Breast milk sugars promote beneficial bacterial balance in infant guts

Sugars contained exclusively in breast milk are helping to feed an important balance of bacteria in babies' developing gut microbiomes, a new study has found.

In a paper published in Nature Communications, a European research team led by Professor Lindsay Hall from the University of Birmingham used deep DNA sequencing to look at stool samples from 41 healthy babies and their mothers in the Netherlands.

The study aimed to see which microbes were there and how they might interact with each other as well as with food sources introduced to the gut. The study is thought to be the first that describes how babies who are breastfed maintain a mutually beneficial co-existence of E. coli and a bacteria called Bifidobacterium, which is a key part of a healthy gut microbiome.

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.

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."

Professor Lindsay Hall from the University of Birmingham, and Quadram Institute, and corresponding author of the study

How strains are passed on

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.

Dr. David Seki from the University of Vienna, Austria and first author of the paper said: "E. coli was first isolated from infant feces in 1885 by Theodor Escherich. Since then, this organism has shaped genetics and molecular biology like no other. However, fundamental gaps remain in our understanding of its ecology. Specifically, what factors determine whether E. coli adopts a commensal or pathological phenotype? To fully understand the underlying mechanisms of such shifts, it is important to recognize that host-microbe interactions are always embedded in broader, more complicated ecological networks comprising multiple co-existing species."