Longitudinal culture-enriched metagenomics reveals persistence and sharing of culturable infant gut and breast milk microbiota

Abstract The importance of gut microbiota in early life and the contribution of breast milk to human health and disease prevention has attracted extensive attention as studied by culture-independent metagenomic technologies. However, the fraction and assembled dynamics of culturable early gut and breast milk microbiota remain unexplored. In this study, longitudinal culture-enriched metagenomic sequencing was applied to examine the proportion, assembly, persistence and sharing of culturable microbiota from the infant gut and breast milk in the first six months of life. Compared to culture-independent sequencing of infant fecal samples, an average of 54% at species level, 69% at subspecies level, and 82% at strain-level resolution of gut microbiota were cultured with 14 different culture media or a representative subset of media, representing 93% of the relative abundance at species level. No difference was observed in the capacity of media used to recover gut microorganisms from infants born vaginally or by cesarean section (C-section). Depletion of culturable Bacteroides and Bifidobacterium and an enrichment of culturable Citrobacter , Klebsiella , and Veillonella were observed in infants born via C-section. The metagenomic assembled genomes from infant fecal samples and breast milk were significantly improved with culture enrichment, particularly for breast milk. By integrating newly assembled and existing genomes from gut microbiota, 31 and 26 culturable strains were persistent (presence in at least two time points) in infants born vaginally or by C-section, respectively, with the former distributed more diversely at phylum level. Twenty culturable strains were shared between breast milk and infant gut samples. Collectively, these results provide the first evidence for the culturable microbiota from infant gut and breast milk regarding their assembly, persistence and sharing status, with potential implications for probiotic development and infant health.