Immunoglobulins (IgA) target bacteria in the breast milk and infant gut microbiomes

Once thought to be sterile, breast milk is now known to contain a diverse community of bacteria that contributes to the development of the microbiome in the gastrointestinal track of the breastfeeding infant. However, only a subset of the bacteria in breast milk take up residence in the infant gut, and the factors that influence which bacterial taxa colonize the infant gut microbiome are not well understood. Breast milk contains a high abundance of maternal immunoglobulins (IgA) that provide passive immunity to breastfeeding infants. While it is well-established that maternal IgA targets bacteria in the infant gut, we sought to determine if IgA also targets bacteria in the breast milk microbiome as a possible mechanism of preventing potentially harmful (pathogenic) bacteria in breast milk from colonizing the infant gut, while at the same time allowing healthful commensal microbes to establish residence. Paired breast milk and infant stool samples (n = 4) were collected from healthy breastfeeding subjects. Bacteria in samples were stained with PE-conjugated anti-IgA antibodies and subjected to fluorescence-activated cell sorting (FACS) to isolate IgA-bound (IgA+) bacteria from unbound (IgA-) bacteria. DNA from IgA+ and IgA- fractions was extracted and subjected to 16S analysis to confirm presence of bacteria in sorted fractions, and to subsequently identify which taxa (family, genus, and species) are targeted by IgA. IgA targets a significant proportion of cells in breast milk (32%, p = 0.020) and infant stool (42%, p = 0.015). PCR of universal bacterial 16S gene confirms presence of bacteria in IgA-bound (IgA+) and unbound (IgA-) fractions, indicating that IgA-bound bacteria are present in both breast milk and infant stool. 16S sequencing and inferred metagenomic analysis of sorted fractions subsequently reveal which bacterial taxa are targeted by maternal IgA in breast milk and the infant gut as well as shared versus discrete similarity between the two fractions. We have provided the first demonstration of an interaction in breast milk between the human humoral immune system and the milk microbiome. We speculate that these novel findings and approach will reveal how the maternal humoral immune response works in concert with microbiota in the breast milk to structure the developing infant gut microbiome.