Microbiome and metabolome dynamics in breastfed infants during dietary transition to solid foods
Background Early-life microbiota plays a crucial role in immune and metabolic development, yet its maturation during the key dietary transition from human milk to solid food remains poorly characterized. Methods In this pilot study, we aimed to characterize changes in the oral and fecal bacteriomes of breastfed infants throughout this period. Oral swabs and fecal samples from twelve mother-infant pairs (breastfed infants) from the CELSPAC:TNG cohort were collected at five time points from two to twelve months postpartum and analyzed using 16S rRNA amplicon sequencing. Whole metabolome profiling of infants' fecal and mothers' human milk samples was conducted using NMR spectroscopy. Results Continual changes in relative abundances of several bacterial genera in oral (particularly Gemella and Streptococcus) and fecal (particularly Blautia and Intestinibacter) samples, as well as in metabolome (including concentrations of short-chain fatty acids) were observed throughout the first year of life. Cross-modal omics analysis revealed a strong negative relationship between the concentration of ß-hydroxybutyrate and genus Bifidobacterium in infants' fecal samples. Conclusion This study provides a detailed description of the changes in oral and fecal bacteriomes throughout the first year of infants' lives and associates these changes with changes in fecal metabolome, including short-chain fatty acids.