Time-specific bidirectional links between the maternal microbiome, milk composition, and infant gut microbiota

Early-life gut microbiome development is shaped by complex maternal and nutritional influences, yet the temporal and directional structure of these interactions remains unclear. In a longitudinal study of 152 mother-infant dyads in rural Burkina Faso, we examine how maternal gut and milk microbiomes, alongside milk components, influence infant gut microbiome development during the first 6 months. At 1-2 months, the infant gut microbiome clusters into three types: Escherichia-dominated, Bifidobacterium-dominated, and a diverse, pathogen-prevalent profile, which become less distinct by 5-6 months. Early infant gut microbiomes associate with maternal prenatal gut microbiota and early milk microbiome and oligosaccharides, while later variation links to other milk nutrients. Furthermore, early infant gut profiles predict subsequent milk composition, suggesting potential bidirectional communication between infant needs and maternal lactational physiology. These findings offer insights into early-life microbial development and inform future mechanistic studies and microbiome-targeted interventions, particularly in low-resource settings.