Bifidobacterium longum subsp. nexus nov., a novel subspecies isolated from infant stool

Ennis, D.; Andreu-Sanchez, S.; Levin, Y.; Goldberger, O.; Mallon, C. A.; Jayaprakash, Y. K.; Shao, Y.; Zhao, S.; Sinha, T.; Fu, J.; Weersma, R. K.; Alm, E.; Amster-Choder, O.; Lawley, T. D.; Harmsen, H. J. M.; van Sinderen, D.; Zhernakova, A.; Yassour, M.

doi:10.1101/2025.06.23.661074

bioRxiv · 10.1101/2025.06.23.661074

Bifidobacterium longum subsp. nexus nov., a novel subspecies isolated from infant stool

Ennis, D.·Andreu-Sanchez, S.·Levin, Y.·Goldberger, O.·Mallon, C. A.·Jayaprakash, Y. K.·Shao, Y.·Zhao, S.·Sinha, T.·Fu, J.·Weersma, R. K.·Alm, E.·Amster-Choder, O.·Lawley, T. D.·Harmsen, H. J. M.·van Sinderen, D.·Zhernakova, A.·Yassour, M.

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Abstract

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.

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Ennis, D., Andreu-Sanchez, S., Levin, Y., Goldberger, O., Mallon, C. A., Jayaprakash, Y. K., Shao, Y., Zhao, S., Sinha, T., Fu, J., Weersma, R. K., Alm, E., Amster-Choder, O., Lawley, T. D., Harmsen, H. J. M., van Sinderen, D., Zhernakova, A., Yassour, M.. 2025-06-23. Bifidobacterium longum subsp. nexus nov., a novel subspecies isolated from infant stool. https://doi.org/10.1101/2025.06.23.661074

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