Just like other body parts and fluids in contact with the external environment, breast milk has its own microbiome that plays a key role in infant health by helping to establish a baby’s gut microbiota. Over the past decade, new genomic techniques have increased our understanding of the human milk microbiome and the factors influencing its composition and activity. However, an in-depth study of maternal and early-life factors that affect the milk microbial community is lacking.

A new study, led by Dr. Meghan B. Azad from the Department of Pediatrics and Child Health at the University of Manitoba (Winnipeg, Canada), explores how maternal and infant factors are associated with milk microbiota composition in nearly 400 mothers.

The researchers used 16S ribosomal ribonucleic acid (rRNA) gene sequencing to profile the milk microbiota in 393 breastfeeding mothers and their infants from the CHILD birth cohort, which represents one of the largest studies of the human milk microbiota to date. The women’s milk microbiota profiles were highly variable and a core milk microbiota—dominated by Proteobacteria and Firmicutes and consisting of four discrete clusters that might reflect different sources of exogenous milk bacteria—was identified in all milk samples.

On the other hand, the researchers explored the relationship between maternal and infant factors and milk microbiota diversity and composition, after adjusting for confounding factors relating to both mother and infant.

Milk microbiota diversity and composition were associated with maternal factors, including body mass index (BMI), parity, mode of delivery, mode of breastfeeding and several milk components.

Among the early-life and infant factors analyzed, having siblings and the sex of infants showed significant associations with milk microbiota composition. Maternal BMI and parity were associated with milk microbiota composition in a sex-specific manner, whereas maternal atopy and smoking were associated with milk microbiota diversity in a phylum-specific manner.

In addition, milk components including human milk oligosaccharides’ compositional profile and the profile of fatty acids found in milk were also relevant in determining milk microbiota composition. These non-bacterial milk components were found to be affected by maternal diet.

From the many factors examined, the method of breastfeeding in the two weeks preceding the collection of a breast milk sample for the study (indirect as at least one serving of pumped and stored milk versus exclusive direct breastfeeding) was the most consistent factor related to milk microbiota composition when using different statistical analysis methods.

The authors found that indirect breastfeeding was associated with a lower abundance of beneficial Bifidobacterium and increased abundance of Enterobacteriaceae and potential opportunistic pathogens Stenotrophomonas and Pseudomonadaceae (possibly pump-associated). In contrast, members of the Actinobacteria phylum and Veilloneallaceae (a family member representative of the oral microbiota) were enriched with direct breastfeeding.

In addition, indirect breastfeeding was associated with lower overall milk microbiota richness and diversity when compared with direct breastfeeding.

The researchers suspect that pumping may prevent the transfer of oral bacteria from the infant to the breast milk microbiota, thus introducing other bacteria from the pump. These findings show that milk bacteria may have its origins in the infant oral cavity. This is in agreement with scientists who have previously shown the infant oral cavity as the origin of breast milk bacteria, while others believe breast milk bacteria originate in the mother’s gut.

The same research group had previously found that modes of infant feeding other than direct breastfeeding—including breastfeeding with some pumped breastmilk—were less beneficial than direct breastfeeding in terms of the increased risk of asthma at 3 years of age.

In conclusion, this study has revealed maternal and infant factors involved in shaping milk microbiota composition. Of all the factors examined, the breastfeeding method was the most consistent factor associated with milk microbiota composition, which highlights the importance of considering this variable in future milk microbiome research.

These findings also highlight the importance of the infant’s mouth as a source of bacteria in breast milk and this, together with maternal gut microbiota, contributes to explaining the origins of milk microbiota. Research monitoring and analyzing the long-term impact on infant health of factors affecting the milk microbiota will provide useful insights for the clinical setting.



Moossavi S, Sepehri S, Robertson B, et al. Composition and variation of the human milk microbiota are influenced by maternal and early-life factors. Cell Host Microbe. 2019; 25:324-35. doi: 10.1016/j.chom.2019.01.011.