Breast milk is often discussed in terms of nutrients, antibodies, and bonding, but it also carries its own community of microbes. New research suggests those microbes may play a direct role in shaping an infant’s developing gut microbiome.
In a study published in Nature Communications, researchers affiliated with the University of Chicago used advanced genomic techniques to examine how bacteria present in human milk contribute to the assembly of infants’ gut microbiomes. The findings provide some of the clearest evidence to date that breastfeeding can transmit specific microbial strains from parent to child.
The research team analyzed 507 breast milk and infant stool samples collected from 195 mother–infant pairs participating in the Mothers and Infants LinKed for Healthy Growth (MILk) study. Using metagenomic sequencing, which allows researchers to identify bacteria at the strain level rather than just by species, the team was able to track whether identical microbes appeared in both milk and infant stool.
“Breast milk is the recommended sole source of nutrition for an infant’s first months of life, but important questions about the milk microbiome remained unanswered because the analytical challenges are intimidating,” said Pamela Ferretti, a postdoctoral researcher at the University of Chicago and the study’s first author. “We decided to tackle this endeavor because our collaboration presented a unique opportunity to combine key resources.”
The researchers found that breast milk contained a distinct mix of bacterial species, with bifidobacteria particularly prominent. More than half of the milk samples contained Bifidobacterium longum, a species found in the gut microbiomes of more than 98% of the infants studied.
“Even though B. longum is well-documented as being highly prevalent in the infant gut, it was surprising to find such a strong signature of that species in the breast milk samples,” Ferretti said. “We think these results will prompt some reevaluation in the field.”
By comparing full bacterial genomes, the team identified 12 cases in which the exact same bacterial strain appeared in a mother’s milk and her infant’s gut. This level of genetic matching provides strong evidence that the microbes were transmitted through breastfeeding rather than acquired independently from the environment.
Not all of the shared microbes were traditionally considered beneficial. Some strains classified as pathobionts, including Escherichia coli and Klebsiella pneumoniae, were also detected. The authors emphasized that all mothers and infants in the study were healthy, and that the presence of these microbes does not imply disease but rather reflects the normal diversity of bacteria that can be transferred early in life.
The study also uncovered evidence that breastfeeding itself may influence the milk microbiome. Bacterial strains commonly found in the mouth, such as Streptococcus salivarius, appeared in some milk samples, suggesting that microbes from the infant’s oral cavity may travel back into milk ducts during feeding.
“This study nearly doubled the number of metagenomic breast milk samples that are publicly available and pairs them with extensive information on mothers’ health and lifestyle,” Ferretti said. “We’re hopeful that our findings and future analyses that use this dataset will really push the field forward.”
The researchers stress that the findings do not link specific milk microbes to health outcomes and do not imply that feeding practices should be changed. Instead, the work helps clarify how early-life microbial ecosystems form and highlights breast milk as one of several contributors to infant gut development.
Future studies will explore how microbial transmission through milk interacts with other factors, including milk sugars, environmental exposures, and long-term health trajectories.
“Ultimately, we’re interested in looking at longer health trajectories to see if factors in breast milk and early life are predictive of health outcomes later in life,” Ferretti said.
The study was supported by funding from the National Institutes of Health and by research grants and institutional support from the University of Minnesota, the University of Chicago, and collaborating medical and research centers. The authors also acknowledged the MILk Study participants and staff, as well as computational and laboratory resources that made the research possible.