A new study published in Nature Communications has provided detailed insights into how bacteria found in breast milk contribute to the development of infants' gut microbiomes. Researchers analyzed 507 breast milk and infant stool samples from 195 mother–infant pairs, finding that breast milk contains a unique mix of bacterial species dominated by bifidobacteria, such as Bifidobacterium longum, B. breve, and B. bifidum.
"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, PhD, postdoctoral researcher at the University of Chicago and first author of the study. "We decided to tackle this endeavor because our collaboration presented a unique opportunity to combine key resources."
The research team combined hundreds of milk samples collected from the Mothers and Infants LinKed for Healthy Growth (MILk) study with advanced metagenomic analysis tools available at the University of Chicago. Ferretti noted her prior experience studying how different maternal body sites influence infant microbiomes contributed to this work.
The study found that more than half of breast milk samples contained B. longum, which was also present in over 98% of 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."
Most earlier studies used amplicon sequencing, which examines only specific genomic regions and may miss much genetic information. The current study used metagenomic analysis to identify bacteria at the strain level. "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.
Researchers identified 12 cases where identical bacterial strains were found in both mother's milk and her infant's gut, suggesting vertical transmission during breastfeeding. These included beneficial species such as B. longum and B. bifidum that help digest human milk sugars and support healthy gut development, as well as pathobionts like E. coli and Klebsiella pneumoniae that can cause infection under certain conditions but were not linked to disease among healthy mothers and infants in this study.
The presence of oral-associated bacteria such as Streptococcus salivarius and Veillonella species suggested possible retrograde flow during breastfeeding—where oral microbes from babies travel back into mammary ducts.
"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."
Future research aims to integrate metabolite analysis—including human milk oligosaccharides—and examine environmental exposures such as PFAS or antimicrobial resistance passed through breast 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.
The article "Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk" appeared online ahead of print in November 2025.
