Environmental and Maternal Imprints on Infant Gut Metabolic Programming

Kvitne, K. E.; Allaband, C.; Onuora, J. C.; Perry, D.; Zuffa, S.; Patel, L.; Charron-Lamoureux, V.; Mohanty, I.; Sejane, K.; Patan, A.; Al Mahmud, A.; Ahmed, T.; Bassani, D. G.; Gonzalez, A.; Hamer, D. H.; Haque, R.; Ho, B.; Hossain, M. I.; Islam, M. S.; McDonald, D.; Pell, L. G.; Qamar, H.; Roth, D. E.; Saha, S.; Shah, P. S.; Siddiqui, M. M.; Sarker, S. A.; Sultana, S.; Thomas, S.; Burnett, L. A.; Tsunoda, S. M.; Bode, L.; Dorrestein, P. C.; Knight, R.

doi:10.1101/2025.07.24.666662

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bioRxiv · 10.1101/2025.07.24.666662

Environmental and Maternal Imprints on Infant Gut Metabolic Programming

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Abstract

Early life is a critical period for immune and metabolic programming, but developmental patterns remain underexplored in populations from low- and middle-income countries. Here, we profiled the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first six months of life. Importantly, we observed 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. While microbial source tracking confirmed maternal fecal seeding, a substantial environmental contribution was also highlighted. Differences in infant fecal metabolic profiles were associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. C-section delivery and untreated drinking water were 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 revealed specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances shape metabolic gut programming through the microbiome.

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Kvitne, K. E., Allaband, C., Onuora, J. C., Perry, D., Zuffa, S., Patel, L., Charron-Lamoureux, V., Mohanty, I., Sejane, K., Patan, A., Al Mahmud, A., Ahmed, T., Bassani, D. G., Gonzalez, A., Hamer, D. H., Haque, R., Ho, B., Hossain, M. I., Islam, M. S., McDonald, D., Pell, L. G., Qamar, H., Roth, D. E., Saha, S., Shah, P. S., Siddiqui, M. M., Sarker, S. A., Sultana, S., Thomas, S., Burnett, L. A., Tsunoda, S. M., Bode, L., Dorrestein, P. C., Knight, R.. 2025-07-24. Environmental and Maternal Imprints on Infant Gut Metabolic Programming. https://doi.org/10.1101/2025.07.24.666662

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