Abstract

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

Shao Y Wang S Gichuki BM Stares MD Rozday TJ Kumar N Browne HP Dawson NJR Njunge JM Tigoi C Ngao N Chisti MJ Singa BO Kariuki S Diallo AH Saleem AF Ali SA Mupere E Mbale E Tickell KD Voskuijl WP Lancioni CL Bandsma RHJ Ahmed T Walson JL Berkley JA Lawley TD
Cell. 2026;

Permenent descriptor

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.