A Strain-Resolved Genome Resource Defines Conserved Infant Gut Microbiome Assembly across Sub-Saharan Africa and South Asia

Infant gut microbiome assembly shapes growth, immunity, and neurodevelopment, yet almost all high-resolution metagenomic data derive from high-income cohorts. We assembled a deep shotgun metagenomic reference from 596 generally healthy children aged 2–23 months across nine sites in six low- and middle-income countries (LMICs) in sub-Saharan Africa and South Asia. From ~5.7 Tbp we reconstructed 7,683 high-quality genomes spanning 1,941 species, including 220 uncultured and five novel core species, with strain-resolved functional annotations and harmonized metadata. Assembly followed a conserved three-stage trajectory (pioneer, transition, expansion) governed by breastfeeding and weaning and reproducible across all nine sites, and potentially host-beneficial functions were maintained despite taxonomic turnover. Against age-matched high-income cohorts, LMIC microbiomes diverged from the first months of life and carried higher species richness, with Bifidobacterium (notably B. infantis), Lactobacillus, and Prevotella depleted in high-income infants. This open-access reference anchors future LMIC cohorts and supports globally inclusive infant microbiome research.