When a newborn attaches, the exchange goes beyond just nourishment. Minute travelers in breast milk (microbes that have evolved to digest milk sugars and aid in initial growth) move directly into the baby’s developing intestinal tract. This quiet microbial transfer influences everything from nutrient absorption in infants to the maturation of their immune systems, yet researchers have not always been certain which microbes participate in this process or how consistently they establish themselves.
Recent research following 195 mother-infant pairs over six months reveals the clearest understanding of this biological communication to date. Featured in Nature Communications, the study scrutinized 507 metagenomic samples and discovered that breast milk harbors a unique microbial community predominantly featuring Bifidobacterium longum. This singular species accounted for most of the similarities between the microbiomes of breast milk and infant guts, and infants with a gut dominated by it exhibited significantly greater stability in their microbial communities over time.
The scientists uncovered 12 instances where matching bacterial strains were found in both a mother’s milk and her child’s stool. This serves as the microbial equivalent of corresponding fingerprints. The shared strains comprised beneficial commensals as well as pathobionts like Klebsiella pneumoniae, microbes that coexist harmlessly in healthy individuals yet can lead to complications under specific circumstances. Since all participants were healthy, their presence signifies normal diversity rather than a risk of disease.
The Dynamics of Microbial Transfer
Achieving these results necessitated overcoming considerable technical hurdles. Breast milk is notoriously challenging to analyze. It is filled with fats and human cells but contains relatively few bacteria. The team employed shotgun metagenomic sequencing instead of older, lower-resolution techniques, enabling them to distinguish bacteria not only by species but by precise strain.
“Metagenomic analysis is more complex and challenging, but it was worthwhile as it allowed us to gather data at the level of individual bacterial strains,” explains Pamela Ferretti.
This accuracy revealed an unexpected finding: the transfer is not entirely one-sided. Streptococcus salivarius and other bacteria associated with the mouth appeared in milk samples, indicating “retrograde flow” where small amounts of the infant’s oral bacteria return to the breast during feeding. It serves as a vivid reminder of the physical connection in breastfeeding, where fluids and microscopic life flow in both directions.
The research also revealed genes associated with antimicrobial resistance shared between the milk of mothers and the gut of their infants. Although resistance genes may sound concerning, the authors stress that this indicates normal microbial inheritance in healthy populations rather than consequences of antibiotic treatment or infection.
When Microbial Transfer is Most Significant
The microbial crossover between milk and the infant gut actually lessens as babies grow older. At one month, approximately 10 percent of bacterial taxa in infant stools were also found in their mother’s milk. By six months, this figure declined to 7 percent. The seeding process is most vigorous during the earliest weeks of life, a time when the gut is essentially an empty landscape being colonized for the first time.
Infants born through vaginal delivery exhibited more stable bacterial strains compared to those born via C-section, adding another layer of complexity to how the method of birth and feeding practices interact. This dataset nearly doubles the existing public metagenomic breast milk data, creating opportunities to explore whether these early microbial patterns can forecast later health issues like asthma or obesity.
At this point, the findings reconceptualize breast milk as more than just a source of nutrition and immunity. It represents a living system that conveys microbes already equipped to establish a functional gut community from scratch. Those initial bacterial travelers, exchanged silently during each feeding, establish a foundation that may resonate throughout a lifetime of health.
Nature Communications: 10.1038/s41467-025-66497-y