Breast milk is often described as a baby’s first food. New research suggests it may also help shape a carefully balanced ecosystem of bacteria in the gut, including some that are usually viewed as harmful.
A study published in Nature Communications found that sugars unique to breast milk help support a relationship between two types of bacteria in infants: Bifidobacterium, which is widely considered beneficial, and E. coli, which is often associated with illness. Researchers say this interaction may play a role in how the infant gut microbiome develops.
“Our previous work, and that of others has already shown that human milk oligosaccharides (HMOs) feed Bifidobacterium,” said Professor Lindsay Hall, corresponding author of the study. “The exciting new development is the way that HMOs being eaten by Bifidobacterium also supports E. coli, something that has not been demonstrated before.”
The study analyzed stool samples from 41 healthy infants and their mothers in the Netherlands using DNA sequencing to identify which microbes were present and how they interact. The researchers focused on human milk oligosaccharides, or HMOs, a group of complex sugars found only in breast milk.
Bifidobacterium can break down these sugars, while E. coli cannot. Instead, E. coli relies on the simpler compounds produced during that process. In turn, E. coli produces substances that support the growth of Bifidobacterium. This exchange creates a form of cross-feeding that may help both types of bacteria coexist.
“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,” Hall said.
The findings challenge the idea that E. coli is always harmful. While certain strains can cause illness, the researchers found that in infants, some forms of E. coli may exist at low, stable levels as part of a balanced gut environment.
“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,” Hall said.
The study also explored how these bacteria are introduced. Several strains of Bifidobacterium were shared between mothers and their babies, suggesting they are passed on early in life. In contrast, E. coli strains were more likely to come from outside the family but were still able to persist in the infant gut.
Researchers say these insights could eventually inform new approaches to infant nutrition, particularly for babies who are premature or do not have consistent access to breast milk. However, they emphasize that more research is needed to understand how these microbial interactions translate to long-term health.
The study was observational and involved a relatively small number of participants, which limits how broadly the findings can be applied. It also focused on early-life microbiome development, meaning the results may not extend to older children or adults.
Still, the findings add to a growing body of research showing that diet does more than provide nutrients. It can help shape how different microbes interact, especially during the earliest stages of life.
This study was funded by the Wellcome Trust, the Biotechnology and Biological Sciences Research Council, and the Austrian Science Fund.