Gut microbes begin developing at birth and are shaped by the mother and environment, but factors scuh as antibiotics can disrupt this process, affecting growth and development. Now, researchers are uncovering how region-specific strains of infant gut bacteria are adapted to local diets and environments.

The findings, published in Cell, show that two early colonizers – Bifidobacterium longum and B. infantis – are distinct species with strains adapted to local diets, highlighting the importance of developing geographically tailored infant probiotics.

B. infantis and B. longum help with nutrient digestion and immune development, making them strong probiotic candidates. Yet, most studies group them together, masking important differences. 

What’s more, commercial B. infantis strains from the US or Europe often fail to colonize infants in places such as Bangladesh or the Philippines, indicating probiotics may need local tailoring. So, researchers led by Yan Shao at the Wellcome Sanger Institute in Hinxton, UK, set out to analyze 4,098 genomes of B. infantis and B. longum from 48 countries. 

Local adaptations

By comparing the bacterial genomes, the team identified four main groups: B. infantis and three subspecies of B. longum. Within one of the B. longum subspecies, the researchers found a group of bacteria specifically adapted to infant guts, separate from strains associated with animals.

The analysis also indicated that B. infantis and B. longum are separate species that are evolving differently, with B. infantis being the more ancestral species. B. infantis is mostly found in infants under one year, especially in low- and middle-income countries, while B. longum dominates in high-income countries and becomes common in adults. 

B. infantis has a wider variety of genes than B. longum, particularly for breaking down nutrients in breastmilk, including vitamins and human milk sugars, which are crucial for infant growth and development. Instead, B. longum has genes better suited for digesting plant-based sugars found in adult diets. 

Tailored probiotics 

The researchers found that not all B. infantis strains can use all milk sugars, suggesting differences depending on geography, breastfeeding patterns, and other environmental factors. Some subspecies seem adapted to formula or solid foods in high-income countries.

B. infantis strains from low- and middle-income countries carry unique genes that help them break down local foods and nutrients, and 36 B. infantis strains from Africa and South Asia—which are better adapted to local diets and gut environments—could be promising candidates for region-specific probiotics. 

While the findings could open the door for precision infant probiotics, more research is still needed to confirm metabolic activity, colonization ability, and safety, the authors say. What’s more, they add, “whether similar ecological and evolutionary principles apply more broadly across early-life bifidobacteria remains to be established.”