Newborns have one of three pioneer bacteria in their gut shortly after birth, one of which could be used to develop new personalized therapeutic probiotics for infants, researchers show.
In the largest UK infant microbiome study to date, researchers from the Wellcome Sanger Institute, University College London (UCL) and the University of Birmingham used whole genome sequencing to analyse stool samples from 1,288 healthy infants, all under one month old, from the UK Baby Biome Study.
This research, published in Microbiology of naturediscovered that one of these beneficial pioneer bacteria was genetically adapted to fully utilize the nutrients in breast milk, suggesting that it is best suited to thrive in a baby’s microbiome. The team found that this bacteria can also prevent pathogens from colonizing the baby’s gut, highlighting its important potential as a natural probiotic.
These findings could help develop infant formulas and therapeutic probiotics that contain the most effective natural strains for the baby’s gut. Currently, most commercially available infant probiotics contain a different bacterial strain that is absent from the early microbiomes of infants in industrialized societies such as the UK and US.
In addition to the two beneficial pioneer bacteria, the researchers identified a third bacterium that is considered dangerous because it can lead to the colonization of antibiotic-resistant bacteria. This can interfere with the development of the infant’s microbiome and increase the risk of colonization of the intestine by pathogens.
In the future, it may be possible to predict the development of a baby’s gut microbiota by mapping their gut microbiota profile right after birth to assess which pioneer bacteria they carry. If necessary, a personalized probiotic could be administered to promote healthy microbiota development and protect against potentially pathogenic infections.
Further research, such as the Microbes, Milk, Mental Health and Me (4M) project, is needed to understand the impact of pioneer bacteria on health. This project, co-led by the Wellcome Sanger Institute, is part of the Children Growing Up in Liverpool study, which is looking at 10,000 mothers and infants. This wide-ranging research aims to explore how factors such as the infant gut microbiome and early nutrition affect brain development, behaviour, emotions and mental health in later life.
The gut microbiome is a complex ecosystem composed of millions of microbes that are essential to human health and important for immune system development. Because it begins to form immediately at birth, the first month is the prime window to intervene with probiotics that could be used to restore or boost the microbiome. However, prior to this study, there was a lack of high-resolution data showing how the microbiome develops during this period of life and which bacteria would be most helpful in healthy newborns.
Building on a previous UK study of the baby microbiome that showed that babies born vaginally had a different microbiome to those born by caesarean section, the new research analysed an expanded dataset of 2,387 stool samples from 1,288 UK infants born in hospital and some of their mothers. The team from the Wellcome Sanger Institute, UCL and the University of Birmingham found that all the newborns fell into one of three microbiome profiles, each characterised by a different dominant pioneer bacteria.
Among these pioneer bacteria, Bifidobacterium longum subsp. longum (B. longum) and Bifidobacterium breve (B. breve) are considered beneficial because they promote stable colonization of other beneficial microbes, and Enterococcus faecalis (E. faecalis) is considered risky.
B. longum was found to originate in the mother’s gut during childbirth. However, the team found that B. breve was not transmitted in this way. The team also found that B. breve was genetically adapted to fully utilize the nutrients present in breast milk and can prevent potentially dangerous pathogens from colonizing the babies’ gut.
About 85% of the babies studied were breastfed in the first few weeks of life. The researchers found that breastfeeding versus formula feeding did not appear to influence the type of pioneer bacteria present in the baby’s gut, unlike antibiotic use. The researchers note that other factors such as the mother’s age and the number of times a person has given birth may also play a role, but more research is needed to explore this and its impact on long-term health outcomes.
They also showed that a bacteria commonly found in commercial infant probiotics, known as Bifidobacterium longum subsp. infantis (B. infantis), was not a pioneer bacteria and was rare in British infants. This finding is consistent with research from other Western industrialised countries that also shows an absence of naturally occurring B. infantis in the microbiomes of young infants and suggests that B. breve may be a more effective natural probiotic.
Dr Yan Shao, lead author from the Wellcome Sanger Institute, said: “If we think of a newborn’s gut as an ecosystem that starts to take shape from birth, very little was known about the microbes that plant the very first seeds to establish themselves prior to the findings of the UK Baby Biome Study. By analysing high-resolution genomic information from over 1,200 babies, we identified three pioneer bacteria that drive the development of the gut microbiota, allowing us to group them together into infant microbiome profiles. Being able to see the composition of these ecosystems and how they differ is the first step in developing effective personalised interventions to help support a healthy microbiome.”
Professor Louise Kenny, lead researcher on the Children Growing up in Liverpool study at the University of Liverpool, added: “Decisions about birth mode and breastfeeding are complex and personal, and it is important to note that there is no one-size-fits-all approach when it comes to determining the best options for you and your baby. It is also important to note that we still do not have a complete understanding of how the role of birth mode and different infant feeding methods influence the development of the microbiome and how this affects later health. This research is therefore essential. We must continue to find new ways to ensure that all children get the best possible start in life.”
Professor Nigel Field, co-author of the UCL study, noted: “While our study has selected three pioneer bacteria as important for the development of the baby microbiome, it remains unclear whether and how different pioneer bacteria affect health and disease, both in infancy and later in life. The UK Baby Biome Study is actively following participants to provide clues about this, and now even larger cohorts are needed to study the role of the infant microbiome in health.”
Dr Trevor Lawley, lead author from the Wellcome Sanger Institute, observed: “The development of a person’s microbiome early in life could have huge implications for them later in life. This is also a time when the use of infant probiotics could be very effective, if we know which bacteria are both important and relevant to the target populations.
“Our study highlights a highly beneficial pioneer bacterium that can fully digest breast milk and protect the newborn from harmful microbes. It has the potential to be a highly effective natural probiotic, as it can already establish itself in the infant’s gut. I hope that our open-access study will encourage the rational selection of probiotic strains and the development of new microbiome-based therapies based on genomic research.”
More information:
Primary succession of bifidobacteria drives pathogen resistance in the neonatal microbiota assembly, Microbiology of nature (2024). DOI: 10.1038/s41564-024-01804-9
Provided by the Wellcome Trust Sanger Institute
Quote:Natural probiotic discovered in microbiomes of British newborns (2024, September 6) retrieved September 6, 2024 from
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