A recent study conducted by a number of scientific research institutions in the United States shows that human breast milk is not only a source of nutrients and antibodies in the early stages of a baby's life, but also forms a microbial ecosystem of its own. The bacterial community in it is likely to play a key role in the early establishment of the baby's intestinal microbiome. The research team used advanced metagenomic sequencing technology to track the correspondence between the bacterial lineages in breast milk and the infant's intestinal flora, providing one of the clearest evidence to date showing that some bacteria in breast milk can be "vertically" transferred to the baby during the breastfeeding process.
Traditionally, discussions about breast milk have focused on aspects such as nutritional content, immune antibodies, and parent-child attachment, while relatively limited attention has been paid to bacteria in breast milk. However, there is a small but structurally stable "milk microbiota" in human milk. These bacteria may affect the colonization path of the infant's intestinal flora, thereby affecting multiple physiological processes such as nutrient absorption, metabolism, and immune system maturation. The new study, published in Nature Communications, systematically analyzed how the composition of different breast milk flora is related to the formation of infant intestinal microorganisms.
Because breast milk is rich in fat and overall low in bacteria, obtaining enough genetic material from it for in-depth analysis has been technically difficult. Although breast milk is widely recommended as the sole source of nutrition for infants in the first months of life, there are still many unanswered questions about the milk microbiome, in part because it is so difficult to analyze, said lead author Pamela Ferretti, a postdoctoral researcher in Blekhman's lab at the University of Chicago Medical Center. This study was able to systematically break through this bottleneck by relying on hundreds of milk samples collected from the "Maternal and Infant Health Linkage (MILk)" large-scale cohort study and combined with the team's experience in metagenomic and infant microbiome research.
The research team analyzed a total of 507 samples from 195 mother-infant pairs, covering both breast milk and infant feces. Data show that there is a characteristic bacterial combination in breast milk, among which Bifidobacterium is dominant, including Bifidobacterium longum (Bifidobacterium longum), Bifidobacterium breve (B. breve), and Bifidobacterium bifidum (B. bifidum). Bifidobacterium longum was detected in more than half of the breast milk samples, and in the infant gut microbiome, this species was present in high abundance in more than 98% of the samples. This high overlap is regarded as an important clue that breast milk is involved in the construction of intestinal flora.
Ferretti points out that it is well established that Bifidobacterium longum is highly prevalent in the infant gut, but finding such a strong "signature" of the same species in breast milk samples was unexpected. Previous studies on breast milk bacteria reported more on Staphylococcus, Streptococcus and other bacterial genera, reflecting the limitations of previous detection methods and depth of analysis. The new results are expected to prompt the academic community to re-evaluate the composition and structure of breast milk microbiota and its biological significance.
Unlike previous studies that mostly used amplicon sequencing, this study used metagenomic sequencing technology, which can reconstruct a larger range of genomic information in mixed bacterial samples and is accurate to the strain level. This kind of resolution is crucial for tracing the "transmission path" between breast milk and the infant's gut, because only when there is a match at the strain, rather than species, level can researchers infer the existence of an actual transmission event. The research report documented 12 cases of the same bacterial strain co-occurring in the mother's milk and the intestines of her infant, which is seen as strong evidence of vertical transmission through breastfeeding.
These include beneficial symbiotic bacteria such as Bifidobacterium longum and Bifidobacterium bifidum, which can break down human milk oligosaccharides (HMOs) and support healthy intestinal development of infants; they also include "opportunistic pathogenic bacteria" such as Escherichia coli and Klebsiella pneumoniae. The latter can exist as intestinal commensal bacteria in healthy people, but may cause infection under certain circumstances or immune status. The research team emphasized that the mothers and infants participating in the study were clinically healthy individuals. The presence of these strains in milk does not necessarily mean that they are pathogenic, but rather reflects the diversity of microorganisms that can be transmitted during breastfeeding.
The study also detected strains of bacteria commonly associated with the oral environment in the milk samples, including Streptococcus salivarius and several species of the Veillonella genus. This finding supports the so-called "retrograde flow" hypothesis: During the baby's sucking process, small amounts of oral bacteria may flow back into the mammary gland through the nipple and milk ducts, and then become part of the milk microbiome. This suggests that breast milk flora not only contributes "outwardly" to the mother's multi-site flora, but may also form a dynamic two-way interaction with the baby's own oral environment.
Ferretti said that this study not only advances the understanding of microbial transmission pathways, but also fills a major gap in basic scientific research data. Through this work, the number of publicly available breast milk metagenomic samples has almost doubled, and is accompanied by detailed maternal health status and lifestyle information, providing valuable resources for future research on the relationship between early life health and milk factors. The research team hopes that as more scholars use this data set to carry out multi-omics linkage analysis, research progress in related fields will be significantly accelerated.
Next, the researchers plan to expand the analysis to the level of metabolites and environmental exposure, such as in-depth study of the composition and function of human milk oligosaccharides, and examine how environmental factors such as per- and polyfluoroalkyl substances (PFAS) and antimicrobial resistance are transmitted through milk to affect the infant microbiome and health risks. The team's ultimate goal is to map health trajectories over longer timescales and explore whether breast milk composition and early life exposures predict health outcomes in adulthood. The related paper is titled "Infant Gut Microbiome and Resistance Genome Assembly Associated with Breast Milk Bacterial Strains" and was published in the journal Nature Communications on November 22, 2025.
Compiled from /ScitechDaily