The entero–mammary pathway is a specialized route that selectively translocates bacteria to the newborn’s gut, playing a crucial role in neonatal development. Previous studies report shared bacterial and archaeal taxa between human milk and neonatal intestine. However, the functional implications for neonatal development are not fully understood due to limited evidence. This study aimed to identify and characterize the microbiota and metabolome of human milk, mother, and infant stool samples using high-throughput DNA sequencing and FT-ICR MS methodology at delivery and 4 months post-partum. Twenty-one mothers and twenty-five infants were included in this study. Our results on bacterial composition suggest vertical transmission of bacteria through breastfeeding, with major changes occurring during the first 4 months of life. Metabolite chemical characterization sheds light on the growing complexity of the metabolites. Further data integration and network analysis disclosed the interactions between different bacteria and metabolites in the biological system as well as possible unknown pathways. Our findings suggest a shared bacteriome in breastfed mother–neonate pairs, influenced by maternal lifestyle and delivery conditions, serving as probiotic agents in infants for their healthy development. Also, the presence of food biomarkers in infants suggests their origin from breast milk, implying selective vertical transmission of these features.

In the early days, maternal immunoglobulins are essential for sustaining a balanced gut environment by influencing the interaction between the host and the microbiome. The successional establishment of the pioneer strains is an interesting topic of research where maternal immunoglobulins appear to be important. This proof-of-concept study explored the binding pattern of IgA1, IgA2, IgM, and IgG classes to a commensal bacterial in human colostrum and the stool of breastfed neonates. We used flow cytometry coupled with 16S rRNA gene sequencing in human colostrum and neonatal feces samples to characterize this Ig-microbiota association. We observed that in human colostrum samples, IgA2 and IgM bind alfa and beta Proteobacteria, which can potentially stimulate neonatal immune system development in the gut. Other immunoglobulins like IgG predominantly bind facultative anaerobes belonging to the Firmicutes phylum, reported as part of human milk microbiota and pioneer colonizers of the neonatal gut. Maternal immunoglobulins also bind a wide diversity of bacteria in the neonatal stool. For instance, IgA2 and IgM bound more members of the phylum Bacteroidetes in comparison to IgG, these Bacteroidetes and some firmicutes have been reported as late colonizers of the neonatal gut, and their presence is important due to their ability to produce important short chain fatty acids like propionate and butyrate. Our results support the current view that microbial and immunoglobulin transference is crucial for developing the neonate's immune system and individual gut microbiota.