Microbial Profile Along the Maternal–Infant Axis: Early Characterization and Associations in Breastfeeding Women and Their Newborns in Colombia

There is growing interest in understanding the origins of the bacterial taxa involved in the assembly of the infant microbiome. The mother has been recognized as a key source in this process, potentially contributing over 50% of the neonatal microbiota through various maternal niches. Despite this importance, knowledge about microbiota dynamics during the first 1,000 days of life remains limited in the Latin American context. In this study, we characterized the maternal–infant microbiota and examined the relationships among the maternal gut, human milk, and infant gut microbiomes in a cohort of Colombian women and their newborns during the first three months postpartum. A total of 90 samples including maternal feces, infant feces, and human milk from healthy mother–infant dyads were analyzed to assess bacterial composition and diversity. The maternal gut microbiota was characterized by Subdoligranulum spp., Akkermansia spp., Christensenellaceae_R-7_group, and Bacteroides spp., while the human milk microbiota was dominated by Streptococcus spp. and Staphylococcus spp. In contrast, the infant gut microbiota was primarily composed of Escherichia-Shigella spp. and Bifidobacterium spp. A total of 644 ASVs were shared between the maternal gut and human milk, belonging mainly to the orders Bifidobacteriales and Enterobacterales. Our findings demonstrate that the maternal gut, human milk, and infant gut microbiomes represent distinct yet interconnected ecosystems, establishing early microbial relationships in which the maternal gut microbiota plays a key role in shaping the milk microbiome. These insights highlight the importance of implementing strategies to enhance nutritional and healthcare interventions targeting lactating women.