Analysis of the human breast milk microbiome and bacterial extracellular vesicles in healthy mothers

The microbiota of human breast milk (HBM) contribute to infant gut colonization; however, whether bacterial extracellular vesicles (EVs) are present in HBM or might contribute to this process remains unknown. In this study, we characterized the HBM microbiota of healthy Korean mothers and measured the key bacteria likely affecting infant gut colonization by analyzing both the microbiota and bacterial EVs. A total of 22 HBM samples were collected from lactating mothers. The DNA of bacteria and bacteria-derived EVs was extracted from each sample. In alpha-diversity analyses, bacterial samples showed higher richness and evenness than bacterial EV samples, and beta-diversity analyses showed significant differences between bacteria and bacterial EVs within identical individual samples. Firmicutes accounted for the largest proportion among the phyla, followed by Proteobacteria, Bacteroidetes, and Actinobacteria, in both bacteria and bacterial EV samples. At the genus level, Streptococcus (25.1%) and Staphylococcus (10.7%) were predominant in bacterial samples, whereas Bacteroides (9.1%), Acinetobacter (6.9%), and Lactobacillaceae(f) (5.5%) were prevalent in bacterial EV samples. Several genera, including Bifidobacterium, were significantly positively correlated between the two samples. This study revealed the diverse bacterial communities in the HBM of healthy lactating mothers, and found that gut-associated genera accounted for a high proportion in bacterial EV samples. Our findings suggest the existence of key bacteria with metabolic activity that are independent of the major bacterial populations that inhabit HBM, and the possibility that EVs derived from these bacteria are involved in the vertical transfer of gut microbiota.