The Role of Probiotics in Supporting Children’s Gut Health

Gut health has never been more in the spotlight. With a growing interest in how the community of bacteria in our gut, known as the gut microbiome, impacts health and well-being, there is an increasing focus on what this means for children. The early-life gut microbiome is known to play a significant role in shaping lifelong health, with the community of gut bacteria formed in the early years influencing everything from immune development to behaviour¹.

As a clinician working directly with children and their families, I understand that supporting children’s gut health is crucial. An area that is increasingly being questioned is the role of probiotics in digestive wellness and health. This article discusses why gut health matters, what influences gut microbiome development in children, and how probiotics can help nurture a healthy gut for life.

Children’s gut health – why does it matter?

When you think of gut health, most people immediately think of digestion; however, thanks to scientific research over the past twenty years, we now know that the gut plays a far more vital role in overall health. This is never truer than during childhood, where the early life microbiome is rapidly developing². Arguably, the first few years of life represent the most critical window for supporting gut health, as this is when the seeds for lifelong health and well-being are being laid.

The gut microbiome's impact on health

A vital community influences the broader factors affecting health – the gut microbiome. While invisible to us, the gut microbiome comprises a vast ecosystem of bacteria, viruses, and other microbes that, although small, can have a significant impact on health. Within the first three years of life, children accumulate a gut microbiome that will accompany them for life. A healthy gut from childhood and beyond is now well known to support¹⁴:

• Digestive wellness in children – not only helping to digest and absorb nutrients from food, but also helping to avoid common tummy troubles like constipation.

• Immune health – with over 70% of the body’s immune cells found in the gut, a healthy gut means a happy and well-functioning immune system. Research has shown that changes in the gut microbiome are associated with a range of immune-related conditions, including allergies and autoimmune conditions⁵⁶.

• Brain development, mood and behaviour – the gut and the brain are in regular conversation along a ‘phone line’ called the gut-brain axis. In the early years (especially the first three years), rapid brain development occurs simultaneously with booming gut development¹. Scientific studies have linked gut health with everything from emotional regulation and sleep quality to cognitive development and behaviour⁷⁸.

• Long-term health – early gut health, and the community of bacteria building during this time have been found to influence risk of conditions like diabetes, obesity and Alzheimer’s¹.

So, while thinking about a child’s gut health may not be at the top of your agenda as a professional or parent, children’s gut health is one of the most important factors to consider for both their current and future well-being, and something we can have a hand in supporting.

Factors that influence a healthy gut microbiome for children

A baby’s gut begins to colonise from the moment a child is born, and the early-life microbiome starts to develop from there. This community of gut bacteria rapidly populates and evolves, a process impacted by a wide range of variables – some we can control, and others we cannot. There are lots of ways to support children’s gut health, but here are some of the key ingredients we know can influence a healthy gut microbiome for children.

1. Breast milk – Breast milk is powerful fuel for a child’s gut microbiome. It contains helpful bacteria (probiotics) and prebiotics (specifically human milk oligosaccharides), which feed beneficial bacteria, shaping the early gut microbiome.

2. Dietary variety and balance – What food we offer our children can have a profound influence on their gut. Once babies begin solids and beyond, a diverse and balanced diet that includes a wide variety of fibre-rich plant foods, which will feed beneficial gut bacteria, is ideal. Think fruits, vegetables, beans, legumes, wholegrains, nuts and seeds (in age-appropriate forms). The greater the diversity, the better it is to build a robust and resilient community of bacteria⁹. Including fermented foods like yoghurt or kefir can also be a natural source of probiotics (more on these below).

3. Socialising with other children (and pets!) – Exposure to other children (yes, even with bugs!) and furry friends can naturally boost microbial diversity. For bonus points, playing outside has been shown to increase beneficial microbes too¹⁰.

4. Minimal use of certain medications – Whilst medications like antibiotics are sometimes a necessity, overuse, particularly in early life, can disrupt the balance of gut bacteria. Supporting recovery during and/or after a course of antibiotics, perhaps with a targeted bacterial (probiotic) strain for kids or probiotic-rich foods, can be a helpful step in restoring bacterial balance.

The role of probiotics in supporting children’s gut health

Probiotics, often referred to as ‘friendly’ or ‘beneficial’ bacteria, are more formally known as “live bacteria (or microorganisms) that, when consumed in adequate amounts, can provide health benefits to the host.” For children’s health, probiotics may help support digestive wellness, restore balance to the gut microbiome, and impact wider aspects of health, such as those mentioned above.

Probiotics are generally available in two forms: food and supplements. Below is a brief overview of both.

Food sources of probiotics

These are typically fermented foods, such as live yoghurt, kefir, and foods like kimchi. They naturally contain bacteria due to the process of fermentation, where microorganisms break down parts of the food, e.g. sugars, and produce bacteria in the process. These foods can be an easy way to include live bacteria (probiotics) into your child’s diet, but it’s worth being aware that some children may struggle with the palatability of some of these foods. From my experience, options like live yoghurt, aged cheese, and kefir are most easily incorporated into a child’s diet.

Scientific evidence has shown that these foods can contribute to a more diverse community of gut bacteria, support regular bowel habits, and may even enhance immunity (e.g., reduce risk of respiratory tract infections)¹¹¹².

Supplement sources of probiotics

These can come in various forms, including powders, drops, and even drinks. Typically, these contain specific strains (or species/types) of bacteria in measured doses (or amounts of bacteria). Not all kids’ probiotic supplements are made equal, and ideally, you want to choose a product that has:

• • Evidence that the bacteria reach the gut alive

  • A high ‘dose’ of bacteria (look for CFU, known as colony-forming units)

  • A strong science backing (e.g. the bacteria strain is shown to be of benefit)

Whilst probiotic supplements for kids are just one puzzle piece in supporting children’s gut health, research has shown they can be particularly helpful when there is a need for targeted support, e.g. after antibiotics or tummy bugs, during periods of tummy troubles (like colic, functional abdominal pain, or diarrhoea¹³), or when dietary intake of probiotic-rich foods or overall dietary variety is limited.

Key takeaways

As a professional or parent/caregiver, remember that one of the most effective tools for supporting a child’s gut health is their diet. Think about how you can nourish their evolving gut microbiome with dietary diversity, fibre-rich whole foods, and consider probiotics from fermented foods or suitable supplements. A well-rounded and balanced diet is a cornerstone of lifelong health and well-being, and it starts early!

References

1. Sarkar, A., Yoo, J. Y., Ozorio Dutra, S. V., Morgan, K. H., & Groer, M. (2021). The Association between Early-Life Gut Microbiota and Long-Term Health and Diseases. Journal of Clinical Medicine, 10(3), 459. https://doi.org/10.3390/jcm10030459

2. Arrieta, M., Stiemsma, L. T., Amenyogbe, N., Brown, E. M., & Finlay, B. (2014). The Intestinal Microbiome in Early Life: Health and Disease. Frontiers in Immunology, 5, 105813. https://doi.org/10.3389/fimmu.2014.0042

3. Laue, H. E., Coker, M. O., & Madan, J. C. (2022). The Developing Microbiome From Birth to 3 Years: The Gut-Brain Axis and Neurodevelopmental Outcomes. Frontiers in Pediatrics, 10, 815885. https://doi.org/10.3389/fped.2022.815885

4. Johnson, D. E., & Jones, R. B. (2025). Predicting child health with gut microbiome development trajectories. Nature Microbiology, 10(2), 265–266. https://doi.org/10.1038/s41564-024-01920-6

5. Hoskinson, C., Petersen, C., & Turvey, S. E. (2025). How the early life microbiome shapes immune programming in childhood asthma and allergies. Mucosal Immunology, 18(1), 26–35. https://doi.org/10.1016/j.mucimm.2024.12.005

6. Hoskinson, C., Dai, D. L., Del Bel, K. L., et al. (2023). Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease. Nature Communications, 14(1), 1–14. https://doi.org/10.1038/s41467-023-40336-4

7. Vaher, K., Bogaert, D., Richardson, H., & Boardman, J. P. (2022). Microbiome-gut-brain axis in brain development, cognition and behaviour during infancy and early childhood. Developmental Review, 66, 101038. https://doi.org/10.1016/j.dr.2022.101038

8. Fan, X., Zang, T., Liu, J., et al. (2023). Changes in the gut microbiome in the first two years of life predicted the temperament in toddlers. Journal of Affective Disorders, 333, 342–352. https://doi.org/10.1016/j.jad.2023.04.073

9. Heiman, M. L., & Greenway, F. L. (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism, 5(5), 317. https://doi.org/10.1016/j.molmet.2016.02.005

10. Zhang, M., Tang, H., Chen, Y., et al. (2023). Impact of environmental characteristics on children's gut microbiota – A pilot study in assessing the role of indoor microbiome and metabolites. Environmental Research, 234, 116114. https://doi.org/10.1016/j.envres.2023.116114

11. Leeuwendaal, N. K., Stanton, C., W., P., & Beresford, T. P. (2022). Fermented Foods, Health and the Gut Microbiome. Nutrients, 14(7), 1527. https://doi.org/10.3390/nu14071527

12. Wang, Y., Li, X., Ge, T., et al. (2016). Probiotics for prevention and treatment of respiratory tract infections in children: A systematic review and meta-analysis of randomized controlled trials. Medicine (Baltimore), 95(31), e4509. https://doi.org/10.1097/MD.0000000000004509

13. Szajewska, H., Berni Canani, R., Domellöf, M., et al. (2023). Probiotics for the management of pediatric gastrointestinal disorders: Position paper of the ESPGHAN Special Interest Group on Gut Microbiota and Modifications. Journal of Pediatric Gastroenterology and Nutrition, 76(2), 232–247. https://doi.org/10.1097/MPG.0000000000003633