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What is the gut microbiome?

5 mins
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.

What does the gut microbiome do?

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.

The baby gut microbiome

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.

Early development of the gut microbiome

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).

  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.


We believe that breastfeeding is the ideal nutritional start for babies and we fully support the World Health Organization’s recommendation of exclusive breastfeeding for the first six months of life followed by the introduction of adequate nutritious complementary foods along with continued breastfeeding up to two years of age. We also recognise that breastfeeding is not always an option for parents. We recommend that healthcare professionals inform parents about the advantages of breastfeeding. If parents choose not to breastfeed, healthcare professionals should inform parents that such a decision can be difficult to reverse and that the introduction of partial bottle-feeding will reduce the supply of breast milk. Parents should consider the social and financial implications of the use of infant formula. As babies grow at different rates, healthcare professionals should advise on the appropriate time for a baby to begin eating complementary foods. Infant formula and complementary foods should always be prepared, used and stored as instructed on the label in order to avoid risks to a baby’s health. The product should be used only on the advice of independent persons having qualifications in medicine, nutrition, pharmacy, or other professionals responsible for maternal and child care.