Infant Gut Bacteria Atlas Reveals Path to Personalized Probiotics
A newly created global atlas of infant gut bacteria is challenging conventional wisdom about probiotics, revealing that many commercially available strains may be ill-equipped to colonize the digestive systems of modern infants. The atlas, compiled by an international team of researchers, maps the genomes of over 4,000 bacterial strains from 48 countries, identifying strains absent from current probiotic formulations.
The research, published in Cell, highlights a significant disparity between the bacterial populations represented in existing probiotics and those currently found in infants worldwide. According to Dr. Yan Shao, first author from the Wellcome Sanger Institute, UK, the strains used in many probiotics are “historical,” no longer commonly observed in infant microbiomes. This suggests a potential disconnect between the intended benefits of these products and their actual effectiveness.
A key finding centers on Bifidobacterium infantis, a bacterium often used in infant probiotics. The atlas reveals a striking geographical difference: while prevalent in the gut bacteria of infants in Africa and South Asia, B. Infantis is often lacking or entirely absent in infants from Western countries, including the UK, Europe, and North America. This absence is particularly concerning given the established role of Bifidobacteria in early gut colonization, nutrient digestion, and immune system development.
“Geo-specificity would enable the industry to move beyond one-size-fits-all formulations toward region-specific products that contain naturally occurring regional strains that are already adapted to infant microbiomes in those areas,” Shao explained. He suggests that the atlas provides a “shortlisted candidate strain pool” for probiotic development, prioritizing strains based on the target population’s geography rather than relying on legacy commercial strains.
The researchers traced all commercial infant probiotic strains to just three historical bacterial strains, genetically similar but marketed under different names. This finding raises questions about the diversity and relevance of current probiotic offerings. The study also suggests that clinical trials should incorporate geographically matched strains and quantify engraftment – the ability of strains to successfully settle and grow in the gut – using strain-resolved markers.
The research team, which included experts from the University of Oxford, UK, and the Kenya-based KEMRI-Wellcome Trust Research Programme, sequenced B. Infantis and B. Longum genomes from publicly available data, the UK Baby Biome Study, and the CHAIN study, which examined children across sub-Saharan Africa and South Asia. The CHAIN study provided crucial data on the microbial composition of infants in regions with vastly different lifestyles and diets compared to Western nations.
Shao attributes the decline of B. Infantis in Western infants to major shifts in industrialized lifestyles since World War II, including increased antibiotic use, changes in diet, and greater access to healthcare and clean water. These factors, he argues, may have altered the conditions necessary for the persistence of B. Infantis in the gut. He cautioned that similar trends may emerge in other regions undergoing rapid industrialization and urbanization.
“Under this industrialization-driven ‘missing microbes’ hypothesis, it is reasonable to expect that similar forces accompanying rapid industrialization and urbanization could lead to similar outcomes in other regions over time,” Shao stated. He emphasized the demand for longitudinal research in under-represented regions to establish baseline microbiome profiles and understand the relationship between microbial losses and infant health outcomes.
The research was funded by Wellcome Trust and the Gates Foundation. Future work will focus on detailing gut bacteria profiles from additional regions worldwide, with researchers noting that infant gut microbiome development in South Asia and Africa appears to follow a different trajectory than that observed in Westernized cohorts.