A new cohort study reveals variations in milk and infant fecal microbiota within and between populations

The human milk microbiota is an important source of commensal microorganisms for the infant gut. Although both maternal and infant microbiomes are shaped by a multitude of factors, including delivery mode, geographic location and the method of breastfeeding, the extent to which bacterial taxa in a mother’s breast milk correlates with an infant’s fecal microbiota across different geographic locations is unclear.

A new multi-cohort study, led by Dr. Michelle K. McGuire from the University of Idaho (United States), has found that human milk and infant fecal microbiomes show variations within and between different populations worldwide.

Breastmilk and infant fecal samples were collected from 11 populations: rural Ethiopia, urban Ethiopia, rural Gambia, urban Gambia, Ghana, Kenya, Spain, Sweden, Peru, California and Washington. The study analyzed 394 milk and 377 infant feces samples, comprising a total of 360 matched infant feces and milk samples.

The mother’s milk and infant fecal microbiome composition were more similar within than across cohorts. However, a significant variation within each cohort was also apparent, which researchers explained as being down to the role of the mother and infant pair’s environment in shaping the milk and fecal microbial communities. These findings highlight that a normal or healthy human milk or infant fecal microbiome cannot be defined based on current data.

In terms of similarities, a small core group of bacteria consisting of Streptococcus and Staphylococcus was shared in breast milk samples across all cohorts. Furthermore, some cohorts had additional taxa that composed their own microbiota core. For instance, Rhizobium genus was more abundant in milk produced by women in rural Ethiopia when compared with the other cohorts.

As with breast milk, a small core group of bacteria, including Streptococcus, Escherichia, Shigella and Veillonella, was found in all infant feces from different cohorts. In addition, some cohorts had their own microbiota core. This is the case of Lactobacillus genus, the abundance of which was highest in infant feces from rural Ethiopia and The Gambia and lowest in those infants from the United States, Sweden, Peru and Spain.

Bacterial diversity also showed variation between all cohorts.

Finally, the authors found that although individual taxa in a mother’s breast milk was not always found in her infant’s stool, positive correlations were found at the community level between microbial communities in both samples. For example, the abundance of Lactobacillus in milk was positively correlated with its abundance in infant feces.

Even in populations in close geographical proximity (Kenya to Ethiopia) and with genetic similarity (rural Ethiopia and urban Ethiopia, and rural Gambia and urban Gambia) significant differences were found between milk and infant fecal microbiota composition.

The fact that Lackey and colleagues have utilized standardized sample collection and analysis procedures reduces the methodology bias. Therefore, genetics and environment—including diet and lifestyle-related factors—can explain variations in the maternal breast milk and infant fecal microbiomes among the populations under study.

On the whole, this is the first large-scale observational study that provides evidence of maternal breast milk and infant feces microbiota variations within and between 11 populations worldwide. To what extent these findings have significance for the health of infants and their mothers should be addressed in future research that considers the contribution made by environmental factors to shaping the gut microbiome.


Lackey KA, Williams JE, Meehan CL, et al. What’s normal? Microbiomes in human milk and infant feces are related to each other but vary geographically: the INSPIRE study. Front Nutr. 2019; 6(45). doi: 10.3389/fnut.2019.00045.

GMFH Editing Team
GMFH Editing Team