Impact of Infant Feeding Mode on Gut Microbiome Composition in Early Life: Evidence from an Egyptian Cohort

Abstract

The infant gut microbiome develops rapidly in early life, shaping immune maturation and metabolic pathways. Data from Middle Eastern populations remain limited. We studied Egyptian infants aged 1 to 6 months to assess feeding related differences in gut microbiome composition. Stool samples were collected and the gut microbiota was profiled using 16S rRNA gene sequencing targeting the V3-V4 region. Sequence processing, denoising, and taxonomic assignment were performed in QIIME2. Differentially abundant taxa between feeding groups were identified using LEfSe. Alpha and beta diversity, and co-occurrence networks were analyzed. Feeding mode was the dominant factor shaping microbiome composition and diversity. Artificial feeding showed Actinobacteria dominance, near absence of Bacteroidetes, and lowest diversity. Breastfeeding was associated with a more balanced phylum distribution, detectable Bacteroidetes, increased Proteobacteria, and significantly higher richness and diversity. Mixed feeding showed the highest alpha diversity and a Firmicutes dominated profile, consistent with a transitional microbial state. Beta diversity clearly separated breastfed from artificially fed infants, with mixed feeding intermediate. Genus level signatures differed by feeding mode. Artificial feeding enriched Bifidobacterium. Breastfeeding enriched facultative anaerobes including Escherichia Shigella and Enterobacter. Mixed feeding enriched fermentative genera such as Subdoligranulum and Eubacterium. Network analysis revealed structured co-variation among anaerobic commensals in breastfed infants and denser opportunistic connectivity in artificially fed infants. Feeding mode strongly influences gut microbiome development in Egyptian infants. Exclusive breastfeeding is associated with greater microbial richness and broader ecological structure, whereas formula feeding is linked to reduced diversity and a narrower community profile. Mixed feeding reflects an intermediate configuration. These findings support breastfeeding promotion for optimal early immune development.