Infant Gut Bacteria Linked to Long-Term Viral Immunity

In the first two years of life, UK newborns with a specific combination of gut bacteria were less likely to be hospitalized for viral lower respiratory tract infections.

A recent study suggests that a baby’s microbiome, the community of gut bacteria that begins forming at birth, may play a role in reducing the risk of viral infections later in childhood.

Researchers at the Wellcome Sanger Institute and University College London (UCL) found that babies with a specific combination of gut bacteria at one week old, seen only in some vaginally born infants, had a lower risk of being hospitalized for viral lower respiratory tract infections (vLRTIs) within their first two years. This finding comes from the largest study of UK baby microbiomes to date.

Published in The Lancet Microbe on June 4, 2025, the study is the first to link early childhood hospitalizations for respiratory infections to the composition of the gut microbiota during the first week of life.

To conduct the study, researchers analyzed stool samples from 1,082 babies using whole-genome sequencing. They then tracked hospital admissions up to age two using electronic health records.

This work builds on earlier findings from the UK Baby Biome Study. It suggests that certain early microbiome profiles may be linked to benefits such as protection against viral infections.

While more research is needed to confirm the connection, the findings may guide future efforts to prevent childhood respiratory illnesses. This could include developing targeted probiotic treatments for newborns.

Overall, the study highlights the potential role of gut bacteria in long-term health. It also underscores the importance of larger follow-up studies, such as the Microbes, Milk, Mental Health and Me (4M) project.

The gut microbiome is a complex ecosystem of millions of microbes that play a key role in human health and immune system development. It begins forming soon after birth, and the first month of life is considered a critical window for potential interventions to support or restore a healthy microbiome.

Previous findings from the UK Baby Biome Study showed that babies born vaginally have a different microbiome composition than those delivered by caesarean section (C-section). However, these differences largely disappeared by the time the child reached one year of age.

Further research by the same team found that, within the first week of life, all UK newborns had one of three types of early colonizing bacteria, known as pioneer bacteria. Two of these—Bifidobacterium longum (B. longum) and Bifidobacterium breve (B. breve)—are believed to support the development of a stable gut microbiome.

In a new study expanding on this earlier work, researchers at the Wellcome Sanger Institute and University College London (UCL) analyzed stool samples from 1,082 infants. They investigated how the presence of these pioneer bacteria in the first week of life might relate to health outcomes in early childhood. Electronic health records were then used to track hospital admissions from birth to age two.

The researchers found that some vaginally born babies had higher levels of B. longum in their gut microbiome, along with other beneficial species such as B. bifidum and Bacteroides dorei. These babies had a lower risk of being admitted to the hospital overnight for viral lower respiratory tract infections (vLRTIs), compared to other infants. This association remained even after accounting for factors such as antibiotic use and whether babies were fed breastmilk, formula, or both.

However, not all vaginally delivered babies had this microbiome profile. The team identified two other distinct microbiota patterns associated with a higher risk of hospitalization for vLRTI. These patterns were seen in both vaginally and C-section–delivered infants.

It is important to note that the study identified a correlation, not a causal relationship. While the findings suggest a possible protective role for B. longum and other early colonizers, further research is needed to confirm any direct effects. This study focused only on one outcome—respiratory viral infections—but future research, including the planned 4M (Microbes, Milk, Mental Health and Me) study, will investigate whether these early microbiome profiles are linked to other health outcomes in childhood.

Viral lower respiratory tract infection is one of the leading causes of hospitalisation in young children, and our research raises the possibility that certain early gut microbiomes might help lower this risk. Further research to confirm and explore the factors behind this, including if there is an interaction between the gut microbiome and the lung microbiome, could lead to new ways to help prevent respiratory infections in childhood.

Dr. Cristina Garcia-Mauriño, Study First Author, University College London

Nigel Field, who is Co-Lead of the Microbes, Milk, Mental Health and Me (4M) project, and the senior study author, added, “While observational, our findings that certain infant microbiomes are linked to a lower risk of viral respiratory infection in childhood are striking and new. This is the first time that this association has been observed, and it was only possible due to the size of the Baby Biome Study, and by combining high-resolution genomics technologies with clinical outcomes.”

Field added, “ To understand more about how our microbiome impacts health, larger studies such as the 4M project are crucial, and I am looking forward to insights from both the Baby Biome Study and 4M that will further shape our understanding of how our microbiomes and our health interact.”

Louise Kenny, Professor and Lead Investigator of the Children Growing up in Liverpool, said,  “A Caesarean section is often a life-saving procedure, and can be the right choice for a woman and her baby. Furthermore, decisions around childbirth are personal and complex, and there is not one single approach that is best for everyone.”

Kenny continued, “While this study suggests that some babies born vaginally may be less likely to experience severe respiratory infections, this was not seen across all babies born this way, suggesting that other factors are at play. Further research is needed to create a full, nuanced picture and to help find new ways to ensure advice and clinical approaches are tailored to personal situations.”

Kenny is a former Consultant Obstetrician and Gynaecologist who was not involved in this study.

Dr. Trevor Lawley, Senior Study Author at the Wellcome Sanger Institute, stated, “Within the first few days of our lives, our microbiomes are already thriving ecosystems that develop and adapt with us as we age. Our study adds to the growing body of evidence that the pioneer gut bacteria acquired in early life may influence health later on, highlighting how gut microbes could help protect us from infections and other diseases.”

Lawley further added, “Different types of infant gut bacteria may provide different benefits, and understanding these could pave the way for developing targeted infant probiotics to support early microbiome development. In the future, we might be able to create personalised interventions that optimise a child’s gut microbiome based on their unique microbial profile, promoting better health and development.”