The human milk microbiome varies by environmental factors and is associated with infant growth: findings from the IMiC Consortium

Human milk (HM) is a complex ecological matrix that connects mothers and infants to the surrounding environment, and promotes infant growth and health. While certain components of HM are well studied, including its macronutrient content and immune properties, the microbial composition of HM (i.e. the microbiome) is poorly characterized and its impact on infant health phenotypes is largely unknown. We hypothesized that the HM microbiome varies by environmental factors and is associated with differences in growth outcomes among HM-fed infants in settings with elevated rates of undernutrition and growth faltering. We leveraged a large dataset of HM samples (N=451) collected from mothers living in rural Tanzania, rural Burkina Faso, and peri-urban Pakistan around 1 month postpartum as a part of the International Milk Composition (IMiC) Consortium. 16S rRNA bacterial gene sequencing revealed geographic and seasonal signatures of the HM microbiome. Machine learning models identified Corynebacterium as a key feature that predicted infant birth season and growth outcomes in each of the three populations, though individual predictive taxa within the genus differed across the models. This study highlights the evolutionary importance of the HM microbiome as a biological system that embeds local environments and is associated with growth phenotypes critical to infant health and survival.