Priority effects, nutrition and HMO-metabolism drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome

Bifidobacterium longum subsp. longum (BLsL) and Bifidobacterium longum subsp. infantis (BLsI) are among the first colonizers of newborns' gut, playing a crucial role in the maturation of the host microbial community. Yet, many of the factors and principles governing their colonization dynamics remain unknown. Here, we analyze fecal samples from 24 mother-infant pairs during the first 6 months of life to identify important features associated with the colonization success and succession outcomes of B. longum subspecies. BLsL was the most abundant and prevalent gut Bifidobacteria at 1 month, being replaced by BLsI at 6 months of age. We find the interplay of priority effects, milk-feeding type and HMO-utilization potential to govern abundance dynamics of B. longum subspecies during the first 6 months of life. By combining strain-tracking, meta-pangenomics and machine learning we were able to provide novel insight into the ecological framework and genomic adaptations associated with the early-life abundance dynamics of B. longum subspecies.