A global atlas of gut bacteria from babies across the world has created a blueprint for early-life probiotics tailored to different local diets and regions that can improve infant health.
The genomic resource could help select geographically bespoke probiotics most beneficial for infants and lead to the development of precision microbiome therapeutics.
The catalog, outlined in Cell, comprises 4098 genomes from the key Bifidobacterium infant gut microbe species B. longum and B. infantis.
Spanning 48 countries, it is well over 10 times larger than similar previous studies and increases representation from low-and-middle income countries 12- to 17-fold.
“Our research has identified region-specific strains that have naturally evolved to thrive in a baby’s microbiome, shaped by regional diets and environments,” explained researcher Yan Shao, PhD, from the Wellcome Sanger Institute in the U.K.
“By creating this resource, we hope that it will support the development of next-generation, tailored probiotics that can more effectively help build a healthy, flourishing microbiome for babies everywhere.”
The microbiome atlas reveals B. infantis bacteria as a “missing microbe”—rarely seen among infants from high-income countries such as Western Europe and North America but dominating early-life microbiota from low-and-middle income countries in Africa and South Asia.
This could be due to lifestyle changes associated with industrialization, the researchers suggest. Earlier weaning, the use of formula, and exposure to antibiotics could all have eroded ecological niches that once favored metabolically diverse B. infantis lineages.
The findings also confirm B. longum and B. infantis as distinct species with different functions.
The 36 B. infantis strains across the globe appear to have adapted to regional diets and lifestyles, with metabolic adaptations to non-industrialized diets consistent with their near-exclusive distribution in low-and-middle income countries. Natural strains appear adapted to local diets rich in plant glycans and substrates derived from breast milk, including urea and B vitamins. Infants from West Africa, for example, carried genes linked with breaking down a local staple grain called fonio millet.
The atlas suggests currently available commercial probiotics, produced to restore or boost the infant microbiome, may be poorly designed. These commercial strains had often partially lost the diverse metabolic loci—including those involved in human milk and plant glycans, lipids and micronutrients—which made regional strains better adapted to their local populations.
“Microbiomes are complex, highly individual ecosystems, yet for decades the infant probiotics industry has taken a one-size-fits-all approach, trying to plant the same bacterial ‘seeds’ in every baby worldwide,” said Shao.
“Our research has identified region-specific strains that have naturally evolved to thrive in a baby’s microbiome, shaped by regional diets and environments.”
Fellow researcher Jay Berkley, PhD, from the University of Oxford, added: “This expanded, more representative atlas will enable us to move beyond relying on ‘legacy’ probiotic strains and instead prioritize testing region-matched strains that are naturally adapted to babies’ local diets and environments.
“This major expansion in known bacterial strains lays the groundwork for developing microbiome-based interventions tailored to the needs of every child, no matter where they are born.”
