Babies, microbes and health

Gut microbes can affect the health of babies in amazing ways

When a baby is born, doctors measure their height and weight, and within the next 1-2 days several tests are made to confirm the baby’s health. In recent years, a whole new aspect of a baby’s health is being studied: gut microbes.

Gut Microbiota at the start of life

maternal baby gut microbiota

The gut microbiota is composed of trillions of bacteria, viruses and fungi. These microbes influence multiple aspects of our body health, including metabolism, immune defence and brain function. Imbalances in the composition of gut microbes, called dysbiosis, have been linked to multiple diseases, including diabetes, obesity, allergies, cancer, chronic liver diseases and neurological disorders. Hence, it’s important to maintain a healthy gut microbiota.  The process of forming your gut microbiota starts very early in life. According to some studies, even before we are born, we are exposed to the bacteria found inside our mother. However, research in this arena is still ongoing and there is some debate about the idea that bacteria found in the stools of newborn babies actually come from the mother, with some studies suggesting it may be due to contamination1-3.

The first, well established, exposure of infants to microbes occurs right at the time of birth. When travelling through the birth canal, babies encounter multiple species of microbes living in the vaginal canal as well as from the intestinal tract and skin of their mum2, 13. These bacteria colonize the baby’s body and represent the first dosage of bacteria reaching the gut.

As the baby grows, further dosages of bacteria come from breast milk and after about two years, a fully functional gut microbiota is established, with billions of microorganisms living in the colon. The makeup of an infant’s gut microbiota can be influenced by many factors, including:

  • Diet – The gut microbiota is differently affected by the baby’s type of feeding, i.e. whether babies are fed breastmilk, formula or weaned to solids4-5.
  • Antibiotic exposure – treating newborn babies with antibiotics can deplete good bacteria and prevent the formation of a healthy gut microbiota6-8.
  • Mum’s health and lifestyle choices – while still in the womb, a foetus is susceptible to mum’s health and lifestyle choices.
    • Certain infections, antibiotic use, or even diet can influence the future microbiome of the baby9-12One study, for example, found that babies born from an obese mother had an altered gut microbiome, which may increase the child’s risk of becoming obese and developing liver disease13.
    • Stress9, infections10, smoking11, and other environmental factors11 can all negatively impact the baby’s capacity of forming a healthy gut microbiota.
  • Type of birth – babies born through caesarean section do not get exposed to the same microbes as babies born through natural birth14,16.
    • A recent study, for example, found that children born through C-section experienced a delay in the build-up of a normal gut microbiota, and had higher levels of potentially harmful gut bacteria and a higher likelihood of developing respiratory infections.

Among these factors one of the most important is the type of birth.

C-section changes the baby gut microbiota

Around 30 million babies are born through C-section every year around the world, according to a 2018 report from The Lancet based on 169 countries15. In recent years, several studies have compared the gut microbiome of babies born through caesarean section (C-section) with those born through the traditional vaginal delivery. Some key findings of these studies include:


  • Babies born through natural birth have a distinct microbiota, characterised by bacteria coming from their mother’s birth canal. Common bacteria found in these babies include LactobacillusPrevotellaBifidobacterium and Bacteroides2, 14.
  • In contrast, babies born from C-section are exposed to a different set of bacteria, mostly those present on the skin of the mother of hospital staff, and to bacteria found in their environment, such as StaphylococcusPropionibacterium or Clostridium16.
baby microbiota

What about health?

A major question in the mind of parents and scientists alike is whether any of these studies say something about the health of babies. The short answer is: probably yes. Several studies have established links between infant gut microbiota, disease and factors like type of birth or early life feeding (breastmilk vs formula). Other factors studied include:

  • Use of antibiotics – Multiple studies have established links between antibiotic use, their effect on the baby gut microbiome and the development of asthma, eczema, obesity and IBD development17-20.
  • Probiotics/prebiotics – Studies have shown that prebiotic supplementation can influence different health outcomes. Two studies, for example, found that infants fed formula milk enriched with prebiotics was associated with a reduction in the incidence of atopic dermatitis, wheezing and urticaria21-22. Further research is reviewed here.
  • Hygiene – One study found that infants whose parents “cleaned” their pacifier by sucking on it were less likely to develop allergic conditions like asthma and eczema23.


Further factors that have been shown to affect the infant gut microbiota and have health consequences include dietetic supplements, exposure to pets and other environmental factors. A good review of current evidence is found here. All in all, the evidence strongly suggest that the gut microbiota has an important role in the health of newborn babies.

If you are expecting a baby or are just planning, consulting with our health team is the first step to design a path that will take you and your baby to optimal health.


  1. Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nature medicine. 2016 Jul;22(7):713. Read it!
  2. Nuriel-Ohayon M, Neuman H, Koren O. Microbial changes during pregnancy, birth, and infancy. Frontiers in microbiology. 2016 Jul 14;7:1031. Read it!
  3. Younge N, McCann JR, Ballard J, Plunkett C, Akhtar S, Araújo-Pérez F, Murtha A, Brandon D, Seed PC. Fetal exposure to the maternal microbiota in humans and mice. JCI insight. 2019 Oct 3;4(19). Read it!
  4. Yoshioka H, Iseki KI, Fujita K. Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants. Pediatrics. 1983 Sep 1;72(3):317-21. Read it!
  5. Savage JH, Lee-Sarwar KA, Sordillo JE, Lange NE, Zhou Y, O’Connor GT, Sandel M, Bacharier LB, Zeiger R, Sodergren E, Weinstock GM. Diet during pregnancy and infancy and the infant intestinal microbiome. The Journal of pediatrics. 2018 Dec 1;203:47-54. Read it!
  6. Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, Dantas G. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nature microbiology. 2016 Apr;1(4):16024. Read it!
  7. Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, Clara G, Ventura M, Margolles A, Gueimonde M. Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics. The Journal of pediatrics. 2015 Mar 1;166(3):538-44. Read it!
  8. Meyer K, Aagaard K. Microbiome: Antibiotics and the infant microflora. Nature microbiology. 2016 Apr;1(4):16040. Read it!
  9. Zijlmans MA, Korpela K, Riksen-Walraven JM, de Vos WM, de Weerth C. Maternal prenatal stress is associated with the infant intestinal microbiota. Psychoneuroendocrinology. 2015 Mar 1;53:233-45. Read it!
  10. Mueller NT, Whyatt R, Hoepner L, Oberfield S, Dominguez-Bello MG, Widen EM, Hassoun A, Perera F, Rundle A. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. International journal of obesity. 2015 Apr;39(4):665. Read it!
  11. Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE, Kim H, Zoratti EM, Lukacs NW, Boushey HA, Ownby DR. Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity. Scientific reports. 2016 Aug 25;6:31775. Read it!
  12. Tang M. Alteration of Microbiome in Colostrum and Infant Health Risks from Exposure to HCHs in Mother-Infant Pairs. InISEE Conference Abstracts 2018 Aug 30 (Vol. 2018, No. 1). Read it!
  13. Soderborg TK, Clark SE, Mulligan CE, Janssen RC, Babcock L, Ir D, Young B, Krebs N, Lemas DJ, Johnson LK, Weir T. The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD. Nature communications. 2018 Oct 26;9(1):1-2. Read it!
  14. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. 2010. Proceedings of the National Academy of Sciences, 107(26), pp.11971-11975. Read it!
  15. Boerma T, Ronsmans C, Melesse DY, Barros AJ, Barros FC, Juan L, Moller AB, Say L, Hosseinpoor AR, Yi M, Neto DD. Global epidemiology of use of and disparities in caesarean sections. The Lancet. 2018 Oct 13;392(10155):1341-8. Read it!
  16. High rate of transfer of Staphylococcus aureus from parental skin to infant gut flora. 2004. Journal of clinical microbiology, 42(2), pp.530-534. Read it!
  17. Kronman MP, Zaoutis TE, Haynes K, Feng R, Coffin SE. Antibiotic exposure and IBD development among children: a population-based cohort study. Pediatrics. 2012 Oct 1;130(4):e794-803. Read it!
  18. Risnes KR, Belanger K, Murk W, Bracken MB. Antibiotic exposure by 6 months and asthma and allergy at 6 years: findings in a cohort of 1,401 US children. American journal of epidemiology. 2010 Dec 29;173(3):310-8. Read it!
  19. Hoskin‐Parr L, Teyhan A, Blocker A, Henderson AJ. Antibiotic exposure in the first two years of life and development of asthma and other allergic diseases by 7.5 yr: A dose‐dependent relationship. Pediatric Allergy and Immunology. 2013 Dec;24(8):762-71. Read it!
  20. Saari A, Virta LJ, Sankilampi U, Dunkel L, Saxen H. Antibiotic exposure in infancy and risk of being overweight in the first 24 months of life. Pediatrics. 2015 Apr 1;135(4):617-26. Read it!
  21. Moro G, Arslanoglu S, Stahl B, Jelinek J, Wahn U, Boehm G. A mixture of prebiotic oligosaccharides reduces the incidence of atopic dermatitis during the first six months of age. Archives of disease in childhood. 2006 Oct 1;91(10):814-9. Read it!
  22. Ivakhnenko OS, Nyankovskyy SL. Effect of the specific infant formula mixture of oligosaccharides on local immunity and development of allergic and infectious disease in young children: randomized study. Pediatria Polska. 2013 Sep 1;88(5):398-404. Read it!
  23. Hesselmar B, Sjöberg F, Saalman R, Åberg N, Adlerberth I, Wold AE. Pacifier cleaning practices and risk of allergy development. Pediatrics. 2013 Jun 1;131(6):e1829-37. Read it!