Using metagenomic data from Irish infants, researchers discovered consistent, early functional shifts in the gut microbiome with the onset of complementary feeding, with a functional shift from simple sugar breakdown towards complex carbohydrate metabolism and short-chain fatty acid fermentation.
The researchers suggest the insights may inform public health strategies providing mothers with tailored, evidence-based guidance on infant feeding.
“The study reveals consistent, early functional shifts in the gut microbiome with the onset of complementary feeding, highlighting the strong influence of feeding mode on microbial metabolism and underscoring the need to consider function alongside taxonomy in early-life microbiome research,” they wrote.
The study
The researchers used metagenomic data from a subset of 125 Irish infants of The Cork Nutrition and Development Maternal-Infant Cohort Study (COMBINE), an observational, longitudinal study describing nutrition and early feeding, growth, health and neurological development in Irish children.
While on average, infants were breastfed up to 20 weeks of age, large variation in duration was observed, ranging from 1 to 95 weeks. Most mothers introduced solid foods between four and six months. Alongside which, 16.8% of infants were still breastfed, 12.8% were mixed-fed, and 69.6% were formula-fed.
The researchers identified stool frequency as a major contributor to variance in microbial profiles. They also reported “a clear pacing effect of breastfeeding”, where the age of breastmilk cessation rather than the introduction of solids drove the most pronounced microbial shifts.
“In line with previous research, our findings highlight dynamic metabolic adaptations of the microbiota to diverse nutritional substrates, differing by milk type consumed alongside solid foods,” the researcher wrote. “These patterns were most evident at the functional level and emerged earlier than previously recognized.”
Strains of interest
The data revealed significant variability between the infants’ microbiomes, but Bifidobacterium remained dominant for all before and after the introduction of solid foods.
During exclusive milk feeding, common species included E. coli, Streptococcus parasanguinis, S. salivarius, Enterococcus faecalis and Bifidobacterium longum. Following the introduction of complementary foods, the microbiomes shifted towards greater representation of Lachnospiraceae, Bacteroidaceae and Veillonellaceae.
Milk-feeding type appeared to shape microbiome diversity more strongly than the timing of solid-food introduction. Before solids were introduced, formula-fed infants had greater microbial diversity and richness than breastfed infants, although these differences disappeared after food introduction.
Conversely, after solids were introduced, formula-fed infants showed slightly lower diversity and numbers of functional pathways than breastfed infants. Mixed-fed infants did not differ significantly from either exclusively breastfed or formula-fed infants.
The introduction of solids altered the abundance of 24 bacterial species overall, but these changes varied according to milk-feeding practice. Notably, significant species-level changes were seen in formula-fed infants, but not in breastfed or mixed-fed infants.
Functional shifts
Solid foods also prompted substantial changes in the microbiome’s metabolic potential, affecting 183 pathways, particularly those involved in carbohydrate, amino acid, nucleotide and lipid metabolism.
Changes included increased pathways associated with starch metabolism, butyrate and acetate production, and some vitamin and cofactor synthesis, alongside decreases in other fermentation and nutrient degradation pathways.
Again, feeding history appeared important. Formula-fed infants underwent far more functional changes following the introduction of solids, with 162 pathways altered compared with just seven in exclusively breastfed infants, suggesting breastfeeding may influence how the infant microbiome responds to the transition to solid foods.
Noting potential limitations of the study, the authors highlighted that because samples collected before and after the introduction of solids occurred at different developmental ages, the independent contributions of age and complementary feeding cannot be disentangled.
They noted that they assessed metabolic potential rather than actual metabolic output.
“Given current limitations of functional databases, future studies should incorporate multi-omics approaches to validate these findings,” they wrote.
They further noted that a large proportion of functional pathway data in each sample was classified as unintegrated, likely reflecting the underrepresentation of infant-associated and understudied bacterial taxa in current reference gene and pathway databases, which are predominantly derived from adult and well-characterised microbial genomes.
They wrote: “This is a common limitation in infant gut metagenomic studies and underscores the need for expanded, age-representative reference databases to more fully capture the functional potential of early-life microbiomes.”
Source: Scientific Reports, https://doi.org/10.1038/s41598-026-71325-4, “Functional maturation of the infant gut microbiome during dietary transition in the first year of life”, Joos, R., Das, A., Ahern, G. et al.
