Most conversations about breast milk tend to focus on topics like nutrients, antibodies and bonding time rather than bacteria. But it turns out that human milk carries its own tiny community of microbes, and those passengers may help shape a baby's developing gut microbiome — which in turn can impact nutrient absorption, metabolic regulation, immune system development, and more.
A new study published in Nature Communications provides one of the most detailed portraits yet of how different combinations of bacteria in human milk contribute to the assembly of infants' gut microbiomes.
Mapping the milk microbiome
The breast milk microbiome is notoriously difficult to analyze because the milk's high fat content and relatively low bacterial load complicate the process of extracting genomic material.
"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 first author Pamela Ferretti, PhD, a postdoctoral researcher in the Blekhman Lab at the University of Chicago. "We decided to tackle this endeavor because our collaboration presented a unique opportunity to combine key resources."
Those resources included hundreds of milk samples collected as part of the Mothers and Infants LinKed for Healthy Growth (MILk) study , led by Ellen Demerath, PhD, at the University of Minnesota and by David Fields, PhD, at the Oklahoma University Health Sciences Center. On the UChicago side, Ferretti and her colleagues had access to metagenomic tools and deep experience with microbiome data, including Ferretti's highly specific expertise in infant microbiomes and transmission analysis. In her previous research, she studied how different maternal body sites — such as mouth, skin, and vaginal cavity — contributed to infant microbiomes.
Analyzing 507 breast milk and infant stool samples from 195 mother–infant pairs, the team found that breast milk contained a distinct mix of bacterial species dominated by the genus bifidobacteria, including Bifidobacterium longum, B. breve, and B. bifidum. More than half of the milk samples carried B. longum, a species abundant in over 98% of the infants' gut microbiomes.
"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 because previous milk studies mostly reported other bacterial taxa like Staphylococcus and Streptococcus," Ferretti said. "We think these results will prompt some reevaluation in the field."
Tracing microbes from milk to the infant gut
Most prior studies analyzing bacterial DNA in breast milk used a relatively inexpensive, fast technique called amplicon sequencing, which targets a limited number of predetermined genomic regions for each experiment. This method is good for efficiently identifying species within a mixed sample, but it leaves most of the bacterial genome unexamined.
"Metagenomic analysis is trickier and more complicated, but it really paid off because it allowed us to obtain information at the level of different bacterial strains — which is key, because that's the only level where we could actually claim to know about transmission," Ferretti said.
The paper reported 12 instances in which the same exact strain was found in a mother's breast milk and in the gut of her infant, which is a very strong indication that the transmission happens vertically via breastfeeding.
Some of these shared strains were beneficial commensal species such as B. longum and B. bifidum, which help digest human milk sugars and support healthy gut development. Others, however, were pathobionts — microbes like E. coli and Klebsiella pneumoniae that can live harmlessly in healthy individuals but have the potential to cause infection under certain conditions. The authors note that all mothers and infants in the study were healthy, indicating that these species' presence in milk does not inherently signal disease but rather reflects the microbial diversity that can be transferred during breastfeeding.
Interestingly, the team also saw specific strains of bacteria usually associated with the mouth — such as Streptococcus salivarius and Veillonella species — in milk samples. They realized this as potential evidence of "retrograde flow" during breastfeeding: as the baby feeds, tiny amounts of oral bacteria may travel back into the nipple and ducts and become part of the milk microbiome.
Expanding human milk research
Ferretti noted that the study not only sheds light on microbial transmission but also fills a major gap in available data for scientists studying early-life health.
"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."
In subsequent studies, the researchers hope to take their analysis to the next level with a multi-omic approach, including analyzing metabolites like human milk oligosaccharides (HMOs) and examining the "exposome" of environmental factors like PFAS and antimicrobial resistance that can be passed along through milk.
"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.
" Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk " was published early access in November 2025 in Nature Communications. Co-authors include Pamela Ferretti, Mattea Allert, Kelsey E. Johnson, Marco Rossi, Timothy Heisel, Sara Gonia, Dan Knights, David A. Fields, Frank W. Albert, Ellen W. Demerath, Cheryl A. Gale and Ran Blekhman.
