Contributions of Household Environmental Exposures and Early-Life Factors to Infant Gut Microbiome Development in a Low-Resource Setting in Mozambique

Household environmental conditions in low-resource settings influence infant gut microbiome development, yet longitudinal evidence from such settings remains limited. We leveraged data from PAASIM, a prospective mother–infant cohort in Beira, Mozambique, to examine how measured household environmental exposures were associated with infant gut microbiome development across the first year of life, and how these associations related to other early-life factors. We collected infant stool samples at 3, 6, 9, and 12 months and profiled them using 16S rRNA gene sequencing. We evaluated visit-specific household environmental indicators, including water, sanitation, and hygiene (WASH) conditions, household water insecurity, animal contact, animal fecal exposure, and household crowding, along with contextual early-life factors such as breastfeeding, diet, socioeconomic status, and food insecurity. Infants with higher Shannon diversity at earlier time points tended to maintain higher diversity later in infancy, suggesting temporal tracking of microbiome development. Measured household environmental exposures showed modest and time-specific associations with Shannon diversity, with the most pronounced exposure–diversity signals observed around mid-infancy. Weighted UniFrac community structure showed substantial overlap across measured environmental exposure groups, indicating that these indicators explained limited variation in overall community composition. However, specific environmental and contextual factors were associated with taxonomic differences. Each additional child under 5 years in the household was associated with a higher relative abundance of Campylobacterota at 6 months (β = 1.28; 95% CI: 0.54–2.03). Early weaning by 3 months was associated with higher 6-month relative abundance of Clostridioides, Bilophila, and Desulfobacterota, and with higher Roseburia at 9 months. Together, our findings suggest that measured household environmental indicators, particularly household crowding, may contribute to infant gut microbiome development. However, their overall contribution to community structure was modest compared with prior microbiome state and feeding-related factors. Limited explained variation should be interpreted cautiously, as commonly measured household indicators may capture only part of the broader environmental microbial exposure landscape relevant to early-life microbiome assembly.