Functional maturation of the infant gut microbiome during dietary transition in the first year of life

Abstract During the first months of life, breastfeeding and/or formula provide an infant’s sole nutrition. The introduction of solid foods marks the complementary feeding period – a major dietary and gut microbial transition. While taxonomic development of the early-life gut microbiome is well described, functional changes and the influence of different milk types remain less understood. This study used metagenomic data from a subset of 125 Irish infants of the COMBINE cohort to examine taxonomic and functional microbiome shifts during early feeding transitions. Consistent with nutritional guidelines, over 80% of mothers introduced solid foods between four and six months. Alongside, 16.8% of infants were still breastfed, 12.8% were mixed-fed, and 69.6% were formula-fed. Microbial diversity increased over time, alongside a shift in community structure toward a more anaerobic gut environment. Functionally, carbohydrate metabolism transitioned from simple sugar degradation to complex polysaccharide degradation and SCFA fermentation. Clear differences emerged between milk types, with a pacing effect of breastfeeding and distinct metabolic adaptations to varying nutritional substrates. 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.