D. Ennis, S. Andreu-Sanchez, Y. K. Jayaprakash, T. Sinha, H. Peng, O. Goldberger, J. A. D. Docherty, N. Kuzub, A. Fernandez-Pato, S. Zhao, Y. Shao, Y. Levin, L. cohort study, O. Amster-Choder, T. D. Lawley, R. K. Weersma, E. Alm, M. C. Collado, J. Fu, A. Kurilshikov, H. J. M. Harmsen, C. A. Mallon, D. v. Sinderen, A. Zhernakova, M. Yassour
Bifidobacterium longum is a foundational, genetically diverse member of the infant gut microbiome, yet resolving its subspecies in metagenomic data remains challenging. Here, we performed a deep phylogenetic characterization of the B. longum species utilizing 4,577 fecal metagenomes from the LLNEXT mother-infant cohort alongside a global dataset of 1,220 genomes and metagenome-assembled genomes (MAGs). We identified a novel, geographically widespread lineage: Bifidobacterium longum subsp. nexti. Using a polyphasic taxonomic analysis, including average nucleotide identity and digital DNA-DNA hybridization, confirms subspecies-level divergence. Distinct from other members of the B. longum species, BL. nexti harbors -amylopullulanase and grows on soluble starch and often pullulan, consistent with -glucan utilization. Within the LLNEXT cohort, BL. nexti is enriched in formula-fed infants and shows evidence consistent with vertical transmission. Globally, while BL. nexti is geographically widespread, it usually persists at low relative abundance across diverse populations. By resolving a major fraction of previously unclassified B. longum diversity, this study provides new insights into the specialized lineages and ecological dynamics driving the assembly of the developing infant microbiome.