Feeding mode was the dominant factor shaping microbiome composition and diversity in Egyptian infants, with exclusive breastfeeding associated with greater microbial richness and broader ecological structure, formula feeding linked to reduced diversity and a narrower community profile, and mixed feeding reflecting an intermediate configuration.
Key Findings
Results
Artificial (formula) feeding was associated with Actinobacteria dominance, near absence of Bacteroidetes, and the lowest gut microbial diversity among the three feeding groups.
Stool samples from Egyptian infants aged 1 to 6 months were analyzed using 16S rRNA gene sequencing targeting the V3-V4 region
Sequence processing, denoising, and taxonomic assignment were performed in QIIME2
Artificially fed infants showed dominance of the phylum Actinobacteria
Bacteroidetes were nearly absent in the artificially fed group
Artificially fed infants had the lowest alpha diversity (richness and diversity metrics) of all three feeding groups
Results
Breastfeeding was associated with a more balanced phylum distribution, detectable Bacteroidetes, increased Proteobacteria, and significantly higher microbial richness and diversity.
Breastfed infants showed a more balanced distribution across phyla compared to artificially fed infants
Bacteroidetes were detectable in breastfed infants, in contrast to their near absence in the artificially fed group
Proteobacteria were increased in breastfed infants
Breastfeeding was associated with 'significantly higher richness and diversity' compared to artificial feeding
Genus-level analysis showed breastfeeding enriched facultative anaerobes including Escherichia-Shigella and Enterobacter
Results
Mixed feeding was associated with the highest alpha diversity of all three groups and a Firmicutes-dominated microbial profile consistent with a transitional microbial state.
Mixed-fed infants had higher alpha diversity than both exclusively breastfed and exclusively formula-fed infants
The mixed feeding group showed a Firmicutes-dominated phylum profile
Mixed feeding was described as 'consistent with a transitional microbial state'
Mixed feeding enriched fermentative genera such as Subdoligranulum and Eubacterium
Beta diversity placed mixed-fed infants intermediate between breastfed and artificially fed infants
Results
Beta diversity analysis clearly separated breastfed from artificially fed infants, with mixed-fed infants occupying an intermediate position.
Beta diversity was used to assess between-sample compositional differences across feeding groups
Breastfed and artificially fed infants showed clear separation in beta diversity space
Mixed feeding was intermediate in beta diversity between the two exclusive feeding groups
Feeding mode was identified as 'the dominant factor shaping microbiome composition and diversity'
Results
Artificial feeding specifically enriched Bifidobacterium at the genus level, while breastfeeding enriched facultative anaerobes and mixed feeding enriched fermentative genera.
Differentially abundant taxa between feeding groups were identified using LEfSe (Linear discriminant analysis Effect Size)
Artificial feeding was associated with enrichment of Bifidobacterium
Breastfeeding enriched Escherichia-Shigella and Enterobacter
Mixed feeding enriched Subdoligranulum and Eubacterium, described as 'fermentative genera'
These genus-level signatures were distinct across all three feeding modes
Results
Co-occurrence network analysis revealed structured co-variation among anaerobic commensals in breastfed infants and denser opportunistic connectivity in artificially fed infants.
Co-occurrence network analysis was performed to assess microbial interaction patterns across feeding groups
Breastfed infants showed 'structured co-variation among anaerobic commensals'
Artificially fed infants showed 'denser opportunistic connectivity', suggesting a different ecological organization
Data from Middle Eastern populations on infant gut microbiome development are limited, and this Egyptian cohort study addresses a geographic gap in the literature.
The study cohort comprised Egyptian infants aged 1 to 6 months
The authors noted that 'data from Middle Eastern populations remain limited'
The study used 16S rRNA gene sequencing of the V3-V4 region on stool samples
The findings were described as relevant for breastfeeding promotion in the context of 'optimal early immune development'
What This Means
This research examined how different feeding methods — exclusive breastfeeding, exclusive formula feeding, and mixed feeding — affect the community of bacteria living in the guts of young Egyptian infants (ages 1 to 6 months). The researchers collected stool samples and used advanced genetic sequencing to identify what types of bacteria were present and in what proportions. They found that how an infant is fed has a strong influence on which bacteria colonize the gut in early life. Formula-fed infants had the least diverse gut bacteria communities, dominated by one bacterial group (Actinobacteria) and missing others (like Bacteroidetes) that were present in breastfed babies. Breastfed infants had a more varied and balanced bacterial community. Interestingly, infants who received both breast milk and formula had the highest overall diversity of bacteria, suggesting their gut microbiome reflects a transitional state between the two extremes.
The study also found that specific types of bacteria were associated with each feeding method. Formula feeding was linked to higher levels of Bifidobacterium, breastfeeding to certain facultative anaerobes like Escherichia-Shigella and Enterobacter, and mixed feeding to fermentative bacteria like Subdoligranulum and Eubacterium. Network analysis further revealed that breastfed infants had more organized bacterial communities, while formula-fed infants had denser connections among opportunistic bacteria. This research suggests that feeding method shapes not just which bacteria are present but also how they interact with each other in an infant's gut.
This study is notable because it comes from an Egyptian cohort, filling a gap in knowledge about infant gut microbiome development in Middle Eastern populations, where such data are scarce. The findings support the idea that exclusive breastfeeding fosters a richer and more ecologically structured gut bacterial community in early infancy, which may have implications for immune system development. This research suggests that the type of bacteria established in early life differs meaningfully depending on how infants are fed, adding to a growing body of global evidence on the importance of early feeding choices for infant gut health.
ELHindi S, Abdalla S, Azab M, Bendary M. (2026). Impact of Infant Feeding Mode on Gut Microbiome Composition in Early Life: Evidence from an Egyptian Cohort.. Scientific reports. https://doi.org/10.1038/s41598-026-66403-6