Ancestral trajectory of infant gut microbiome assembly in non-industrialised populations

Infant gut microbiome assembly influences childhood growth and development. However, current understanding is based almost exclusively on infants from highly industrialised, high-income countries. Here, we present a high-resolution map of gut microbiome assembly in 596 infants from six non-industrialised countries across sub-Saharan Africa and South Asia. Microbiome assembly followed a unified trajectory comprising three distinct stages, characterised by the ordered acquisition and loss of bacterial species and functions. Progression through these stages is governed by breastfeeding and the timing of weaning, revealing an ancestral pattern of microbiome succession conserved across diverse non-industrialised populations. Core microbiome functions are rapidly established by a defined consortium of pioneer species, followed by age-dependent expansions in functional capacity, including pathways implicated in metabolism, immune regulation, and neurodevelopment. Comparison with infant microbiomes from highly industrialised populations reveals that key bacteria underpinning the ancestral assembly trajectory— Bifidobacterium, Lactobacillus and Prevotella —are depleted with industrialisation. Our microbiome assembly map provides a reference for optimising infant microbiome development and supporting child growth through rational design of next-generation infant probiotics, and highlights commensal microbes that should be prioritised for preservation amid global lifestyle transitions.