Tiny Helpers in Tummies: Why the Microbiome Matters for Kids

This is a guest blog post by Children’s Nutritionist, Hannah Daw

Abstract artistic depiction of beneficial gut bacteria for children.

What is the gut microbiome?

Our gut microbiome is a vast community of tiny microorganisms living in our digestive system, along with their DNA and the molecules they produce (1).

Far from being unwanted guests, these microbes help us digest food, make vitamins, support our immune system, and even influence mood and energy (2). But when this community becomes unbalanced through a loss of beneficial bacteria, an overgrowth of ‘bad’ ones, or reduced diversity, it can’t do its job properly (3).

Think of the microbiome like an orchestra. Most microbes play in harmony, creating a beautiful sound. But if the “bad” ones get too loud, the music turns messy and our health can be affected.

The developing microbiome

From the very start of life, a child’s microbiome begins to take shape. Some factors, such as genetics or birth method, are beyond our control. Others, like nutrition and environment, help shape it in powerful ways (4).

The first 1,000 days of life are especially important. These early years lay the foundations for the core microbiome that continues to evolve as your child grows (5).

The role of the microbiome

So why all the fuss? This busy community plays a huge role in your child’s health, both now and later in life. The microbiome:

  • Supports immune system development

  • Trains immune cells to recognise friend from foe

  • Strengthens the gut barrier to stop harmful bacteria sneaking in (6)

But that’s not all. Microbes also:

  • Produce important nutrients, including vitamins

  • Break down fibre into beneficial compounds

  • Influence mood and behaviour by affecting neurotransmitters — the brain’s chemical messengers (7)

What’s new in research?

The microbiome is still a relatively young field of science and researchers continue to uncover exciting connections.

A major UK study from UCL this summer looked at the microbiomes of thousands of babies. Researchers found three distinct microbiota clusters, two of which were linked with an increased risk of hospitalisation from viral lower respiratory infections (8).

It’s important to note that this shows a link, not a cause. More research is needed to fully understand the relationship.

Other emerging areas of study include how microbes may influence:

  • Children’s responses to vaccines

  • The risk of allergies and asthma (9)

This is very much a “watch this space” area of science.

Happy child eating a healthy breakfast with fruit and cereal high in fibre to support a healthy gut microbiome.

Supporting your child’s microbiome

While there’s still much to learn, we already know some simple ways to help children nurture a healthy gut.

Probiotics (live bacteria)
Fermented foods like natural yoghurt and kefir contain probiotics. While they don’t permanently change your child’s microbiome, they offer benefits as they pass through the gut.

  • Start small and build gradually based on your child’s tolerance

  • Watch out for fermented foods high in salt, as children’s kidneys aren’t ready for too much

  • Offer a variety—different foods contain different probiotic strains (10)

Prebiotics (the food for microbes)
Prebiotics are fibre-rich foods that feed the “good” bacteria. These include fruits, vegetables, pulses and wholegrains.

Smiling toddler drinking kefir.

Practical tips to try

  • Encourage a rainbow of plants – add small amounts to familiar meals for fussy eaters

  • Offer wholegrains, pulses, nuts and seeds – try 50:50 swaps (white/brown bread, rice) or add beans to soups and sauces

  • Keep variety going – reintroduce new foods regularly, without pressure

  • Get children involved in food prep – this boosts acceptance

  • Encourage outdoor play and nature time – this supports microbial diversity too

Children playing outdoors in nature to support healthy microbiome development.

Summary

Your child’s gut microbiome is a fascinating, hard-working community that supports everything from digestion and immunity to mood and development.

While the science continues to evolve, one thing is clear: early nutrition and exposure to a wide range of foods and environments help build a healthy foundation (11). By offering fibre-rich plant foods, fermented options, and plenty of outdoor play, you’ll be giving your child’s tiny allies the best chance to thrive.

 

References

Salvadori, M., & Rosso, G. (2024). Update on the gut microbiome in health and diseases. World Journal of Methodology, 14(1). https://doi.org/10.5662/wjm.v14.i1.89196

  1. Clapp, M., Aurora, N., Herrera, L., Bhatia, M., Wilen, E., & Wakefield, S. (2017). Gut microbiota’s effect on mental health: The Gut-Brain axis. Clinics and Practice, 7(4), 987. https://doi.org/10.4081/cp.2017.987

  2. Hrncir, T. (2022). Gut Microbiota Dysbiosis: Triggers, Consequences, Diagnostic and Therapeutic Options. Microorganisms, 10(3), 578. https://doi.org/10.3390/microorganisms10030578

  3. Gaufin, T., Tobin, N. H., & Aldrovandi, G. M. (2018). The importance of the microbiome in pediatrics and pediatric infectious diseases. Current Opinion in Pediatrics, 30(1), 117–124. https://doi.org/10.1097/mop.0000000000000576

  4. Monk 2023

  5. Yoo, J., Groer, M., Dutra, S., Sarkar, A., & McSkimming, D. (2020). Gut Microbiota and Immune System Interactions. Microorganisms, 8(10), 1587. https://doi.org/10.3390/microorganisms8101587

  6. Chaudhry, T. S., Senapati, S. G., Gadam, S., Mannam, H. P. S. S., Voruganti, H. V., Abbasi, Z., Abhinav, T., Challa, A. B., Pallipamu, N., Bheemisetty, N., & Arunachalam, S. P. (2023). The impact of microbiota on the Gut–Brain axis: Examining the complex interplay and implications. Journal of Clinical Medicine, 12(16), 5231. https://doi.org/10.3390/jcm12165231

  7. Garcia-Mauriño, C., Shao, Y., Miltz, A., Lawley, T. D., Rodger, A., & Field, N. (2025). Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics. The Lancet Microbe, 101072–101072. https://doi.org/10.1016/j.lanmic.2024.101072

  8. Ardura-Garcia, C., Curtis, N., & Zimmermann, P. (2024). Systematic review of the impact of intestinal microbiota on vaccine responses. Npj Vaccines, 9(1). https://doi.org/10.1038/s41541-024-01000-0

  9. Park, I., & Mannaa, M. (2025). Fermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes. Foods, 14(13), 2292. https://doi.org/10.3390/foods14132292

  10. Pieri, M., Nicolaidou, V., & Christos Papaneophytou. (2023). Special Issue: The Impact of Early Life Nutrition on Gut Maturation and Later Life Gut Health. Nutrients, 15(6), 1498–1498. https://doi.org/10.3390/nu15061498

  11. Conlon, M., & Bird, A. (2014). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7(1), 17–44. https://doi.org/10.3390/nu7010017

  12. Pantazi, A. C., Balasa, A. L., Mihai, C. M., Chisnoiu, T., Lupu, V. V., Kassim, M. A. K., Mihai, L., Frecus, C. E., Chirila, S. I., Lupu, A., Andrusca, A., Ionescu, C., Cuzic, V., & Cambrea, S. C. (2023). Development of Gut Microbiota in the First 1000 Days after Birth and Potential Interventions. Nutrients, 15(16), 3647. https://doi.org/10.3390/nu15163647

 

About the author of this blog

Hannah is a Registered Associate Nutritionist and Mum to Lucas, who had feeding difficulties and was eventually diagnosed with a paediatric feeding disorder (PFD).

Hannah has a MSc in Eating Disorders and Clinical Nutrition and supports other families with children with PFD.

She has her own practice supporting children and their families with all aspects of nutrition from fussy eating to plant based diets.

For more information about Hannah, you can visit her website www.thechildrensnutritionconsultant.com

Jo Lenz