Breastfeeding, the Gut Microbiome, and Growth among Infants in Lusaka, Zambia

In low- and middle-income countries (LMICs), ∼250 million young children are at risk of not reaching their full growth and developmental potential. Early-life gut microbiota is increasingly recognized as a key factor influencing long-term growth and development, yet data from LMICs, including Zambia, remain limited.

This substudy, nested within a 2 × 2 cluster-randomized trial (NCT05120427) in Lusaka, Zambia, aimed to characterize early-life gut microbiota composition and diversity; examine associations with breastfeeding status, nutritional status, and maternal HIV status; and explore links between the microbiome and child growth and development.

Anthropometry and participant characteristics were assessed at baseline (2-11 mo) and after 18 mo of intervention; child development was measured at endline using the Global Scales for Early Development. Rectal swab stool samples were collected from a subsample of 247 infants at baseline and profiled via 16S rRNA gene sequencing. Microbial abundances were visualized with stacked bar plots and uniform manifold approximation and projection for dimensionality reduction. β-Diversity and its associations with explanatory variables were analyzed using distance-based redundancy analysis and nonmetric multidimensional scaling. Multivariate linear models evaluated genus-level associations with growth indicators, whereas random forest regression and partial least squares regression identified predictors of endline growth and development outcomes.

We found that breastfeeding and nutritional status were significantly associated with microbiota composition. Mixed breastfeeding showed greater microbial diversity and broader taxa, whereas exclusive breastfeeding had higher Bifidobacterium abundance and increasing diversity with age. Despite these distinct trajectories, early microbiota features were weak predictors of later growth.

Overall, further research is needed to clarify early microbiome drivers and their impact on child outcomes, particularly in LMIC settings. This trial was registered at https://clinicaltrials.gov/study/NCT05120427 as NCT05120427.