Breastfeeding and the Microbiome

Mother's milk provides health benefits that last a lifetime

Journal: Cell Host & Microbe
Date: July 2020

Within our intestines is an ecosystem of some 100 trillion living microorganisms, including bacteria, viruses and fungi that play important roles like breaking down food, synthesizing vitamins and defending against pathogens - among other things. We call this ecosystem our intestinal ‘microbiome.’ It turns out that breastfeeding plays an important role in establishing a healthy microbiome in babies, which in turn has long-term implications for our overall health.

Breastmilk contains a rich and varied array of nutrients that are unique to each mom and baby. It also contains beneficial bacteria and prebiotics – “food” for the beneficial bacteria. In an article titled “Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: The Child Cohort Study* researchers found that beneficial bacteria are shared through breastmilk and that feeding directly from the breast is the best way to support this process. The milk itself is amazing enough, but feeding directly at the breast increases the transfer of beneficial organisms. This is because approximately ten percent of the bacteria introduced to the infant is from the skin around a mother’s areola. There is also a beneficial alchemy that occurs with the bacteria and enzymes inside the infant’s mouth, facilitating a healthy oral microbiota in the baby. 

Long-term health implications of a healthy microbiome
A healthy microbiome is developed within the first three years of life and plays a number of critical roles throughout the lifespan, including how well people are able to fight disease and prevent infections. Breastmilk seeds and nurtures the microbiome with beneficial bacteria, until it is fully mature. Beneficial gut bacteria play a role in lowering risk for chronic diseases like asthma, obesity, allergies, dermatitis, inflammatory bowel disease and neurodevelopmental disorders. They also play a role in regulating anxiety, mood, cognition and pain via the brain/gut axis.

It has been well established that breastfeeding is a powerful, modifiable factor in establishing a baby’s microbiome, but the study in the above mentioned journal article was the first to evaluate breastfeeding practices (mode, exclusivity and duration), along with milk bacteria and milk components - and the composition of infant gut microbiota - at multiple points in a baby’s first year. This research involved 1,249 mother/baby pairs who are part of the ongoing Canadian CHILD Cohort Study.

There are many factors involved in establishing a healthy microbiome, including whether the baby was born vaginally or via C-section, the status of the mother’s microbiome and BMI during pregnancy and lactation, whether the baby is born pre- or full-term, the mother’s stress levels, antibiotic use, the duration of breastfeeding, which solid foods are first introduced, whether the baby has siblings, the mother’s diet while breastfeeding, milk composition at various stages of lactation and even if there is a pet in the home. Researchers are just beginning to tease apart these factors in an effort to understand how best to support mothers and babies during the first years of life, for the best health outcomes.

Regardless of all these factors, evidence shows that any amount of breastmilk is beneficial - even if only for a short period of time. And even though the process of pumping, storing and bottle-feeding breastmilk may reduce the transfer of viable milk bacteria from mom to baby, pumped milk still provides many health benefits. This study provides important new knowledge that can help improve recommendations on how to handle and store breastmilk for when moms need to pump.


  • Breastfed babies have higher levels of beneficial gut bacteria and healthier growth patterns than babies who are not breastfed.
  • Breastfed babies have a lower rate of wheezing – one of the most common reasons infants are hospitalized or receive medical care.
  • Breastfed babies have a lower risk of developing asthma as they get older.
  • How a baby is breastfed matters too – meaning, there is a difference between feeding directly from the breast and feeding pumped breastmilk from a bottle.
  • Breastmilk is unique to each mom and baby.

What about formula fed babies?
While there is rock solid evidence that breastfeeding provides health advantages for babies and mothers, the fact that there are millions of adults who were formula fed indicates that women who are unable to breastfeed can still raise normal, healthy children. Women often feel guilty for not nursing, or being able to nurse, their babies. However, there are many circumstances where they are simply unable to. There are a variety of physiological reasons why a woman might not produce an adequate supply of milk. They may have latching problems, pain, medical complications, or need to return to work early and choose not to breastfeed. Some babies are adopted and the parents don’t have access to breastmilk. This study on the microbiome provides important insight into how microbes could be manipulated and used to optimize health for all infants.

Supporting women’s personal goals
The World Health Organization (WHO) and the American Academy of Pediatrics (AAP) recommend that babies are exclusively breastfed until six months of age, and that mothers continue breastfeeding while introducing complimentary foods for at least one year (at least two years or more according to WHO). Oregon has a strong track record in the number of women who breastfeed but due to an overall lack of support, many aren’t able to meet their original breastfeeding goals. According to the Oregon Public Health Division, over 90 percent of Oregon mothers breastfeed their new babies, but only six in ten women are able to continue for as long as they had planned. Families, employers, child care and health care providers, hospitals and communities all play a role in reducing barriers to breastfeeding and ensuring that mothers get the support they deserve. 

Learn more about why breastfeeding matters.

Additional resources:
La Leche League of Oregon

OHSU Center for Women’s Health lactation services
U.S. Breastfeeding Committee

USDA WIC Breastfeeding Support

*The senior author on the study, Dr. Megan Azad, is a widely recognized expert on human pregnancy and nutrition in childhood. She is a valued friend of the Moore Institute. Dr. Azad is Associate Professor of Pediatrics at the University of Manitoba, and co-Directs the new Manitoba Interdisciplinary Lactation Centre (MILC). Her research program is focused on the role of infant nutrition and the microbiome in child growth, development and resilience. Dr. Azad also co-leads the Manitoba site of the CHILD Cohort Study, the largest multidisciplinary, longitudinal, population-based birth cohort study in Canada. It’s designed to be one of the most informative studies of its kind in the world.

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The OHSU Bob and Charlee Moore Institute for Nutrition & Wellness supports human research that seeks to find the links between maternal stresses, including poor nutrition, and elevated disease risks for babies as they become adolescents and adults. 


Kelsey Fehr, Shirin Moossavi, Hind Sbihi, Rozlyn C.T. Boutin, Lars Bode, Bianca Robertson, Chloe Yonemitsu, Catherine J. Field, Allan B. Becker, Piushkumar J. Mandhane, Malcolm R. Sears, Ehsan Khafipour, Theo J. Moraes, Padmaja Subbarao, B. Brett Finlay, Stuart E. Turvey, Meghan B. Azad. (2020). Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study. Cell Host & Microbe 28(2):285-97.e4, ISSN 1931-3128.