Mother and son breast milk

Babies & Nursing

The Body Loves a Healthy Belly Microbiome


Beginning at birth, the microbes in our guts carry out essential tasks supporting our digestion and the metabolism of the food we eat, the development and activation of our immune systems, and the production of neurotransmitters that can affect our behavior and brain function1. There are millions of micro-organisms that live in and on us and work together with our own cells to support our health through our lives1. Their make up is as unique to you as your fingerprint and is known as your microbiome.

The First Years of Life

The first few years of life are important for establishing the microbiome. You are born with very few microbes, and these assemble and grow on and in your body through those first years of your life. Research has shown a number of factors affect the make-up of a baby’s microbiome both during birth and the first 1000 days of life; including how we give birth (vaginal or surgical), whether your baby has antibiotics and how we feed them. This isn’t the whole story though with more recent research suggesting an impact even from maternal stress1.

Three Essential Roles

Starting from birth, our gut microbiota has three essential roles: protective, metabolic, and trophic (feeding other systems)2. First, gut microorganisms serve as a barrier against infection. Secondly, they support the digestion and metabolism of our food, from breastmilk and infant nutrition products to weaning and varied adult diets, in addition to the breakdown of toxins and drugs. Trophic functions include the growth of the cells lining the intestines and supporting the balance of our immune systems. With complete colonization of the gut, which occurs by about the age of 33,4, immune homeostasis is achieved, which in healthy individuals, means the gut is populated by lots of different microorganisms and means we have good resistance to infections and antigens5. Inadequate colonization during this early period, however, may increase how susceptible we are to a variety of immune-related conditions5,6. In this way, the gut microbiome may be viewed as a middle man between environmental factors like diet and stress7, and later health and developmental outcomes8.

When it comes to immunity and our immune function, it isn’t all about our susceptibility to infection but also how our immune system behaves and therefore our risk of developing auto-immune conditions. This includes type 1 diabetes and coeliac disease in addition to allergies, asthma and obesity all being linked with potential disruptors to the development of the microbiome such as C-section deliveries, antibiotics and use of infant nutrition products,9-16.


The TEDDY study (The Environmental Determinants of Diabetes in the Young) study found an association between at least partial breastfeeding and having a higher abundance of Bifidobacterium breve and Bifidobacterium bifidum, two types of bacterial species with probiotic properties known to be prevalent early in life11. The researchers also found an association between vaginal delivery and having a greater abundance of bacteria belonging to the Bacteroides genus. Those who did have more Bacteroides at birth tended to have a greater diversity of microbes early in the first 40 months of life11. The gut microbiome of vaginally delivered infants also displays greater diversity, which is considered health protective1.

The trouble with all of this is that surgical births, antibiotics and infant nutrition products exist for a reason and are, in many cases, life-saving. So what steps can we take to restore the microbiome when these potential disruptors have occurred?

Early Steps to Restore the Microbiome

After surgical delivery, trying to get skin to skin contact where possible, supports immediate colonisation with the maternal skin microbiome1. Supporting breast rather than infant nutrition product feeding can also help, as breast fed infants have reduced colonization of E.coli and C. difficile bacteria17, which are associated with the development of allergies17. Where this isn’t possible, new research supports use of probiotics to help restore the microbiome development.Newer infant nutrition products fortified with prebiotic and probiotic compounds may help in this regard18.

Asthma and Allergies

Many of the studies linking the infant gut microbiota with atopic disease like asthma and allergies emphasize the first six months as a “critical window period,”19 suggesting that colonization of the gut microbiota during this period functions as an important determinant of future health status19. A randomized controlled trial reported that premature babies taking probiotics and prebiotics together, altered the composition of their gut microbiota and decreased their risk of developing atopic diseases20 as well as reducing episodes of fussing and crying21.

Probiotic Strains

While the literature on probiotics is promising, we don’t know the full story yet. Benefits are likely to be strain specific22 so we need to learn more about the best combinations of probiotic strains, the timing of giving them, and whether they work better with prebiotics (such as the oligosaccharide fiber found in breast milk).

Beyond thefirst few months of life,a high fiber diet rich in fruits, vegetables, beans and pulses, wholegrains, nuts and seedsis associated with a more diverse gut microbiome with potentially beneficial bacterial genomes. Lastly, antibiotics should be usedonly where neededacross the lifespan, but perhaps especially so during the first 1,000 days. In cases where antibiotic treatment is necessary, you might consider probiotic supplements as early evidence suggests this may lessen the negativeimpact of antibiotics on the infant gut microbiome23.

In summary, there are many factors that can support and indeed impede the microbiome development, which having an awareness of, allows us to focus on steps to support its restoration through improvements in diet, avoidance of unnecessary antibiotics and use of probiotics following exposure to antibiotics.



  1. Yang I, Corwin EJ, Brennan PA, Jordan S, Murphy JR, Dunlop A. The Infant Microbiome: Implications for Infant Health and Neurocognitive Development. Nurs Res. 2016;65(1):76-88.
  2. Guarner F, Malagelada J-R. Gut flora in health and disease. 2003;361:512–519.
  3. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Ley RE. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences. 2011;108:4578–4585.
  4. Weng M, Walker W. The role of gut microbiota in programming the immune phenotype. Journal of Developmental Origins of Health and Disease. 2013;4:203–214.
  5. Walker WA. Initial intestinal colonization in the human infant and immune homeostasis. Annals of Nutrition and Metabolism. 2013;63:8–15.
  6. Renz H, Brandtzaeg P, Hornef M. The impact of perinatal immune development on mucosal homeostasis and chronic inflammation. Nature Reviews Immunology. 2012;12:9–23.
  7. Sudo N. Microbiome, HPA axis and production of endocrine hormones in the gut. In: Lyte M, Cryan JF, editors. Microbial endocrinology: The microbiota-gut-brain axis in health and disease.New York, NY: Springer; 2014. pp. 177–194
  8. Grenham S, Clarke G, Cryan JF, Dinan TG. Brain-gut-microbe communication in health and disease. Frontiers in Physiology. 2011;2:94.
  9. Decker E, et al. Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children. Pediatrics. 2010;125:e1433–e1440
  10. Ege MJ, et al. Exposure to environmental microorganisms and childhood asthma. N Engl J Med. 2011;364:701–709.
  11. Tommi Vatanen, Eric A. Franzosa, Randall Schwager, Surya Tripathi, Timothy D. Arthur, Kendra Vehik, Åke Lernmark, William A. Hagopian, Marian J. Rewers, Jin-Xiong She, Jorma Toppari, Anette-G. Ziegler, Beena Akolkar, Jeffrey P. Krischer, Christopher J. Stewart, Nadim J. Ajami, Joseph F. Petrosino, Dirk Gevers, Harri Lähdesmäki, Hera Vlamakis, Curtis Huttenhower, Ramnik J. Xavier. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature, 2018; 562 (7728): 589 DOI: 1038/s41586-018-0620-2
  12. Algert CS, et al. Perinatal risk factors for early onset of type 1 diabetes in a 2000-2005 birth cohort. Diabet Med. 2009;26:1193–1197.
  13. Aumeunier A, et al. Systemic Toll-like receptor stimulation suppresses experimental allergic asthma and autoimmune diabetes in NOD mice. PLoS ONE. 2010;5:e11484.
  14. Huh SY, et al. Delivery by Caesarean section and risk of obesity in preschool age children: a prospective cohort study. Arch Dis Child. 2012;97:610–616.
  15. Ajslev TA, et al. Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics. Int J Obes (Lond) 2011;35:522–529
  16. Blustein J, et al. Association of caesarean delivery with child adiposity from age 6 weeks to 15 years. Int J Obes (Lond) 2013;37:900–906.
  17. Penders J, Thijs C, van den Brandt PA, Kummeling I, Snijders B, Stelma F, Stobberingh EE. Gut microbiota composition and development of atopic manifestations in infancy: The KOALA Birth Cohort Study. 2007;56:661–667.
  18. Guaraldi F, Salvatori G. Effect of breast and formula feeding on gut microbiota shaping in newborns. Front Cell Infect Microbiol. 2012;2:94.
  19. Penders J, Stobberingh EE, van den Brandt PA, Thijs C. The role of the intestinal microbiota in the development of atopic disorders. 2007;62:1223–1236.
  20. Luoto R, et al. Prebiotic and probiotic supplementation prevents rhinovirus infections in preterm infants: a randomized, placebo-controlled trial. J Allergy Clin Immunol. 2014;133:405–413.
  21. Partty A, et al. Effects of early prebiotic and probiotic supplementation on development of gut microbiota and fussing and crying in preterm infants: a randomized, double-blind, placebo-controlled trial. J Pediatr. 2013;163:1272–1277.
  22. Wallace TD, et al. Interactions of lactic acid bacteria with human intestinal epithelial cells: effects on cytokine production. J Food Prot. 2003;66:466–472.
  23. Johnston BC, Goldenberg JZ, Vandvik PO, Sun X, Guyatt GH. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Library. 2011