Breast Milk’s Connection to the Gut Microbiome

Human milk is considered the perfect food for infants and is the recommended sole source of nutrition for at least the first sixth months of the infant’s life. After this, complementary foods should be introduced, but continuing to provide human milk is still important. The child and nursing parent should continue nursing until one or both decide it is no longer desired. There is not an age limit for when one should stop nursing.

There are instances, of course, where feeding your child solely human milk, or any human milk for that matter, is not possible due to maternal physical abilities, mental health, or a personal choice. My goal as a pediatrician and IBCLC are, first and foremost, is to ensure a child is adequately fed. I will only choose how my own children are fed, never another’s. My phrase I say to parents is always “not my baby, not my body, not my choice.” I just want to make sure your child is being provided a sufficient amount of safe and appropriate food, whatever it is you choose.

I would like to talk about the benefits of human milk, particularly in regards to the human microbiome.

There has been a lot of discussion about the microbiome lately, so I would like to start there. Humans are covered in bacteria. In fact, there is about 4-6 pounds worth on the average adult. It is on our skin, in our mouths, and lining our gastrointestinal tract. How do we get that bacteria? Well, it starts at birth.

Our microbiome is created by multiple factors. For example, our mode of delivery (vaginal or cesarean) and the bacteria from our birthing parent can affect the development of our microbiome. Another significant factor is what we are fed, which has been shown to contribute to nearly 30% of all bacteria found in our gut. Our microbiome is also affected by antibiotics, which selectively kill certain bacteria. Probiotics and our physical environment (where you live, animals you’re exposed to, etc.) also affect our gut health.

So, why is the microbiome important?

We are learning that our microbiome has the ability to alter our health for life. It affects things like our metabolism, immune tolerance, and what diseases we might be prone to (e.g. asthma, autoimmune disease, eczema, inflammatory bowel disease, diabetes, colon cancer, our weight, etc.). Pretty important!

Now how does human milk contribute to this?

Human milk is made up of water, protein, sugar, fat, vitamins, hormones, antibodies, and about 800 strains of bacteria. When we are born, we have a completely sterile gastrointestinal tract. The bacteria we are exposed to nutritionally are the first ones to grow in our body and begin the creation of our microbiome. There is also something called human milk oligosaccharides that select the good bacteria to colonize and grow. Lactoferrin, a protein found in human milk, is antibacterial, antifungal, antiviral, and antiparasitic. This all functions to protect infants from all sorts of diseases. It decreases the risk of infection, certain types of cancer, type 1 diabetes, ear infections, respiratory infections, diarrhea, and eczema just to name a few.  It improves vision, IQ, and immune responses.

It is important to note, however, that feeding your infant human milk does not mean they will never be ill or get any of these diseases nor does it mean feeding your child formula (aka science milk) will guarantee these illnesses either.

What is also interesting is that human milk also affects a child’s future education and career. For children, feeding human milk is correlated with higher levels of education, higher adult earnings, and overall healthier families.

Furthermore, a mother’s decision to breastfeed will also affect her personal health. In the nursing parent, there is a reduction in breast and ovarian cancer, type 2 diabetes, and osteoporosis (bone thinning), cardiovascular disease, and postpartum depression. I would argue (and this is solely my opinion based on my own clinical experience) that nursing can be a strong source for maternal anxiety and depression.

Overall, the benefits of providing human milk to children have been proven. We know that it’s not only the best choice for the child, but may also have positive implications for the overall family unit as well. One suggestion I can offer though, is that you make the choice prior to the birth of your child!



  1. JAMA Pediatr. 2017;171(7):647-654. doi:10.1001/jamapediatrics.2017.0378
  2. Victora, C. G. et al. Breastfeeding in the 21st century: epidemiology, mechanisms, and lifelong effect. The Lancet 387(10017), 475–490 (2016).
  3. The Biologist 64(3) p10-13
  4. Rautava, S. (2016). Early microbial contact, the breast milk microbiome and child health. Journal of Developmental Origins of Health and Disease, 7(1), 5-14. doi:10.1017/S2040174415001233
  5. Clinical Benefits of Lactoferrin for Infants and Children Paolo Manzoni MD, PhD.
  6. Le Doare K, Holder B, Bassett A, Pannaraj PS. Mother’s Milk: A Purposeful Contribution to the Development of the Infant Microbiota and Immunity. Front Immunol. 2018;9:361. Published 2018 Feb 28. doi:10.3389/fimmu.2018.00361

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Dr. Lauren Hughes, MD, IBCLC

Dr. Hughes is a board-certified pediatrician, international board certified lactation consultant (IBCLC), and a mother of three. She is the founder and lead physician of the first pediatric direct primary care clinic in Kansas City, Bloom Pediatrics and Lactation ( She is also Kansas City's only breastfeeding medicine physician. She started her practice as a way to provide quality, convenient, and accessible care to the children of Kansas City. She lives in the Kansas City metro with her husband, son, and twins.