Breast milk bacteria found to influence infant gut microbiome formation - Video

Breast milk isn't just nutrition-it's also a delivery system for trillions of tiny passengers. A new study published in Nature Communications reveals that human milk carries its own unique community of bacteria that seeds a baby's developing gut microbiome, shaping everything from nutrient absorption to immune system strength. Researchers analyzed 507 milk and infant stool samples from 195 mother-infant pairs, uncovering how specific bacterial strains travel from mother to child through breastfeeding—and sometimes in unexpected ways.

The breast milk microbiome has long been a mystery because milk's high fat content and low bacterial load make it notoriously difficult to study. Most prior research used quick but limited techniques that only examined a small slice of bacterial DNA. A team led by Pamela Ferretti at the University of Chicago and collaborators from the University of Minnesota and Oklahoma University Health Sciences Center took a different approach—they used metagenomic analysis, a deep-dive technique that examines nearly the entire bacterial genome. This allowed them to track not just which bacteria were present, but which exact strains moved from mother to infant.

The findings surprised researchers. Breast milk was dominated by bifidobacteria, particularly Bifidobacterium longum, which showed up in over 50% of milk samples and colonized 98% of infants' guts. Previous studies had reported other bacteria like Staphylococcus and Streptococcus as dominant.

Even more intriguing, the team identified 12 instances where the exact same bacterial strain appeared in both mother's milk and baby's gut—definitive proof of vertical transmission through breastfeeding. Some strains were beneficial, while others were potentially harmful bacteria like E. coli and Klebsiella that can cause infection under certain conditions. All mothers and infants in the study were healthy, suggesting these microbes reflect normal microbial diversity rather than disease.

The researchers also discovered evidence of "retrograde flow"—oral bacteria from the baby traveling back into the mother's breast during feeding, enriching milk's microbial composition. This groundbreaking work nearly doubled available data on milk microbiomes and opens doors to understanding how early-life microbial exposure shapes lifelong health.

REFERENCE: Ferretti, P., et al. (2025). Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk. Nature Communications. DOI: 10.1038/s41467-025-66497-y. https://www.nature.com/articles/s41467-025-66497-y