Baby sat and looking at his belly

The gut microbiome is the name given to the trillions of microbes1 and their genetic material living in our gastrointestinal tract2. This population includes both commensal (good) and pathogenic (bad) bacteria, viruses, protozoa, and fungi.


The gut microbiome is connected to many aspects of health including digestion and metabolism4. It is also essential for the development of a healthy immune system4. The gut microbiome works with the immune cells that live in the gut, supporting appropriate immune response4,5.


Babies are born with an immature immune system, so they need a balanced gut microbiome for their immune function and development3. A suboptimal gut microbiome is associated with higher risk of asthma, allergies and obesity in later life4-6. Early life provides a unique opportunity to support the development of a healthy gut microbiome in order to promote long-term health.


The infant’s gut microbiome rapidly develops during and post-birth through vaginal, faecal and skin exposure6. Breastfeeding is crucial for the development of the gut microbiome as breast milk contains many microbes that colonise the baby’s gut3-4,6. Breast milk also contains unique prebiotics called Human Milk Oligosaccharides that promote the growth of good bacteria and help fight off bad bacteria6. Some factors negatively influence the development of the gut microbiome, including: Caesarean delivery, gestational age of the infant, unnecessary antibiotic use and exclusive formula feeding3,6.

Recommendations to promote the development of a healthy gut microbiome
  • Exclusive breastfeeding for the first 6 months of life with the introduction of appropriate, diverse complementary foods, alongside continued breastfeeding3,6.
  • Human Milk Oligosaccharides (HMOs): If formula is being used, clinically tested infant formula milk supplemented with prebiotics such as HMOs7-8.
  • Avoidance of unnecessary antibiotics use in early life

Explore our CPD accredited webinar on Early life and gut health: A webinar with Dr Caroline Childs, view on demand

This article was written by Nutritionist and PhD Candidate, Maude Grant (Nutrition & Scientific Affairs Manager for SMA Nutrition).

References Show all Hide all
  1. Sender et al. PLoS Biol 14(8):2016

  2. Swanson et al. Nat Rev Gastroenterol Hepatol. 17(11) 2020

  3. Moore & Townsend et al. Open Biol. 9:2019

  4. Turroni et al. Italian Journal of Pediatrics 46(16)2020

  5. Vighi, G et al. Clinical and Experimental Immunology 153:2008

  6. Muller et al. Trends Mol Med 21(2):2015

  7. Puccio et al. JPGN (64) 624–631 2017

  8. Berger et al., mBio 2020.

IMPORTANT NOTICE: Breast milk is best for babies and breastfeeding should continue for as long as possible. Infant formula milks should only be used on the advice of a doctor, midwife, health visitor, public health nurse, dietitian or pharmacist, or other professionals responsible for maternal and childcare.