Breast milk enables major symbiotic relationship in infant gut microbiome

Researchers have found that sugars in breast milk support a beneficial balance of gut bacteria in infants. They hope that their findings could inform future treatments to support gut health in pre-term babies or those lacking consistent breast milk. 

The European team led by the University of Birmingham, UK, analyzed stool samples from 41 healthy babies and their mothers to learn about the interaction between the pathogen Escherichia coli and healthy bacteria Bifidobacterium.

The study in Nature Communications found that Bifidobacterium uses human milk oligosaccharides (HMOs) from breast milk, providing nutrients to E. coli, which helps contribute to a stable gut environment — essential for infant development.

The researchers note that their study is the first to describe how breastfed babies maintain a mutually beneficial co-existence of E. coli and Bifidobacterium.

Cross-feeding system 

The study explains that E. coli in the gut cannot break down HMOs. Instead, the bacteria scavenge simple sugars, which are already broken down by the Bifidobacterium.

“Our previous work, and that of others, has already shown that HMOs feed Bifidobacterium. The exciting new development is the way that HMOs being eaten by Bifidobacterium also support E. coli, something that has not been demonstrated before,” comments corresponding author professor Lindsay Hall from the University of Birmingham and the Quadram Institute, UK.

“This discovery sheds light on a mutualistic relationship in which each bacterium supports the other, and both may be required for stable co-existence. This is particularly significant in early life, because Bifidobacterium is well recognized 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.”

Through this system, feeding through the Bifidobacterium byproducts called cysteine is essential for a healthy balance. The researchers add that the mutual cross‑feeding might help keep E. coli at low, stable levels while supporting a Bifidobacterium‑rich ecosystem in early life.

The study underscores the beneficial role of E. coli in the development of the gut microbiome and immune system.

Uncovering the origins

The researchers examined how the strains are passed on through sequencing techniques. Several Bifidobacterium strains were shared between mothers and babies, revealing the pathways in which babies first take in and culture beneficial gut bacteria.

Concurrently, E. coli strains tend to come from outside the family but can persist in the baby over time. 

The researchers say that knowing 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.

“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,” says first author Dr. David Seki from the University of Vienna, Austria. 

“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.”

The new study findings are expected to help professor Hall and researchers worldwide introduce infants to Bifidobacterium and E. coli strains to help gut microbiome development. 

New treatments may potentially be developed as supplemental feeding for babies who don’t have access to breast milk. 

In related research, a patented method uses metabolites from Bifidobacteria to reduce the risk of allergies and asthma in children. The finding could have a major impact in preventing these chronic conditions, which are some of the most common diseases among children.

Another study found that probiotic supplementation can help restore the gut microbiomes of infants who have been exclusively breastfed.

Beneficial gut bacteria, specifically B. infantis, in high-resource regions, are declining in infants according to recent trends. Missing Bifidobacteria in US babies drive allergies, asthma, and eczema.