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Ten Things IBCLCs Need to Know About the Gut Microbiome

New understanding of how human milk affects the gut microbiome is helping to explain exactly how the benefits of human milk are achieved.

We hear a lot these days about the gut microbiome—and with good reason. Evidence suggests that the bacteria in our gut influence virtually every aspect of our functioning, from our stress and anxiety responses, to our metabolism and appetite, to the robustness of our immune system, to even our experience of gender and mating. And when our gut microbiome is out of balance, research suggests negative consequences can result: depression and anxiety, obesity, irritable bowel syndrome, Alzheimer’s Disease, and asthma have all been linked to microbiome disruption.

What does the gut biome have to do with breastfeeding? A lot, as it turns out. A webinar hosted by ILCA, Jarold “Tom” Johnston, DNP, CNM, IBCLC, explores that connection. Here, based on Johnston’s talk, are the 10 things lactation consultants need to know about the maternal-infant gut microbiome.

1. The microbiomes of baby and birthing parent are inextricably linked.

When a person gives birth, they pass their microbiome to their baby—first through exposure to their normal flora in the birth canal and then through their milk during breast- or chestfeeding.

2. Communication is a two-way street.

The milk ejection reflex is a muscular contraction that pushes milk out to the baby. But did you know that once the milk ejection reflex slows, muscles relax and pull baby’s saliva back in? Lactocytes respond to saliva exposure by producing particular macrophages. If the baby has been exposed to an infection, at the next feeding, he will get leukocytes and antibodies to fight that specific infection.

3. Colostrum is not really food.

You read that correctly! Babies get very few calories at the breast during the first 48 hours, because the calories in colostrum are not intended for digestion. They come from immune cells, designed to populate the immune system. Rather than thinking of colostrum as calories, think of it as an immune system transfer.

4. Breastmilk sugars are more than food.  

Human Milk Oligosaccharides (HMOs) play a key role in developing the infant’s gut microbiome. Human milk contains more than 100 types of HMOs. (In contrast, cows’ milk contains only two.) Each HMO has a specific benefit for the infant’s gut microbiome. Some are prebiotics, acting to increase good bacteria in the gut. Others block the attachment of invading viruses and bacteria like RSV and e.coli by providing harmless “decoy” attachment sites. Another type coats the baby’s gastrointestinal tract, preventing pathogens from sticking.  But none of them are digested by baby as carbohydrates until the baby is more than four months old.

5. A breasted baby’s gut microbiome is optimized for nutrition delivery.

The breastfed infant’s gut contains a specialized group of bacteria known as the phosphotransferase system. This system transports lactose and makes it available for use. Breastfed babies have higher levels of phosphotransferase then formula-fed babies. This means breastfed babies can access the maximum amount of energy available in their breastmilk. This ensures a constant source of carbohydrate for the developing, glucose-dependent brain.

Breastfed babies have higher numbers of gut bacteria that produce Vitamin A, B Vitamins, Vitamin K-2, and more. When they drink breastmilk, it feeds the bacteria colonies in their gut that make these micronutrients. Are you ever asked whether breastmilk contains enough iron, Vitamin K, or other nutrients? That question is misleading! Babies actually do not “get” these important micronutrients from the breastmilk they drink; what they get from breastmilk are the ingredients to feed a microbiome that can synthesize these micronutrients.

6. There are “bonus” calories in breastmilk.

Epithelial cells in human milk (formerly thought to be dead) are actually alive, active, and functional. They form clusters (called mammospheres) in the baby’s gut and continue to make more milk! This means that for every calorie of breastmilk a baby takes in, he gets bonus calories as the epithelial cells continue to generate milk inside his gut.

7. Exclusively breastfed babies have “less mature” gut microbiomes, and that is a good thing.

At birth, babies have very different proportions of specific bacteria in their gut microbiome compared to their birthing parent’s. Over the first 12 months of life, the baby’s microbiome shifts to strongly resemble the birthing parent’s. However, this shift is accelerated by the introduction of formula or the feeding of solid foods. As soon as the baby ingests anything other than human milk, the gut microbiome changes rapidly, and it does not go back. This may explain why formula fed infants experience more auto-immune and infectious illness.

8. Birth interventions affect the microbiome.

Cesarean section birth reduces microorganism exposure. While infants born via vaginal birth show 135 of their mother’s 187 bacteria strains after birth, infants born via surgical delivery show only 55. Antibiotics given to Group Beta-Strep-positive parents during birth also have an effect, since they wipe out good flora in the birth canal. Exactly how these interventions affect long-term health is not yet clear, but continuing to think carefully about birth interventions is key.

9. What about special situations?

Many of the mechanisms of microbiome transfer rely on birth and direct feeding. What about parents who exclusively pump, rely on donor milk, or induce lactation for an adopted baby? Exclusive pumping and the use of donor milk both impact the microbiome to some extent. Pasteurization of donor milk inactivates some of the living organisms in human milk, and exclusive pumping does not allow for the two-way communication discussed earlier where baby’s saliva is taken into the breast and informs lactocytes of the baby’s specific infection exposure. However, as you address parents’ concerns, what the science tells us now is that receiving human milk is more important than how it is the baby receives the milk.

10. Microbiome science is only a baby itself.

According to Johnston, it is important to remember that our understanding of the gut microbiome is just getting started. There is a long way to go, and much more to learn. However, for those of us who work with lactating families, the exciting news is: Understanding how the unique components of human milk interact with the infant’s gut organisms is helping us begin to understand how those benefits occur—they operate through the microbiome.

Want to learn more? ILCA members, access the entire webinar here. Not a member yet? Learn more about how you can access this and other continuing education at ILCA here.

14 Responses to Ten Things IBCLCs Need to Know About the Gut Microbiome

  1. ECBrooks 15 February 2020 at 06:53 #

    Great blog! Thanks!

  2. Jenny Weyman 15 February 2020 at 15:19 #

    In your article you say ‘glucose-dependant brain’, however I believe babies are often in nutritional ketosis so fueling from ketones. Do you have any information about this
    Thanks. Jenny.

    • lactationmatters 17 February 2020 at 11:49 #

      We will reach out to Tom Johnson for his input. Thanks for asking!

      • SV 21 February 2020 at 14:56 #

        I would love to read more about epithilials cells secrete milk in the gut. In wich study can i find more info? Can you please add a link?

      • Jarold Johnston 26 February 2020 at 16:01 #

        That comes from this article: Hassiotou, F., Geddes, D., Hartmann, P (2015) Cells in Human milk: State of the science. J Human Lactation, 29(2) 171-182
        Now, to be clear, the research demonstrates that the epithelial cells form mammospheres and secrete B-casein outside the body, I hypothesize that it may be rudimentary form of breast milk, and may be an additional source of kcals. Sometimes these things get a little over simplified in a blog post.

        Hope that helps

    • Jarold Johnston 26 February 2020 at 15:53 #

      That’s odd, I know that I replied to this question, but I don’t see it here. I’ll do so again.
      Your question asked about babies being in “nutritional ketosis” I’m no dietician, but I’ll try to answer that question. Ketone bodies are not a source of energy, but rather the waste product of gluconeogenesis (the making of glucose from fat). So when you deprive yourself (or the baby) of glucose you break down protein and fat to provide glucose thus building up ketone bodies and entering the state of “ketosis”.
      Now, this is supposed to happen during the colostral phase of breastfeeding, which is why all exclusively breastfed newborns lose weight in the first 2-3 days of life. In essence, they pack a lunch and take it with them when they are born. Of course, that assumes that the baby is full term and not IUGR. Babies born under stressful conditions may not have had the time or the opportunity to build up a healthy layer of fat before birth, which explains why they have so much trouble maintaining their blood glucose levels at birth.

      I hope that answers your question, and I’m sorry that I didn’t respond earlier.
      Jarold Johnston

  3. Johanna Sargeant 17 February 2020 at 14:55 #

    Brilliant article!

  4. Esen Dönmezer 23 February 2020 at 07:25 #

    Hi! Thanks for such a great article! Would you please give references? Especially about the mammospheres, I really would love to read more!

    • Jarold Johnston 26 February 2020 at 15:47 #

      Here are the ones that I like the most. Backhed, Bode, and Hassiotou were probably the three that specifically address this posting. Hassiotou, I believe, is the one the specifically addresses mammospheres.
      Hope that helps.

      Borre, O’Keefe, Clarke, Stanton, Dinan, Cryan (2014) Microbiota and neurodevelopmental windows: implications for brain disorders. Trends in Molecular -Medicine, 20(9); 509-518. DOI:
      -Gomez de Aquera, M, Ganal-Vonarburg, S., McCoy, K., Macpherson, A. (2016) The maternal microbiota drives early postnatal innate immune development. Vol. 351, Issue 6279, pp. 1296-1302 DOI: 10.1126/science.aad2571
      -Backhed, F., Roswall, J, Dahlgren, J., Wang, J. (2015) Dynamics and stabilization of the Human Gut Microbiome during the first year of life. Cell Host & Microbe, 17, 690-703
      -Bloomfield, S., Rook, G., Scott, E., Shanahan, F., Stanwell-Smith, R., Turner, P. (2016) Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspecitves in Public Health, 136(4) 213
      -Mayer, E.,. Tillisch, K., Gupta, A (2015) Gut/Brain axis and the microbiota. J of Clinical Investigation, 125(3) 926
      vanDe Sand, M., vanBuul, V., Brouns, F. (2014) Autism and nutrition: the role of the gut-brain axis. Nutrition research reviews, 27 p 199-214
      -Bode, L (2015) The functional biology of human milk oligosaccharides. Early Human Development, 91 p. 619-622
      -Bode, L (2012) Human milk oligosaccharides: Every baby needs a sugar mama. Glycobiology, 22(9) p 1147-1162
      -Hassiotou, F., Geddes, D., Hartmann, P (2013) Cells in Human milk: State of the science. J Human Lactation, 29(2) 171-182
      -Levy, M., Thaiss, C., Elinav, E. (2015) Metagenomic cross-talk: The regulatory interplay between immunogenomics and the microbiome. Genome Medicine 7:120

  5. Wilma 23 February 2020 at 20:58 #

    Very Interesting article. Our bodies are so amazing! Can you address the issue of Vitamin D for infants who are breast fed?

    • Jarold Johnston 26 February 2020 at 16:03 #

      I’m sorry, I have not spent any time on Vitamin D from an academic perspective. Perhaps there are others who can address that?

  6. Ruth Jameson 4 March 2020 at 11:10 #

    Thanks for a great article. Is there new research that has led to elevating the hypothesis of retrograde milk flow to an understood feature of lactation? The literature up to 2015 is tantalizing, but far from conclusive. I’m also very curious about the ability of lactocytes to produce macrophages. Could you help me find that research, as well?

    • doulatron 28 April 2020 at 15:35 #

      Yes, I’m keen to learn more about this too.

  7. doulatron 28 April 2020 at 15:28 #

    You wrote: “Human Milk Oligosaccharides (HMOs) play a key role in developing the infant’s gut microbiome. Human milk contains more than 100 types of HMOs. (In contrast, cows’ milk contains only two.)”

    Is that a typo or am I missing something? Why would we expect *Human* Milk Oligosacchrides in cow’s milk?


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