BackgroundGut microbiota promote and maintain infant health. Vertical transmission of bacteria from the maternal gut through breast milk to an infant is an important source of microbial colonisation in human offspring. However, the causative active/culturable bacteria and mechanisms responsible for their mother-neonate vertical transfer via breastfeeding remain unclear. Secretory immunoglobulin A (sIgA) may mediate this vertical transmission; however, evidence supporting this hypothesis is required. In this study, we aimed to investigate whether sIgA-coated bacteria in the maternal intestine may migrate to breast milk and colonise the infant gut.ResultsMaternal faeces, breast milk, and neonatal faeces were collected from 19 mother-infant dyads during lactation stages specific to colostrum, transitional, and mature milk. sIgA-coated bacteria were enriched using magnetic-activated cell sorting, and live bacteria were cultured in lactic acid bacteria- and gut bacteria-specific medium. 16S ribosomal RNA gene amplicon sequencing showed that microbiota diversity in maternal faeces, breast milk, and infant faeces decreased sequentially from colostrum to transitional milk to mature milk. Significant beta diversity existed between sample types (p < 0.05). However, high similarity was found between sIgA-coated microbiota of the three types of samples at the mature milk stage. Source track analysis showed that sIgA-coated microbiota in breast milk and maternal gut are major contributors of sIgA-coated microbiota in infant gut. Genera with co-occurrence in sample types included Bifidobacterium, Enterococcus, Streptococcus, Lactobacillus, Klebsiella, Escherichia-Shigella, and an unclassified genus of Enterobacteriaceae. Shotgun sequencing of three dyads identified co-occurring species Lactobacillus and Bifidobacterium, including Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Lactobacillus jonsonii, Lactobacillus oris, Bifidobacterium longum, and Bifidobacterium breve. ConclusionsBreastmilk and infant faeces samples showed unique microbial composition and diversity in the three lactation stages. The fractions of sIgA-coated microbiota in maternal faeces, breast milk, and infant gut showed similar bacterial abundance patterns. This study will facilitate development of strategies to adjust aberrant microbial establishment and reduce the risk of disease by providing essential information for effective probiotic administration to the neonate and/or breastfeeding mother.