How baby microbiomes in the West differ from those everywhere else

An unprecedented look at how the gut microbiome varies among babies in different parts of the world reveals that infants in the West lack a microbe that is common elsewhere. This could aid the development of probiotics, which are sometimes given to premature babies, that are tailored according to where the infant lives, to maximise the chance of these bacteria becoming established.

The first 1000 days of a child’s life are very important for seeding their microbiome, which influences everything from their immune function and mental health to their future disease risk. Our understanding of this was almost exclusively limited to infants in the West, but now, a global atlas of baby microbiomes is finally providing a broader picture.

Yan Shao at the Wellcome Sanger Institute in South Cambridgeshire, UK, and his colleagues sequenced more than 1900 genomes of a bacterium called Bifidobacteria longum, which has been linked to the development of a stable gut microbiome.

These were taken from stool samples collected across the UK, Sweden, the US, and seven countries in South Asia and sub-Saharan Africa: Bangladesh, Pakistan, Kenya, Malawi, Burkina Faso, Uganda and Zimbabwe.

They zeroed in on two subspecies of B. longum: B. longum longum and B. longum infantis, which have been the focus of most previous infant gut microbiome studies. By combining their data with genomes sequenced in prior studies, the researchers found that around 70 per cent of infants from the African and South Asian countries had B. longum infantis in their guts by 2 months old, compared with fewer than 2 per cent of babies from the UK, US and Sweden. “Infantis is basically missing in Western settings,” says Shao.

In contrast, B. longum longum had established in the guts of about a third of infants from these Western countries by 2 months, compared with fewer than 10 per cent of those across the African and South Asian countries.

This suggests that B. longum longum and B. longum infantis – which both help to develop the immune system and prevent gut and blood infections – are primarily found in distinct regions, says Shao.

This is probably because they thrive on different diets, he says. “Bifidobacteria help to digest nutrients from breast milk, and the composition of this varies with the mother’s diet, so it could be that longum [longum] is better adapted to a Western diet while infantis thrives on diets in other regions,” he says. The babies without either B. longum longum or B. longum infantis probably had other, similar bacteria established in their gut microbiome, like Bifidobacterium breve, says Shao.

This study increased the number of B. longum genomes from South Asia that scientists have ever analysed by about 17 times, and those from Africa by around 11 times. “This is a huge step forward for underrepresented populations,” says Lindsay Hall at the University of Birmingham, UK.

Probiotics are not generally recommended for full-term babies, but are sometimes given to premature ones. Off the back of this study, probiotics could be tailored to the region that the premature infant is from, says Hall. For instance, B. longum infantis probiotics may benefit those in parts of Africa and Asia, but it may not persist as well in the guts of Western infants. “Only by understanding how bacteria differ in various places can we understand which probiotics are going to be the best for kids in particular parts of the world,” she says.