Infant Microbiome Tied to Reduced Risk of Viral Infections

As part of the largest study of UK baby microbiomes to date, researchers at UCL and the Wellcome Sanger Institute found that babies with a specific mix of gut bacteria at one week old were less likely to be hospitalized for viral lower respiratory tract infections (vLRTI) in the first two years of life.

This particular microbiome was only found in some babies who had been born vaginally.

The new study, published in the Lancet Microbe, is the first study to show an association between the makeup of the gut microbiome in the first week of life and hospital admissions for lower respiratory infections in early childhood.

For the research, the team used metagenomic sequencing (a method that allows researchers to examine all of the microbial genetic information to understand what species are present) of stool samples from 1,082 newborns.

They then used electronic healthcare records to track admissions to hospitals in these children up to the age of two years old.

Building on previous findings from the UK Baby Biome Study, this new research suggests that certain microbiome compositions could give different benefits, such as protection against viral infections.

While further research is needed to prove this link, these findings could help shape future research and prevention efforts for childhood respiratory diseases, including the development of effective infant therapeutic probiotics to reduce the risk of respiratory infections in infants.

First author, Dr. Cristina Garcia-Mauriño (UCL Institute for Global Health), said: “Viral lower respiratory tract infection is one of the leading causes of hospitalization in young children, and our research raises the possibility that certain early gut microbiomes compositions 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.”

The gut microbiome is a complex ecosystem of millions of microbes that are vital for human health and important in immune system development. As it begins to form immediately at birth, the first month is the earliest window for intervention that could be used to restore or boost the microbiome.

Previously, the team found that babies born vaginally have a different microbiome compared to those born via cesarean section (C-section), although the differences largely evened out by the time the child was one-year-old.

A different study from the same team also found that all UK babies have one of three bacteria within the first week of life, called pioneer bacteria. Two of these, Bifidobacterium longum (B. longum) and Bifidobacterium breve (B. breve), are considered beneficial as they help promote the development of a stable microbiome.

The new research builds on both of these studies, as the researchers found that some babies born vaginally with a higher amount of pioneer bacteria B. longum in their early gut microbiome, alongside other similarly beneficial Bifidobacterium and Bacteroides species, such as B. bifidum and B. dorei, had a lower risk of being admitted overnight to hospital for vLRTI, when compared to all other babies.

This was still seen after taking account of important confounders, such as babies receiving antibiotics, and whether babies were fed with breastmilk, formula, or both.

Senior author, Professor Nigel Field (UCL Institute for Global Health) who is also co-lead of the Microbes, Milk, Mental Health and Me (4M) project, said: “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.

“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.”

Not all babies born vaginally had the same microbiome composition. The team found that two other groups of babies had similar risk of hospital admission for vLRTI, and these babies had microbiome profiles that were found in babies born both vaginally and by C-section.

It’s important to note that the team observed this finding as an association and further research is needed to prove any causal links. While this study has examined only one common health outcome in children —lower respiratory viral infections — future research with a much larger cohort is needed to investigate whether the possible protective effects of B. longum, or other potentially beneficial pioneer bacteria such as B. breve, may be linked to other health outcomes. The study authors aim to explore this in the upcoming 4M study.

Dr. Trevor Lawley, senior study author at the Wellcome Sanger Institute, and co-lead of the Microbes, Milk, Mental Health and Me (4M) project, said: “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.

“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 personalized interventions that optimize a child’s gut microbiome based on their unique microbial profile, promoting better health and development.”

Reference: Garcia-Mauriño C, Shao Y, Miltz A, Lawley TD, Rodger A, Field N. Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics. Lancet Microbe. 2025. doi: 10.1016/j.lanmic.2024.101072

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