Cited by 17Gut microbiota and healthInfant Nutrition and HealthProbiotics and Fermented Foods

Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design

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Shao, Yan, Wang, Shuyi, Gichuki, Bonface M., Stares, Mark D., Rozday, Timothy J., Kumar, Nitin, Browne, Hilary P., Dawson, Nicholas J.R. +19 more·2026·Cell

Abstract

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.

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Crossref · 10.1016/j.cell.2026.01.007

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  • Similar patterns, in which non-Westernized or rural cohorts exhibit greater strain-level and accessory genome diversity than Westernized populations, have been reported within the genus Bifidobacterium.

    “Similar patterns, in which non-Westernized or rural cohorts exhibit greater strain-level and accessory genome diversity than Westernized populations, have been reported within the genus Bifidobacterium [34,76] .”
  • The inclusion of metagenome-assembled genomes (MAGs) provides a far more complete genetic landscape, as recently observed with B. adolescentis and B. longum pangenome reconstruction.

    “As recently observed with the B. adolescentis and B. longum pangenome reconstruction, the inclusion of metagenome-assembled genomes (MAGs) provides a far more complete genetic landscape [33,34] .”
  • The B. bifidum pangenome is closed.

    “By incorporating a large number of MAGs, following an approach previously applied to B. adolescentis and B. longum [33,34] , this study provides a robust framework allowing genomic investigation within a closed B. bifidum pangenome.”

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Authors
Shao, Y., Wang, S., Gichuki, B. M., Stares, M. D., Rozday, T. J., Kumar, N., Browne, H. P., Dawson, N. J. R., Njunge, J. M., Tigoi, C., Ngao, N., Chisti, M. J., Singa, B. O., Kariuki, S., Diallo, A. H., Saleem, A. F., Ali, S. A., Mupere, E., Mbale, E., Tickell, K. D., Voskuijl, W. P., Lancioni, C. L., Bandsma, R. H. J., Ahmed, T., Walson, J. L., Berkley, J. A., & Lawley, T. D.
Affiliations
  • Wellcome Sanger Institute (GB)
  • Kenya Medical Research Institute (KE)
  • International Centre for Diarrhoeal Disease Research (BD)
  • Université Joseph Ki-Zerbo (BF)
  • Aga Khan University (PK)
  • The Childhood Acute Illness and Nutrition Network (KE)
  • University of Washington (US)
  • Emma Kinderziekenhuis (NL)
  • Oregon Health & Science University (US)
  • University of Malawi (MW)
  • Johns Hopkins University (US)
Corresponding author
  • Shao, Yan
  • Lawley, Trevor D.
Venue
Cell
Publisher
Elsevier BV
Published
2026-03
Volume
189
Issue
6
Pages
1854-1873.e17
ISSN
0092-8674 (ISSN-L)
OpenAlex
W7130370638
Cited by
17
References
113
Citations by year
2026: 17
FWCI
34.74
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eCommons - AKU (Aga Khan University) (submittedVersion)
Funders
  • China Scholarship Council (202306010298)
  • Wellcome Trust (206194, 220540/Z/20/A)
  • Bill and Melinda Gates Foundation (INV-000791, OPP1131320, INV-003225)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
Keywords
Bifidobacterium infantis, Bifidobacterium longum, phylogenomics, low- and middle-income countries, neonatal gut microbiota, strain selection, species delimitation
MeSH terms
Bifidobacterium longum, Bifidobacterium longum subspecies infantis, Humans, Infant, Phylogeny, Genome, Bacterial, Probiotics, Genomics

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