Environmental and maternal imprints on infant gut metabolic development

Early life is a critical period for immune and metabolic development, but these patterns remain underexplored in populations from low- and middle-income countries. Here, we profile the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first 6 months of life. Importantly, we observe an increase in microbially derived bile amidates and N-acyl lipids with age in conjunction with reads matching the bile salt hydrolase/transferase (bsh) gene. Although microbial source tracking confirms maternal fecal seeding, a substantial environmental contribution is also highlighted. Differences in infant fecal metabolic profiles are associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. Cesarean section (C-section) delivery and untreated drinking water are linked to transient metabolic differences, including increases in bile amidates, N-acyl lipids, and other host-microbe co-metabolic products, including acylcarnitines. Multi-omics analysis reveals specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances influence gut metabolic development through the microbiome.