An Irish study of 125 babies found that feeding history influenced the microbiome’s shift towards complex carbohydrate breakdown and short-chain fatty acid production when solids were introduced.
Researchers analysing stool samples from Irish infants have found that the move from milk to solid foods triggers an early, measurable change in the gut microbiome, with bacteria shifting away from simple sugar metabolism and towards the breakdown of complex carbohydrates and the production of short-chain fatty acids.
The study, published in Scientific Reports, drew on metagenomic data from 125 babies in the Cork Nutrition and Development Maternal-Infant Cohort Study, a long-running Irish project tracking nutrition, growth, health and neurological development. It found that the timing and type of milk feeding mattered as much as, and in some cases more than, the introduction of solids itself. Breastfeeding typically continued until around 20 weeks, although there was wide variation, and most mothers introduced complementary foods between four and six months.
The researchers said stool frequency explained a notable share of the variation in microbial profiles, but they also identified what they described as a “clear pacing effect of breastfeeding”, in which the age at which breast milk stopped appeared to drive the strongest microbiological changes. Before solids were introduced, formula-fed infants showed greater microbial diversity and richness than breastfed infants. Once complementary foods were added, those differences largely disappeared, although formula-fed babies then tended to have slightly lower diversity and fewer functional pathways than breastfed babies.
Across all infants, Bifidobacterium remained a dominant genus before and after solid foods began. Other common species during exclusive milk feeding included E. coli, Streptococcus parasanguinis, S. salivarius, Enterococcus faecalis and Bifidobacterium longum. After solids were introduced, the microbiome moved towards a higher presence of Lachnospiraceae, Bacteroidaceae and Veillonellaceae, a pattern consistent with a gut environment adapting to more complex dietary substrates. Earlier studies, including work indexed in PubMed, have likewise found that the biggest microbiome changes in the first year of life often occur around the introduction of solid foods, rather than later during diet diversification.
The functional changes were even more striking than the taxonomic ones. The Irish study reported changes in 183 metabolic pathways after solids were added, including pathways involved in carbohydrate, amino acid, nucleotide and lipid metabolism. There were also shifts linked with starch processing, butyrate and acetate production, and some vitamin and cofactor synthesis. But the response depended heavily on feeding history: formula-fed infants showed 162 altered pathways after solids, compared with just seven in exclusively breastfed infants, suggesting that breast milk may shape how the microbiome adapts to the transition.
The authors said the findings could help guide public health advice for parents by strengthening evidence-based feeding support in the first year of life. They also cautioned that the study could not fully separate the effects of age from those of complementary feeding, because samples taken before and after solids were collected at different developmental stages. In addition, the team measured metabolic potential rather than direct metabolic output, and noted that many pathways could not yet be assigned confidently because infant-associated microbes remain under-represented in reference databases. That limitation, they said, underlines the need for broader, age-specific microbiome resources and for future studies that combine metagenomics with other “multi-omics” methods to confirm how early feeding choices shape gut function.
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