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Home » Breast-Feeding’s Role in Establishing the Microbiome in Infancy

Breast-Feeding’s Role in Establishing the Microbiome in Infancy

Today's DietitianToday's Dietitian5 Mins ReadSeptember 16, 2025
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By Sherry Coleman Collins, MS, RDN, LD

Developing a healthy gut begins at birth. In fact, the route of a baby’s birth impacts colonization of the infant body and gut in a significant and measurable way. Vaginal delivery ensures the baby is inoculated with the mother’s microbes and starts the process of developing a diverse microbiome, as compared with a less diverse and less robust microbiome after cesarean birth. Instead of benefiting from the mother’s microbes, the early microbiome of babies born via cesarean is mostly influenced by the environment. Further and ongoing colonization of the skin and gut continues with early feeding (eg, breast-feeding vs formula) and environmental factors (eg, pets), as well as the influence of genetics and medications (eg, antibiotics).1

When it comes to nutrition, most experts agree that breastmilk represents the ideal for infant feeding. With thousands of unique components, breastmilk provides the perfect ratio of macronutrients at just the right time during infant growth, adjusting to meet a baby’s needs. Current infant feeding recommendations encourage mothers to breast-feed exclusively for the first six months. It has long been understood that breastmilk confers short- and long-term benefits to both mother and baby. These benefits include reducing the risk of infections, potentially decreasing the development of type 2 diabetes and obesity in the breast-fed infant, and lowering the risk of breast cancer in the mother and possibly the risk of type 2 diabetes and ovarian cancer.2

With regard to gut health, breast-feeding helps transfer bacteria from the mother’s milk and skin to the baby’s gastrointestinal tract.3 Among the bacteria transferred from mother to baby are proteobacteria and firmicutes, which are the most common. However, there’s great diversity in both the bacteria found in the mother’s milk and on the mother’s skin, which help promote greater bacterial diversity in the gut of breast-fed infants compared with formula-fed infants. In addition to bacteria, breastmilk contains a variety of other immunomodulatory components such as immunoglobulin A, lactoferrin, and defensins. It also provides prebiotics, including human milk oligosaccharides (HMOs), which feed beneficial bacteria in the infant gut and downregulate inflammatory markers.1

HMOs are complex indigestible sugars that are the third most abundant substances in human milk by volume, after carbohydrate and fat (not including water). While babies can’t digest HMOs, they serve as prebiotics for infant-specific strains of Bifidobacterium and likely for other beneficial species. Increased early colonization of Bifidobacterium is considered normal, healthy gut development. Interestingly, there are many different variations of HMOs in breastmilk, which may depend on genetics, environment, and even when breast-feeding occurs.4 Researchers still are trying to understand the significance of and contributing factors to these differences and how each may influence the immune system. Perhaps it’s tied to the changes in the bacteria found in breastmilk. Yet, experts agree that HMOs are beneficial.

In addition to functioning as prebiotics, it’s believed that HMOs serve other important functions in the gut to support healthy infants. In fact, HMOs may prevent pathogens from adhering to the gut lining altogether, averting or reducing illness by inhibiting them from staying in the gut. In one in-vitro study, HMOs reduced the ability of rotavirus, a particularly dangerous virus that causes potentially dehydrating diarrhea in infants and young children, to adhere to the gut lining by more than 70%.5 Other studies have shown similar results for E coli.4 These observations could explain some of the infection-prevention benefits breast-fed babies experience.

Formula companies recently have begun adding HMOs to some infant formulas. In fact, in a randomized controlled trial published in the Journal of Nutrition and supported by Reverri and colleagues, infants fed formula including 2’-Fucosyllactose HMO (one of the most abundant and well-studied HMOs) experienced lower numbers of inflammatory cytokines “similar to those of breastfed infants.”6,7 Though the research is limited, the results are encouraging. Other studies have shown conflicting results regarding the formula’s ability to protect against E coli but have established the safety of the addition of HMOs to infant formula.4

Breast-feeding remains the gold standard for infant feeding for its role in helping to establish a healthy gut microbiome. However, advances in the understanding of breastmilk composition, the role of components such as HMOs, and the ability to create infant formulas that more closely resemble breastmilk, including the addition of bioidentical HMOs, may help improve outcomes when mothers can’t or choose not to breast-feed. With more than 100 different types of HMOs identified, it’s likely that additional HMOs will be added to infant formula in the future. For now, it’s important to know that infant formulas with HMOs are an option for non-breast-fed infants.

— Sherry Coleman Collins, MS, RDN, LD, is president of Southern Fried Nutrition Services in Atlanta, specializing in food allergies and sensitivities, digestive disorders, and nutrition communications. Find her on Twitter, Instagram, and Facebook as @DietitianSherry, via the Southern Fried Girlfriends podcast, and at www.southernfriednutrition.com.

References
1. Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nature Med. 2016;22(7):713-722.

2. Section on Breastfeeding. Breastfeeding and the use of human milk. Pediatrics. 2012;129(3):e827-e841.

3. Pannaraj PS, Li F, Cerini C, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171(7):647-654.

4. Triantis V, Bode L, van Neerven RJJ. Immunological effects of human milk oligosaccharides. Front Pediatr. 2018;6:190.

5. Laucirica DR, Triantis V, Shoemaker R, Estes MK, Ramani S. Milk oligosaccharides inhibit human rotavirus infectivity in MA104 cells. J Nutr. 2017;147(9):1709-1714.

6. Goehring KC, Marriage BJ, Oliver JS, Wilder JA, Barrett EG, Buck RH. Similar to those who are breastfed, infants fed a formula containing 2’-Fucosyllactose have lower inflammatory cytokines in a randomized controlled trial. J Nutr. 2016;146(12):2559-2566.

7. Reverri EJ, Devitt AA, Kajzer JA, Baggs GE, Borschel MW. Review of the clinical experiences of feeding infants formula containing the human milk oligosaccharide 2’-Fucosyllactose. Nutrients. 2018;10(10):1346.

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