How baby microbiomes in the West differ from those everywhere else

An unprecedented look at how the gut microbiome varies between babies in different parts of the world reveals that babies in the West are missing a microbe common elsewhere. This may aid the development of probiotics, which are sometimes given to premature babies, that are tailored to where the infant lives, to maximize the chance of these bacteria becoming established.

The first 1,000 days of a child’s life are crucial for seeding the microbiome, which affects everything from their immune function and mental health to their future disease risk. Our understanding of this was almost entirely limited to infants in the West, but now a global atlas of baby microbiomes finally provides a broader picture.

Yan Shao at the Wellcome Sanger Institute in South Cambridgeshire, UK, and his colleagues sequenced more than 1,900 genomes of a bacterium called Bifidobacteria longumwhich has been linked to the development of a stable gut microbiome.

These were taken from faecal 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 infantiswhich has been the focus of most previous studies of the infant gut microbiome. By combining their data with genomes sequenced in previous studies, the researchers found that about 70 percent of infants from the African and South Asian countries had B. longum infantis in the intestines at 2 months old, compared to fewer than 2 percent of babies from the UK, US and Sweden. “Infantis basically lacking in Western settings, says Shao.

In contrast, B. longum longum had established themselves in the guts of approximately one-third of infants from these Western countries by 2 months, compared to fewer than 10 percent of infants in the African and South Asian countries.

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

It is probably because they thrive on different diets, he says. “Bifidobacteria helps digest nutrients from breast milk, and the composition of this varies with the mother’s diet, so it may be that longum (longum) is better adapted to a Western diet while infantis thrive 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 the gut microbiome, which Bifidobacterium brevesays Shao.

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

Probiotics are generally not recommended for full-term babies, but are sometimes given to premature babies. On the back of this study, probiotics can be tailored to the region the premature baby comes from, says Hall. For example B. longum infantis probiotics may benefit those in parts of Africa and Asia, but may not persist as well in the guts of Western infants. “Only by understanding how bacteria are different in different places can we understand which probiotics are going to be best for children in certain parts of the world,” she says.