Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design
Open accessAbstract
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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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] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [34]
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] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [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.”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [34]
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Human Milk Oligosaccharide Compositions Illustrate Global Variations in Early Nutrition
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Adaptation of host transmission cycle during Clostridium difficile speciation
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The human milk component myo -inositol promotes neuronal connectivity
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Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
- 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.
- ORCID
- Shao, Yan
- Gichuki, Bonface M.
- Stares, Mark D.
- Rozday, Timothy J.
- Browne, Hilary P.
- Dawson, Nicholas J.R.
- Njunge, James M.
- Tigoi, Caroline
- Ngao, Narshion
- Chisti, Mohammod Jobayer
- Singa, Benson O.
- Kariuki, Samuel
- Diallo, Abdoulaye Hama
- Saleem, Ali Faisal
- Mupere, Ezekiel
- Mbale, Emmie
- Tickell, Kirkby D.
- Voskuijl, Wieger P.
- Lancioni, Christina L.
- Bandsma, Robert H.J.
- Ahmed, Tahmeed
- Walson, Judd L.
- Berkley, James A.
- 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
- hybrid
- doi.org
- Licence
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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