What New Parents Should Know about Breastmilk and the Microbiome

by Dr. Harriet Holme
While I’m a great believer that #fedisbest I do think that women should be able to make an informed decision about how they feed their baby, free from mum guilt or societal judgment and that unbiased accurate information is sometimes lacking.

What is the microbiome?

Not all bacteria are harmful, in fact, many are key to our health. The microbiome is the term used to cover the trillions of bugs, including bacteria, that live on our skin and in our gut. 

Why is the microbiome important?

With increasing research, we know that these single-cell organisms play a huge role in our health1.

How are baby’s microbiomes established?

When breastfeeding, the mother and baby are referred to as a dyad and this describes that although they are two individuals, there is an interactive relationship between them; this is highlighted by the formation of friendly microorganisms in breastmilk (milk microbiota). Initially, a healthy gut microbiome was thought to be established by firstly exposure through vaginal delivery and secondly through the transfer of bacteria through breastmilk1,2 but there is evidence that this is simplified, with many factors playing a role2.
Even before a mother has breastfed her baby, live microorganisms are already found in her breastmilk, providing evidence of maternal origin (called entero-mammary pathway) 2. Additionally, the microorganisms in the baby’s mouth are similar to the mother’s breastmilk, with some evidence to suggest that in addition to maternal transfer, there is also communication via the baby’s saliva back into the breast, which has a role in determining the microbiome2.
Mode of delivery, older siblings, complementary feeding with formula milk, maternal and infant antibiotic exposure, and even mode of feeding (pumped breastmilk versus directly at the breast) are all thought to play a part in determining the baby’s gut microbiome2. Although some of these factors may only act in the short term, for example, there is some evidence to suggest that mode of delivery has no persistent effect at 8 months3, so may have a more long term effect. For example, stool microbiome profiles of children at 1 year were significantly different in those that were still breastfed, compared to those that weren’t, independent of the mode of delivery or previous antibiotic exposure4. More research is needed to determine why the microbiome is different with pumped breastmilk compared with the direct transfer, whether it is the act of pumping or lack of contact with the baby’s mouth2.
Ultimately whether breastmilk provides the microorganisms to colonise the baby’s gut, or provides nutrients and prebiotics to foster a specific environment for selective growth of certain microorganisms or a mixture of both, has yet to be fully established 2. However, maturation and maintenance of the lining of the infant gut depend on bacterial colonisation5 and with evidence to support a long term health impact2,6,7

Why is breastmilk different?

Breastmilk contains a number of different components that make it different to formula milk and are hard to replicate. In addition to the microorganisms, other components of breastmilk such as immune cells, antibodies, fatty acids, and also human milk oligosaccharides (HMOs), also have a role in shaping the diversity of organisms 2.

 Human milk oligosaccharides

Human milk oligosaccharides (HMOs) are short-chain carbohydrates that are present in breastmilk, which are essentially undigested by the baby but are an important nutrient source for specific types of bacteria in the gut8. One of the bacteria commonly seen in the gut of healthy babies is Bifidobacterium longus infantis that metabolizes HMOs into lactate and acetate9. These are compounds are acidic, and change the pH of the infant stool, which associated with lower levels of potentially harmful bacteria and those that harm the lining of the gut9. HMOs may also prevent the formation of other bacteria which are potentially harmful thereby shaping the formation of the microbiome, improve the barrier function of the lining of the gut, and have a role in immune function8.


Lactoferrin, found in breastmilk, binds iron for transfer and absorption through the infant gut lining 8. While the baby can use this iron as an important nutrient, reducing the quantity of iron in the gut, prevents harmful bacterial growth 8.

 Antibodies in Breastmilk

Antibodies are used to tag microbes like viruses and bacteria, for destruction by other immune cells. Levels of certain antibodies (IgA, IgG and IgM), have been found to be higher in the guts of babies who are breastfed10. When babies are born, they are initially unable to produce the antibodies they need.
Breastmilk functions to supply these antibodies for the first few weeks until the baby is able to produce enough themselves10. These supply of these antibodies from breastmilk mean babies who are breastfed, have a lower risk of some childhood infections8. Also, low levels of IgA antibodies as a baby is associated with increased risk of development of allergies and asthma during childhood11, and development of Crohn’s disease in children12.

 Xanthine oxidase

Interestingly breastmilk contains an enzyme called xanthine oxidase, while neonatal saliva contains the substrates for this enzyme (xanthine and hypoxanthine). When the enzyme mixes with these substrates in the mouth and intestinal tract of the baby, a chemical reaction occurs, releasing hydrogen peroxide. This is antibacterial, and regulates the growth of some bacteria, possibly with a role in creating the different microbiome seen in breastfed babies 13

Does the type of milk matter?

Animal studies in monkeys have found that there are changes in the immune system in exclusively breastfed babies compared to babies fed formula and that these changes persist for 3-5 years after birth, long after weaning14.
In humans, gut bacteria have been found to differ between exclusively breastfed and formula fed5. Prebiotic like compounds added to formula milk, predict a microbiome distinct to that seen in an exclusively breastfed baby3. While mixed fed babies have a microbiome that appears to be on a spectrum between that of breastfed and formula-fed babies15.

What about weaning?

The introduction of complementary foods (weaning) changes the microbiome in the baby’s gut. Early weaning starting at 4 months or before, has been associated with a 30% higher risk of being overweight or obese in childhood, and a less diverse gut microbiome16. A high BMI in childhood is associated with a higher future risk of high cholesterol profile, high blood pressure, diabetes, and cardiovascular disease17.  However, those children who were breastfed for more than 4 months, did not have a higher BMI at 5 years, regardless of age at weaning16, so breastfeeding appears to be protective.

Are there benefits of breastmilk long term?

The first 1000 days of life is a critical period for the development of the immune system4, and up to 70% is associated with the gut18. In the first few months of life, patterns are established for recognizing self and non-self (highly important in autoimmune diseases), that have life-long consequences6,7.
There is evidence that the incidence of eczema, and wheezing in the first 2 years of life can be decreased by exclusive breastfeeding for 3 to 4 months19. There is also some evidence that longer duration of breastfeeding may protect against asthma after the age of 5 years19. Breastfeeding has not been shown to prevent or delay the onset of specific food allergies19

Maternal benefits of breastfeeding

For mothers, in addition to the psychological aspect of bonding, breastfeeding decreases the risk of breast cancer and may protect against ovarian cancer and type 2 diabetes20.
About Dr Harriet Holme MA Cantab MBBS Lond MRCPCH PhD RNutr
After over a decade as a medical doctor, ultimately specializing in treating children with cancer, I decided to focus on the aim of prevention of disease through healthy eating. Completing a PhD in genetics inspired my interest in how genes are turned on and off (epigenetics) and understanding the microbiome (the trillions of microbes which live in our digestive systems), which ultimately fueled my interest in nutrition. There is still much research to be done, but with the scientific information already available, there are healthy choices that you could be making now which mean a rich array of tasty nutritious food, that may improve the quality of your life and reduce your future risk of disease. For more information look at my health page, where you will find articles on the the science of wellness.
I studied medicine at Trinity Hall, University of Cambridge and University College London. I have completed a PhD in cancer genetics from UCL and hold a postgraduate Membership of the Royal College of Paediatrics and Child Health. I have an accreditation for Applied Human Nutrition from The University of Cambridge. I no longer practice as a doctor, but instead provide nutritional consultancy, and lecture on culinary science and nutrition. I am a Registered Nutritionist with the Association for Nutrition.
  1. Lynch, S. V. & Pedersen, O. The Human Intestinal Microbiome in Health and Disease.https://doi.org/10.1056/NEJMra1600266 375, 2369–2379 (2016).
  2. Moossavi, S., Sepehri, S., Robertson, B., Bode, L., Goruk, S., Field, C. J., Lix, L. M., de Souza, R. J., Becker, A. B., Mandhane, P. J., Turvey, S. E., Subbarao, P., Moraes, T. J., Lefebvre, D. L., Sears, M. R., Khafipour, E. & Azad, M. B. Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors. Cell Host & Microbe 25, 324–335.e4 (2019).
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  6. Arrieta, M.-C., Stiemsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist-Doutsch, S., Kuzeljevic, B., Gold, M. J., Britton, H. M., Lefebvre, D. L., Subbarao, P., Mandhane, P., Becker, A., McNagny, K. M., Sears, M. R., Kollmann, T., Investigators, T. C. S., Mohn, W. W., Turvey, S. E. & Finlay, B. B. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Science Translational Medicine 7, 307ra152–307ra152 (2015).
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  11. Dzidic, M., Abrahamsson, T. R., Artacho, A., Björkstén, B., Collado, M. C., Mira, A. & Jenmalm, M. C. Aberrant IgA responses to the gut microbiota during infancy precede asthma and allergy development. J. Allergy Clin. Immunol. 139, 1017–1025.e14 (2017).
  12. De Palma, G., Nadal, I., Medina, M., Donat, E., Ribes-Koninckx, C., Calabuig, M. & Sanz, Y. Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol. 10, 63–7 (2010).
  13. Sweeney, E. L., Al-Shehri, S. S., Cowley, D. M., Liley, H. G., Bansal, N., Charles, B. G., Shaw, P. N., Duley, J. A. & Knox, C. L. The effect of breastmilk and saliva combinations on the in vitro growth of oral pathogenic and commensal microorganisms. Sci Rep 8, 1–9 (2018).
  14. Narayan, N. R., Méndez-Lagares, G., Ardeshir, A., Lu, D., Van Rompay, K. K. A. & Hartigan-O'Connor, D. J. Persistent effects of early infant diet and associated microbiota on the juvenile immune system. Gut Microbes 6, 284–289 (2015).
  15. Borewicz, K., Suarez-Diez, M., Hechler, C., Beijers, R., de Weerth, C., Arts, I., Penders, J., Thijs, C., Nauta, A., Lindner, C., Van Leusen, E., Vaughan, E. E. & Smidt, H. The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life. Sci Rep 9, 1–13 (2019).
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  17. Juonala, M., Magnussen, C. G., Berenson, G. S., Venn, A., Burns, T. L., Sabin, M. A., Srinivasan, S. R., Daniels, S. R., Davis, P. H., Chen, W., Sun, C., Cheung, M., Viikari, J. S. A., Dwyer, T. & Raitakari, O. T. Childhood adiposity, adult adiposity, and cardiovascular risk factors. N Engl J Med 365, 1876–1885 (2011).
  18. Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., Khan, M. T., Zhang, J., Li, J., Xiao, L., Al-Aama, J., Zhang, D., Lee, Y. S., Kotowska, D., Colding, C., Tremaroli, V., Yin, Y., Bergman, S., Xu, X., Madsen, L., Kristiansen, K., Dahlgren, J. & Wang, J. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host & Microbe 17, 690–703 (2015).
  19. Greer, F. R., Sicherer, S. H., Burks, A. W., COMMITTEE ON NUTRITIONSECTION ON ALLERGY AND IMMUNOLOGY. The Effects of Early Nutritional Interventions on the Development of Atopic Disease in Infants and Children: The Role of Maternal Dietary Restriction, Breastfeeding, Hydrolyzed Formulas, and Timing of Introduction of Allergenic Complementary Foods. Pediatrics 143, e20190281 (2019).
  20. Victora, C. G., Bahl, R., Barros, A. J. D., França, G. V. A., Horton, S., Krasevec, J., Murch, S., Sankar, M. J., Walker, N., Rollins, N. C.Lancet Breastfeeding Series Group. Breastfeeding in the 21st century: epidemiology, mechanisms, and lifelong effect. Lancet 387, 475–490 (2016).

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