Environmental and maternal imprints on infant gut metabolic development
Kine Eide Kvitne, Celeste Allaband, Jennifer C. Onuora, Daniela S. Perry, Simone Zuffa, Lucas Patel, Vincent Charron‐Lamoureux, Ipsita Mohanty, Kristija Sejane, Abubaker Patan, Abdullah Al Mahmud, Tahmeed Ahmed, Diego G. Bassani, Antonio González-Torres, Davidson H. Hamer, Rashidul Haque, Benjamin Ho, Md. Iqbal Hossain, Mohammad Shahidul Islam, Daniel McDonald, Lisa G. Pell, Huma Qamar, Daniel Roth, Samir K. Saha, Prakesh S Shah, Md Muniruzzaman Siddiqui, Shafiqul Alam Sarker, Shamima Sultana, Sydney P. Thomas, Lindsey A. Burnett, Shirley M. Tsunoda, Lars Bode, Pieter C. Dorrestein, Rob Knight
Abstract
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.