Back-to-school season brings the usual mix of excitement and chaos: new shoes, packed lunches. And, almost inevitably, the first coughs, colds and sniffles of the school year... If you've ever wondered why your child seems to catch every bug going after returning to school, you're certainly not alone – but it's not just bad luck.
As our kids return to school, they move into a completely different environment where they are exposed to new microbes through shared classrooms, busy corridors, playgrounds and close contact with classmates.
This shift, which we at SMART STRAINS like to call the “classroom microbiome effect”, plays an important role in shaping how their immune system responds during the school term and helps explain why sniffles and infections tend to rise at this time of year.
What is the classroom microbiome?
On a typical school day, children spend about 40% of their waking hours in a classroom. But they're not just sharing that space with their classmates – they're also sharing it with millions of microscopic organisms.
Just like our gut and mouth, indoor environments also have a microbiome too(1). This is the intricate ecosystem of bacteria, fungi, viruses and other microorganisms that thrive in the places we live, work, and for our children, where they learn. More specifically, the classroom microbiome refers to the collection of microbes found within school environments, and is influenced by ventilation, exposure to natural light, construction materials, classroom density, cleaning routines, seasonality, and how much time children spend indoors versus outdoors (2). In that respect, every classroom develops its own shifting microbial fingerprint that evolves across the school term.
As scientists continue to explore indoor microbiomes, we're discovering that these environments may influence far more than we once thought – including children's immune health, respiratory health and even aspects of emotional wellbeing.
Why does this matter for your child's immune system?
Exposure to a wide variety of microbes is actually one of the ways the immune system learns.
On a positive note, exposure to a diversity of microbes helps train the immune system – you can think of it as an important part of the immune system’s ‘curriculum’. Without these early lessons, the immune system can overreact to harmless stimuli, which may increase the risk of allergies or conditions, such as asthma, hay fever, and eczema, later in life (3). This means that early microbial encounters children have from exposure to the classroom microbiome may shape their immune system responses throughout life.
This is particularly relevant when it comes to the respiratory infections children encounter at school and nursery. Exposure to a variety of microbes may help the immune system build and refine its responses, potentially supporting greater resilience when children encounter common respiratory illnesses like colds, flu and bronchitis (4). It doesn’t mean that microbial exposure will stop children from getting ill, but these everyday microbial encounters are part of the broader process through which the immune system develops and learns.
But not all microbial exposure is beneficial. In classrooms with poor ventilation or excess moisture, harmful microbes are more likely to build up. Damp or mouldy conditions have been linked to respiratory issues such as asthma and allergies (5). Busy indoor environments with limited airflow can also increase the spread of respiratory viruses, as microbes pass more easily between children through shared air and close contact.
This does more than just raise the risk of illness. It increases what we can think of as the overall immune workload, with the body needing to respond more frequently and adapt to a higher volume of exposures. In the first few weeks of term in particular, this adjustment period can feel more intense as the immune system recalibrates to new routines, environments, and social interactions. It's no surprise, then, that the first few weeks of term often feel like an endless cycle of sniffles.
Beyond immune health, there is also growing interest in how the classroom environment may influence children’s mental wellbeing (6). This is partly linked to the gut brain axis, the communication pathway between the gut microbiome and the brain, which plays a role in mood and behaviour.
Children who spend most of their time in indoor, urban environments may be exposed to a narrower range of microbes, which could influence gut microbiome diversity (6). While research here is still emerging, this suggests that the classroom environment may play a role not just in immune health, but also in supporting overall mental wellbeing during school years.
How can you support your child’s immune health this back-to-school season?
While you can't control the classroom environment, there are plenty of simple ways to support your child's immune system throughout the school year.
Eat the rainbow
One of the most effective ways to do this is through diet. Eating the rainbow is a helpful way to think about it. Different coloured fruits, vegetables, legumes, nuts, and whole grains feed the beneficial bacteria in the gut, helping them produce compounds like short-chain fatty acids (SCFAs) that support immune balance. You do not need perfection here, just variety across the week. The more diverse the diet, the more diverse the gut microbiome tends to be.
Get plenty of ZZZs
Sleep is one of the most important foundations of immune health in children. It is during sleep that much of the body’s immune regulation and repair takes place. A consistent bedtime routine during term time can make a noticeable difference, especially in the early weeks back at school.
Stay active
Regular movement also plays an important role in supporting immune function. It helps keep the immune system responsive and well regulated. It doesn’t need to be an organised sport. Walking to school, playground time, cycling, or simply being active throughout the day all contribute. The key is consistency rather than intensity.
Reduce stress
Stress is another factor that is often overlooked. New routines, social pressures, and busy mornings can all affect how children feel and how their bodies respond. Predictable routines, calm mornings, and some downtime after school can help support overall resilience during term time.
Stay up to date with immunisations
Staying up to date with immunisations remains one of the most effective ways to protect against serious infectious diseases. It is an important part of keeping children safe during the high contact school months when infections tend to circulate more easily.
Outdoor time
Time outdoors is another simple but powerful support. It encourages movement, reduces time spent in crowded indoor air, and gives children a broader environmental experience (7). Even short daily periods outdoors before or after school can help balance the more intense indoor exposure that comes with classrooms.
Consider a live bacterial supplement
During periods like the back-to-school transition, a high-quality live bacterial supplement can offer an extra layer of immune support (8). A review publication of 23 studies from the Cochrane Library (9) found that live bacterial supplements:
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Likely reduce the recurrence of upper respiratory tract infections (URTIs) by 41%
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May shorten the duration of URTIs by more than a day
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Likely reduce the need for antibiotics by 42%
Clinically studied strains such as Lactobacillus rhamnosus LGG® and Bifidobacterium lactis BB-12® have been shown to reduce both the number and severity of respiratory infections in children and adults (10-11). Remember, not all probiotics are created equal. Look for products containing the right strain, at the right dose, supported by strong clinical evidence.
Takeaway
The return to school doesn't just mean new teachers, new classrooms and new routines. It also marks a significant shift in the microbes your child encounters every day.
While those extra exposures can temporarily increase your child's immune workload, they're also helping educate and strengthen their immune system over time. The goal isn't to avoid every germ, instead, it's about giving your child's immune system the support it needs to respond well.
A varied, plant-rich diet, good sleep, regular movement, time outdoors and managing stress all help lay the foundations for a healthy gut microbiome and resilient immune system. And during periods of increased exposure, such as the back-to-school transition, targeted live bacterial supplements containing clinically studied strains may provide additional support.
References
1. Ben Maamar, S., Hu, J. and Hartmann, E.M. (2020) ‘Implications of indoor microbial ecology and evolution on antibiotic resistance’, Journal of Exposure Science & Environmental Epidemiology, 30, pp. 1–15. doi:10.1038/s41370-019-0171-0.
2. Ramos, T., Dedesko, S., Siegel, J.A., Gilbert, J.A. and Stephens, B. (2015) ‘Spatial and temporal variations in indoor environmental conditions, human occupancy, and operational characteristics in a new hospital building’, PLoS One, 10(3), e0118207.
3. Okada, H., Kuhn, C., Feillet, H. and Bach, J.-F. (2010) ‘The hygiene hypothesis for autoimmune and allergic diseases: an update’, Clinical and Experimental Immunology, 160(1), pp. 1–9. doi:10.1111/j.1365-2249.2010.04139.x.
4. Bloomfield, S.F., Stanwell-Smith, R., Crevel, R.W. and Pickup, J. (2006) ‘Too clean, or not too clean: the hygiene hypothesis and home hygiene’, Clinical & Experimental Allergy, 36(4), pp. 402–425. doi:10.1111/j.1365-2222.2006.02463.x.
5. Holden, K.A., Lee, A.R., Hawcutt, D.B. and Sinha, I.P. (2023) ‘The impact of poor housing and indoor air quality on respiratory health in children’, Breathe, 19(2), 230058. doi:10.1183/20734735.0058-2023.
6. Hoare, E., Jacka, F. and Berk, M. (2019) ‘The impact of urbanization on mood disorders: an update of recent evidence’, Current Opinion in Psychiatry, 32(3), pp. 198–203. doi:10.1097/YCO.0000000000000487.
7. Marja I. Roslund et al., Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children.Sci. Adv.6,eaba2578(2020).DOI:10.1126/sciadv.aba2578
8. Wang, X., Li, Y., Zhang, Z. et al. (2021) 'Probiotics Regulate Gut Microbiota: An Effective Method to Improve Immunity' Molecules, 26, p.6076.
9. Zhao, X., et al. (2022). Cochrane Database of Systematic Reviews, Issue 8, Art. No. CD006895. Probiotics for preventing acute upper respiratory tract infections - PubMed
10. Rautava, S., et al. (2009) ‘Probiotics and the immune system’, British Journal of Nutrition, 101, pp. 1722–1726.
11. Smith, T.J., et al. (2013) ‘Effects of probiotics on immune function’, British Journal of Nutrition, 109, pp. 1999–2007.
Written by Rachel Redman - Registered Dietitian
Reviewed by Nichola Ludlam-Raine, Specialist Registered Dietitian
