Gut microbiome variations across lifestyles and life stages

Cross-population microbiome studies are limited by heterogeneous data, cross-sectional designs, and lack of integrated health and omics datasets. The Nepali Maternal and Infant Microbiome Study (NeMaSiMa) addresses these gaps with a longitudinal, multi-omics investigation of host–microbiome interactions from pregnancy through the first three years of life. The study includes ~1,000 genetically and geographically matched individuals from foraging, agrarian, peri-urban, and urban communities, enabling rigorous lifestyle comparisons. Biospecimens (feces, breastmilk, saliva, vaginal swabs) are collected with detailed diet, health, sanitation, and maternal/child care metadata and flash-frozen in liquid nitrogen to preserve integrity for strain isolation and functional genomics. Longitudinal host genomic, ultra-deep metagenomic, and metabolomic datasets enable integrative analyses.

Preliminary sequencing (104M read pairs/adult; 33M read pairs/infant) shows high quality and lifestyle-driven microbiome differences. Pregnancy-associated shifts suggest enhanced gut integrity, energy harvest, and immune modulation. Infant microbiomes differ by environment, with urban infants showing distinct trajectories and Bifidobacterium infantis as a key early colonizer. Ongoing work examines maternal–infant strain transmission and links to long-term outcomes, including childhood stunting. Experimental innovations, including gut-on-chip models, probe host–microbe–immune interactions for microbiome-based therapeutics.

NeMaSiMa also advances community engagement via antenatal care initiatives, health worker training, and adolescent girl fellowships as peer health advocates, recognized by the Gates Foundation and Nepal Health Research Council, establishing it as a global platform for early-life microbiome research in underrepresented populations.