Missing microbes in UK infant gut and probiotics highlighted by global microbiome atlas
An international collaboration, including experts at the Wellcome Sanger Institute, the University of Oxford, the KEMRI-Wellcome Trust Research Programme, and the Childhood Acute Illness and Nutrition (CHAIN) Network, has created a global atlas of over 4,000 gut bacterial genomes from 48 countries, making a freely accessible microbiome resource that is 15 times larger than previous studies.
Published today (18 February) in Cell, this catalogue shows that a key infant-gut species — Bifidobacterium infantis (B. infantis) — is a ‘missing microbe’ in UK babies and other Western countries in Europe and North America, despite being highly common in infants in African and South Asian countries.
Additionally, the team uncovers that all commercial infant probiotic strains trace back to three historical bacterial strains that are no longer found in today’s infant populations, and are highly similar genetically, despite being marketed under different names. The researchers suggest that bacterial strains found naturally in different regions are better adapted to the infant gut and may be more effective for new probiotics.
This atlas showcases a wealth of previously unknown diversity in B. infantis and identifies 36 strains that are specific to particular regions across the globe. These results enable the design of new infant probiotics that can be tailored to local diets and regions.
The gut microbiome is a complex ecosystem of millions of microbes that are vital for human health and shaped by lifestyle, environment, and diet. This ecosystem begins forming at birth, when pioneer bacteria such as Bifidobacteria are among the first to seed the microbiome1. As infants grow, new microbes arrive in their gut, compete with one another for space and interact with the developing infant, helping to digest nutrients and train the immune system, with only the most successful bacteria able to settle and flourish.
Bifidobacterium longum (B. longum) and B. infantis bacteria are widely used in commercial infant probiotic products to help restore or boost the microbiome. However, there are growing questions about the clinical effectiveness of some commercial probiotic strains2, and probiotic safety has also drawn increased scrutiny from regulatory bodies3.
To create a more representative and in-depth resource, experts at the Sanger Institute worked with international collaborators to catalogue the genomes of 4,098 B. infantis and B. longum strains. They sequenced genomes from the UK Baby Biome study4 and the CHAIN study5 — a cohort including children from six countries across sub-Saharan Africa and South Asia — and combined these with all publicly available genomes.
As well as expanding the known diversity of B. infantis and B. longum strains, the atlas confirms that B. infantis is rare in babies in the UK and other Western countries, despite being found widely in babies in African and South Asian countries. The researchers suggest that lifestyle changes may have contributed to the loss of B. infantis in Western babies. As B. infantis is an early pioneer microbe, its absence may shape microbiome development in ways that could have lasting effects on infant health.
Knowing how infant microbiomes differ around the world can help researchers choose and develop probiotic strains tailored for babies in different populations. The new atlas highlights dozens of B. infantis strains with genetic differences linked to local diets and lifestyles6, which may help strains take hold more successfully in the infant gut. For example, strains commonly found in West Africa carry genes linked to breaking down fonio millet, a staple grain in parts of the region.
The team sequenced genomes from all B. infantis probiotic products available on the market and found that these strains are no longer seen in infant microbiomes worldwide. This suggests commercial probiotic strains have not successfully taken hold in today’s infant populations, raising questions about their effectiveness and suitability as probiotics.
This new resource offers a blueprint to help select probiotic strains and design future clinical trials7, matched to specific regions, and track how well these bacteria are at settling in the infant gut. The team also found that, despite their close relationship and frequent classification as subspecies, B. infantis and B. longum should be treated as distinct species, impacting how infant microbiome information is analysed in research and clinical settings.
“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. Our research has identified region-specific strains that have naturally evolved to thrive in a baby’s microbiome, shaped by regional diets and environments. 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.”
Dr Yan Shao, first author at the Wellcome Sanger Institute
“For too long, our understanding of infant microbiomes has been heavily skewed towards data from Western countries, which means we know far less about the regional differences that could matter for child health worldwide. By bringing in data from six countries across sub-Saharan Africa and South Asia through the CHAIN cohort, we set out to correct that imbalance, boosting representation from these countries by 17-fold. This expanded, more representative atlas will enable us to move beyond relying on ‘legacy’ probiotic strains and instead prioritise 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.”
Professor Jay Berkley, co-senior author at KEMRI-Wellcome Trust Research Programme and co-lead of the CHAIN network
“Our microbiomes support us every day by helping us digest food, absorb nutrients and support the immune system. As our diets and lifestyles differ around the world, so do the microbes we carry, and therefore, our microbiomes can look very different. Our atlas highlights this global variation and shows that Bifidobacterium infantis, one of the most important microbes in early life, is a ‘missing microbe’ in many Western populations, including the UK. Yet it remains highly common in babies from countries in sub-Saharan Africa and South Asia. This offers a striking example of how modern lifestyle changes may be reshaping our microbiome from the very beginning of life. Further research is now needed to understand what the loss of B. infantis means for infant health in Western babies, and whether reintroducing it could be beneficial in these settings.”
Dr Trevor Lawley, co-senior author at the Wellcome Sanger Institute and co-lead of the UK Baby Biome Study
More information
- Bifidobacteria are among the most important pioneer microbes in the gut microbiome and are closely linked to healthy development of the infant gut, the immune system and the brain.
- Barratt MJ, Nuzhat S, Ahsan K, et al. (2022) ‘Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition’. Science Translational Medicine. DOI: 1126/scitranslmed.abk1107.
- The Food and Drug Administration (US) has previously warned healthcare providers about risks associated with certain probiotic products and companies illegally selling probiotic products. Full announcement: https://www.fda.gov/news-events/press-announcements/fda-raises-concerns-about-probiotic-products-sold-use-hospitalized-preterm-infants
- The UK Baby Biome study is a large-scale UK birth cohort study and biobank, with longitudinal follow-up through electronic health data linkage. It aims to understand how interactions between microorganisms, the immune system, and clinical, social, and behavioural factors during pregnancy and early life influence later health and disease. Stool samples were collected from newborns and mothers, along with vaginal swabs from the mothers and umbilical cord blood. Funded by Wellcome, it was a collaboration between the Wellcome Sanger Institute, UCL, the University of Birmingham and collaborating hospitals.
- This research used samples from the CHAIN Nested Case-Cohort study, a sub-cohort of the Childhood Acute Illness and Nutrition (CHAIN) Network. CHAIN is a cohort that, between November 2016 and January 2019, recruited 3,101 children under 2 years old at nine hospital sites in six countries across sub-Saharan Africa and South Asia: Dhaka and Matlab Hospitals (Bangladesh), Banfora Referral Hospital (Burkina Faso), Kilifi County, Mbagathi County, and Migori County Hospitals (Kenya), Queen Elizabeth Hospital (Malawi), Civil Hospital (Pakistan), and Mulago National Referral Hospital (Uganda). Ethical approvals were obtained from all recruiting site-affiliated or collaborating institution and all caregivers provided written informed consent for their child to participate in the CHAIN study.
- The team found genetic differences in strains that meant they had adapted to breaking down different substances in local diets, including plant and breastmilk-related nutrients such as urea and B vitamins.
- This resource combines complete genomic sequences with a matched biobank of culture strains, allowing clinical trials to be designed that match bacterial strains with regional populations. While this study did not directly test probiotic safety or efficacy, the atlas can also support screening for safety-related markers, such as antimicrobial resistance.
Publication:
Y. Shao, S. Wang, B. M. Gichuki, et al. (2026) ‘Genomic Atlas of Bifidobacterium infantis–longum Complex to Accelerate Probiotic Discovery for Infant Health’. Cell. DOI: 10.1016/j.cell.2026.01.007
Funding:
This research was funded in part by Wellcome and the Gates Foundation. A full acknowledgement list can be found in the publication.
Author interests:
Alongside his role as Group Leader at the Wellcome Sanger Institute, Dr Trevor Lawley is also a co-founder and Chief Scientific Officer of Microbiotica. This is a clinic-ready biopharmaceutical company specialising in the development of precision live biotherapeutic products for adults, with lead products in immuno-oncology and inflammatory bowel disease.
