic acid. PCA showed OTU composition (Dim1, 72.6%) and SCFA profiles (Dim2, 19.8%) and distinguished control and milk-inoculated groups. Feeding type was the dominant factor shaping microbiota and metabolite profiles, exerting a stronger influence than incubation time (PERMANOVA p < 0.05). These findings underscore the pivotal role of early feeding choices in directing both microbial colonisation and microbial metabolic activity in the infant gut.

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