Out now in Nature Communications: Breastfed babies balance bacteria in developing microbiome

In the new study, the team looked at how Bifidobacterium breaks down the sugars contained in breastmilk called HMOs (Human Milk Oligosaccharide). E. coli in the gut cannot break down HMO itself, but can scavenge simple sugars, which are already broken down by the Bifidobacterium. E. coli feed and maintain a colony in the gut, and a byproduct of their presence is a critical nutrient source for Bifidobacterium called cysteine. The team believe that this mutual cross‑feeding may help keep E. coli at low, stable levels while supporting a Bifidobacterium‑rich ecosystem in early life, essential for healthy infant development.

The findings also highlight the potentially beneficial role of E. coli in the development of the gut microbiome and immune system, rather than solely a harmful presence as often thought.

Professor Lindsay Hall from the University of Birmingham, and the Quadram Institute, and corresponding author of the study, said: “Our previous work, and that of others has already shown that human milk oligosaccharides (HMOs) feed Bifidobacterium. The exciting new development is the way that HMOs being eaten by Bifidobacterium also supports E. coli, something that has not been demonstrated before.

“This discovery sheds light on a mutualistic relationship in which each bacterium supports the other, and that both may be required for stable co-existence. This is particularly significant in early life, because Bifidobacterium is well recognised as a key contributor to healthy infant development, while E. coli, rather than being viewed solely as harmful, may, at low levels, play a beneficial role in immune system maturation.

The team also looked at how strains of the bacteria are passed on. Sequencing found that several Bifidobacterium strains were shared between mothers and babies, highlighting the pathways in which babies first receive and begin to culture the beneficial bacteria in their gut. The study also found that E. coli strains tend to come from outside the family but persist within an infant over time. The identification of the source of Bifidobacterium and E. coli strains is important in considering how infants are exposed to bacteria that have a benefit in the gut.

These findings will help Professor Hall and researchers around the world to start considering other ways to introduce infants to Bifidobacterium and E. coli strains to support typical gut microbiome development. Taken together, new treatments could be developed that could supplement feeding for pre-term babies or those who don’t have access to consistent breastmilk.