Evolutionary historical past and microbial cross-feeding form lifestyle-stratified dominance of Bifidobacterium longum subspecies in infants

Abstract

Bifidobacterium longum (Bl.) is a key early-life intestine symbiont, but its evolutionary origin and mechanisms underlying the worldwide biogeographic distribution of its subspecies stay poorly resolved. Here, we compiled a world genomic atlas of >7,000 MAGs/genomes from infants, domesticated animals, non-human primates, and historical people. High-resolution phylogenomic and purposeful analyses expanded infant-associated subspecies to 5. Compared with non-human primates, B. longum was extra prevalent in domesticated animals and historical people courting from 150 to 1,500 years in the past. Moreover, human- and livestock-derived lineages from the identical geographic areas clustered collectively, suggesting potential host-associated transmission. Ecologically, Bl. infantis and Bl. longum predominated in non-Western and Western infants, respectively, impartial of breastfeeding, supply mode, or antibiotic publicity. Instead, their distribution was related to co-occurring microbes and HMO-driven cross-feeding interactions. These findings clarify subspecies differentiation within the intestine microbiota of Western and non‑Western infants and supply a framework for community-mediated interventions in youth.