The browser you are using is too old for our website. Please visit from Chrome and you will be able to browse normally.


      The importance of your baby's gut health


      The importance of your baby's gut health

      Read time: 10 minutes

      Expert advice

      Get the support you need, the moment you need it

      Join now for free

      Nurturing your baby’s gut is one of the best things you can do for their future health. Aside from helping them get the most out of their food, it can influence many things long into the future – from their ability to fight off infections to their mental wellbeing. No wonder it’s sometimes referred to as ‘the second brain’.

      The gut is home to 70-80% of immune cells1.

      Tummy timeline

      From the moment of conception through to your baby’s second birthday is exactly 1,000 days. It’s also a critical time for establishing a healthy gut ‘microbiota’. Let’s explore how.


      Day 1


      By 20 weeks, your baby’s gut is fully formed2. It is highly debated as to whether you pass your bacteria to your baby in the womb. Although some evidence suggests it may be passed through the amniotic fluid3, it's largely believed that the womb is sterile (no bacteria present) and so bacteria isn't passed until birth. Whatever the way you share your bacteria with your baby, it's important to nurture your own gut microbiota, ready to pass to your baby. And one of the most important ways to do that is by eating a varied and Healthy Pregnancy Diet4.

      (Once your baby's born, the best way to support their digestive system is through breastfeeding. Read our guide to breastfeeding before your baby arrives to help yourself get off to a good start.)

      Day 280


      During vaginal birth your baby’s body is exposed to a whole range of beneficial bacteria as they pass through your birth canal.


      Your baby’s immune system is immature and needs to quickly learn how to fight off all the infectious agents they’re now exposed to. Their gut undergoes an intense period of growth and development5. In fact, a whole new ecosystem is created in their gut, known as the gut microbiota. It’s as unique as their fingerprint and made up of over 1,000 different types of bacteria, along with other microorganisms6. These bacteria support your baby's overall health, strengthening your baby's immune system7.    

      Day 283

      Breast milk

      Breast milk is tailor made especially for your baby, and helps to develop their gut. Breast milk is made up of many components, including elements which are very important in the development of the gut. For example, human milk oligosaccharides (HMOs), which feed the bacteria in the gut8. Other factors which help to develop the gut include lactose, nucleotides and fatty acids9. Breast milk also contains whole proteins, as well as a small amount of proteins broken down into small pieces. These broken down proteins are called peptides9.

      What you eat and drink can also affect your breastmilk, so eating a varied and healthy, balanced diet while you’re breastfeeding won’t just keep you healthy, but your baby too. Discover more about the benefits of breastfeeding. Or if you’re struggling, read our guide to breastfeeding success.

      As your baby continues to grow, so does the number and variety of bacteria in their gut.

      Day 462


      From 6 months, introducing solid foods and working towards a varied and balanced diet is another opportunity to increase and diversify your baby’s gut microbiota10, supporting their immune system and helping them fight infections and diseases for the rest of their life.

      Day 1,000 +


      By the age of around 3 years, your baby’s gut microbiota is fully developed11, although it can still change temporarily12. Going forward, having a balanced and varied diet will continue to maintain their gut health long into the future. Many foods naturally contain prebiotics (such as onions, bananas, tomatoes and many other fibre rich foods) which also help to maintain a healthy gut13.

      Day 1,000+

      As your child continues to grow, their gut microbiota can change for many reasons, such as diet, stress or taking a course of antibiotics. The best way to maintain a healthy gut is by eating a varied and healthy diet, getting plenty of sleep and avoiding stress14.

      1. Furness JB et al. Am J Physiol, 1999;277(5,Pt1):G922-8.

      2. Lebenthal E., Lee P. and Heitlinger, L. J Pediatr 1983; 102(1):1-9.

      3. Collado, M. et al. Sci Rep, 2016;6(1).

      4. Lozupone CA, et al. Nature,2012;489(7415):220-230.

      5. Xu, R. Reprod Fertil Dev, 1996;8(1):35.

      6. Lee KN, Lee OY. World J Gastroenterol 2014;20:886-8897

      7. Wopereis H. et al., Pediatr Allergy Immunol 2014;25:428-438

      8. Ayechu-Muruzabal, V et al. Front Pediatr, 2018;6:239

      9. Ballard O. and Morrow A. Pediatr Clin North Am. 2013;60(1):49-74)

      10. Scholtens P et al. Ann Rev Food Sci Technol. 2012;3:425–427.

      11. Koenig, J., et al. Pro Natl Acad Sci U.S.A, 2010;108(Suppl 1):4578-4585.

      12. Voreades N, Kozil A, Weir TL. Front Microbiol. 2014;5:494.

      13. Sousa V, Santos E, Sgarbieri V. Food Nutr Sci. 2011;2(2):133-144.

      14. Karl J, et al. Front Microbiol. 2018;9.

      Last reviewed: 13th August 2019

      Read Next:

      Your baby's future health begins here

      Your baby's future health begins here

      At Aptaclub, we believe that experience helps to build resilience; that each new encounter, whether in pregnancy or after birth, can shape your baby’s future development. With our scientific expertise and one-to-one round the clock support, we can help you and your baby embrace tomorrow.

      Join Aptaclub

      Questions about feeding and nutrition?

      Our midwives, nutritionists and feeding advisors are always on hand to talk about feeding your baby. So if you have a question, just get in touch.