The role of human milk oligosaccharides in shaping and restoring infant gut microbiota: population-based cohort study

Background Infant gut microbiota colonization is important for supporting normal development and long-term health of children. Human milk oligosaccharides (HMOs) influence the composition of the gut microbiota, but their specific effects, particularly after breastfeeding, remain poorly understood. Objectives We aimed to deepen the understanding of how HMOs associate with the gut microbiota composition at 3 mo and at 13 mo of age. In addition, we assessed the role of HMOs as microbiome-rebalancing agents in cesarean-delivered infants. Methods We analyzed fecal samples from infants at 3 mo ( n = 517) and 13 mo ( n = 522), along with human milk samples at 3 mo, from a population-based cohort. Gut microbiota was profiled by 16S rRNA sequencing, and 19 HMOs were quantified by high-performance liquid chromatography with fluorescent detection. Dirichlet multinomial mixtures clustering was used to identify bacterial fecal community types (FCTs) and multinomial logistic regression models to study the association between HMOs and FCTs. Permutational multivariate analysis of variance and linear regression models were used to associate HMOs with gut microbiota diversity measures and Spearman correlation to bacterial genera. Results HMOs were associated with gut microbiota FCTs, diversity measures, and bacterial genera at 3 and 13 mo of age. At 3 mo, disialyllacto-N-tetraose and the structurally related lacto-N-sialyllactose b showed notable associations with the gut microbiota, whereas at 13 mo, fucodisialyllacto-N-hexaose was associated with multiple gut microbiota metrics. Maternal secretor status was associated with the gut microbiota beta diversity ( R 2 = 0.003, P < 0.05) and decreased Shannon diversity ( b = –0.24, P < 0.05) at 3 mo, with diminishing associations at 13 mo (observed richness, b = –11, P < 0.05). Although no individual HMOs showed microbiome-rebalancing effects in cesarean-born infants, infants fed by nonsecretor mothers exhibited stronger cesarean-related microbiota patterns compared with those fed by secretors. Conclusions HMOs exhibit age-dependent and structure-specific associations with infant gut microbiota, extending beyond breastfeeding.