Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design
Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.
Authors
- Robert Bandsma (ORCID: https://orcid.org/0000-0001-6358-4750)
- Christina Lancioni (ORCID: https://orcid.org/0000-0002-0821-1211)
- Bonface M. Gichuki (ORCID: https://orcid.org/0000-0001-8766-7470)
- James Alexander Berkley (ORCID: https://orcid.org/0000-0002-1236-849X)
- Caroline Tigoi (ORCID: https://orcid.org/0000-0003-2750-7533)
- Judd L. Walson (ORCID: https://orcid.org/0000-0003-4836-720X)
- James M. Njunge (ORCID: https://orcid.org/0000-0002-8524-9133)
- Wieger P. Voskuijl (ORCID: https://orcid.org/0000-0001-5825-2831)
- Narshion Ngao (ORCID: https://orcid.org/0000-0002-0144-9577)
- Kirkby D. Tickell (ORCID: https://orcid.org/0000-0002-4108-1236)
- Timothy Rozday (ORCID: https://orcid.org/0000-0001-7016-0665)
- Ali Faisal Saleem (ORCID: https://orcid.org/0000-0003-1804-9868)
- Kaede V. Sullivan (ORCID: https://orcid.org/0000-0001-6654-5861)
- Benson O. Singa (ORCID: https://orcid.org/0000-0002-6605-324X)
- Mohammod Jobayer Chisti (ORCID: https://orcid.org/0000-0001-9958-3071)
- Syed Asad Ali
- Emmie Mbale
- Mark Stares
- Nitin Kumar
- Shuyi Wang
- Nicholas J.R. Dawson
- Tahmeed Ahmed
- Hilary P. Browne
- Yan Shao
Institutions
- International Centre for Diarrhoeal Disease Research (BD)
- Wellcome Sanger Institute (GB)
- Kenya Medical Research Institute (KE)
- The Childhood Acute Illness and Nutrition Network (KE)
- Centre Muraz (BF)
Publication Details
- Journal
- Cell
- Published
- 2026-02-18
- DOI
- https://doi.org/10.1016/j.cell.2026.01.007
- Primary Topic
- Probiotics and Fermented Foods
- Type
- article
- Field-Weighted Citation Impact
- 0.00