Pioneer bacteria analysed in newborns' microbiomes

In the largest known study of UK baby microbiomes to date, researchers have discovered that newborn babies have one of three pioneer bacteria in their gut shortly after birth. Their findings, published in the journal Nature Microbiology, could support the development of infant formulas and therapeutic probiotics containing the most effective natural strains for the baby’s gut.

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 with probiotics that could be used to restore or boost the microbiome. However, before this study, there was a lack of high-resolution data showing how the microbiome develops in this period of life, and which bacteria would be the most useful in healthy newborns.

Building on a previous UK Baby Biome Study that showed babies born by vaginal birth had a different microbiome compared to those born via caesarean, this new research analysed an expanded dataset of 2387 stool samples from 1288 UK infants born in hospitals and some of their mothers. The research team from the Wellcome Sanger Institute, University College London and the University of Birmingham found that all newborns fell into one of three microbiome profiles, each characterised by a different dominant pioneer bacterium.

Out of these pioneer bacteria, Bifidobacterium longum subsp. longum (B. longum) and Bifidobacterium breve (B. breve) are considered beneficial as they promote the stable colonisation of other beneficial microbes. In particular, B. breve has been genetically adapted to fully utilise the nutrients found in breast milk and can block potentially damaging pathogens from colonising the babies’ guts. This highlights its significant potential as a highly effective natural probiotic, as it can already establish itself in the child’s gut.

The third pioneer bacteria, Enterococcus faecalis (E. faecalis), is meanwhile considered risky as it can lead to the colonisation of antibiotic-resistant bacteria. This can interfere with the development of the infant microbiome and increase the risk of pathogens colonising the gut.

The researchers also found that a bacterium commonly found in commercial infant probiotics, known as Bifidobacterium longum subsp. infantis (B. infantis), was not a pioneer bacterium and is rare in UK infants. This finding is aligned with research from other Western industrialised countries that also shows a lack of naturally occurring B. infantis in early infant microbiomes, and suggests that B. breve could be a more effective natural probiotic.

Breastfeeding versus formula feeding did not seem to influence the type of pioneer bacteria in the baby’s gut, but the use of antibiotics did. Other factors such as maternal age and how many times someone has given birth may also play a role, but further research is needed to investigate this and the impact on long-term health outcomes.

In the future, it could be possible to predict how a baby’s gut will develop by mapping their gut microbiome profile right after birth to assess which pioneer bacteria they have. If needed, a personalised probiotic could be provided to help promote healthy microbiome development and protect against potentially pathogenic infections.

“If we think of a newborn baby’s gut as an ecosystem that starts to establish right from birth, there was very little known about which and how microbes plant the very first seeds to establish themselves before the findings of the UK Baby Biome Study,” said Dr Yan Shao, first author on the study, from the Wellcome Sanger Institute.

“By analysing the high-resolution genomic information from over 1200 babies, we have identified three pioneer bacteria that drive the development of the gut microbiota, allowing us to group them into infant microbiome profiles. Being able to see the make-up of these ecosystems and how they differ is the first step in developing effective personalised interventions to help support a healthy microbiome.”

Study co-author Professor Nigel Field, from UCL, added, “While our study has shortlisted three pioneer bacteria as important for babies’ microbiome development, it remains to be determined if and how different pioneer bacteria affect health and diseases, both in childhood and later in life. The UK Baby Biome Study is actively following up participants to give clues about this, and now even bigger cohorts are needed to investigate the role of the infant microbiome on health.”

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