Your Child’s Microbiome: Dr Kate's Complete Guide

Dr Kate Stephens PhD Food and Microbial Sciences; Gut Microbiology (University of Reading), BSc Medical Microbiology

It's never too late to start learning about your child's gut health. Make sure they get the best start in life, from birth to secondary school, by understanding how nurturing their gut microbiome can help optimise their overall health.

Meet the gut microbiome

Our gut is home to trillions of microbes. They are essential in many aspects of our health including: digestion, immunity, energy and skin. That's why many scientists are now realising that health begins in the gut.

All of these microbes make up our microbiome – a microscopic ecosystem that lives inside us. Like any living ecosystem, the most important thing is balance. Getting this balance right and looking after your child’s gut could really benefit them as they continue to grow. And the sooner you start, the better! The early years of life are especially important for your child's gut microbiome. Here's some key facts for any beginners to the world of the growing microbiome:

Child Microbiome

Birthing mode

The way a baby is delivered can have a real impact on their health in the future. This is because different modes of birth affect your child's gut health and development. Let's take a look at how...

When a baby is born through the vaginal canal, they engulf a huge variety of bacteria in the vaginal tract. This includes lots of good bacteria. Caesarean-born babies, however, are exposed to a much smaller number of microbes. The main types of bacteria that they do come into contact with are mainly associated with the hospital environment, along with those on the skin of the doctor or midwife.

C-section births are becoming increasingly common worldwide. In Europe alone, C-section rates have increased 14% from 1990 to 20141. As Caesarean births do not deliver the diversity of microbes that vaginally-born children usually receive, research has now shown that children born via C-section are at higher risks of food allergiesasthma and obesity2-4.

As well as the process of birth, emerging research also tells us that the health of the mother during pregnancy impacts the baby’s microbiome. Expectant mothers should consider eating well, keeping stress levels as low as possible and looking after their gut and vaginal health. If antibiotics are required, then this can also deplete the microbes that are passed on to the baby. Consider topping up with a probiotic supplement that is suitable during pregnancy and alongside antibiotics, to help restore your own microbial balance.

Smiling Baby
The early years are vital for gut microbiome development


The first 18 months of life are considered crucial to the development of the microbiome. As well as breastfeeding and weaning, a baby’s environment in particular can play a huge role in the types of microbes living in their guts.

As your baby changes and grows, new challenges (and new bacteria) await. This includes when your little one become mobile. In fact, just the crawling action helps to build your child’s immune system. During early years, the immune system starts to mature as it learns how to distinguish between friend and foe. Exposure to new bacteria is crucial for immune development, so a healthy home doesn't necessarily have to be a clean one!

Here's the science: a study in 2017 showed that crawling resulted in the creation of ‘clouds of microbes’. These clouds introduced the infant to a variety of microbes and dust particles5. These results suggest the exposure to new microbes provided a challenge to the infants’ immune systems, and aided the process of early immune development.

And that's not all - another study on 467 children showed that exposure to household germs, dusts and pet allergens during the first year of life also reduced the risk of asthma and allergies6. Babies come into contact with lots of bacteria when they start to crawl. So, don’t worry too much if you forget to hoover this week, because a little exposure can be a good thing.

Colic has also been associated with an imbalance in the microbiome, as certain nasty bugs may be contributors to this condition. If your child is suffering, it might be worth looking into supplementing their friendly bacteria, to help rebalance the microbiome (and hopefully give you a bit more sleep!).


We've all heard of the terrible twos! For toddlers, the microbiome and immune system are still learning and developing, so there's lots of experiences that continue to challenge their guts.

Nursery is one example that can throw a child’s microbiome into flux. This is a whole new world of other children and their microbes. Nurseries can be a breeding ground for harmful bacteria, with nearly two thirds of children under 4 visiting their GP annually due to a cough7.

Whilst it’s likely that your child will get ill during the nursery years, you may be able to reduce the risk, severity and duration of illness by looking after their microbiome. Remember: a healthy gut microbiome is key for good immunity.

Exposure to pets in early life can help build immunity later on

As toddlers get older, they also start having more interactions with animals and foreign environments. Worried about germs from pets? Actually, one study investigated 474 children over a seven-year period, and found that children exposed to a pet in the first few years of life experienced a protective effect against eczema and allergies throughout childhood8. Talk about man’s best friend! Another study even showed having a dog during pregnancy could reduce the risk of eczema9.

There is also some evidence that living on a farm may reduce the risk of allergy development in childhood, extending into adulthood10. However, it should be noted that the evidence on animal interaction and gut health is still emerging and there are some inconsistencies.

Another interesting area that the gut microbiome can play a role in is toddler’s behaviour. A study in 2015 demonstrated that toddlers who were more engaged, happy and interactive had a wider diversity of microbes in the gut11. This shows that a healthy gut microbiome is positively associated with mood. This connection is known as the gut-brain axis (and it's a favourite of mine).


At approximately aged 3, the development of the microbiome tends to stabilise. However, it can still be influenced by numerous lifestyle factors.

When the microbiome becomes unbalanced - meaning there is a reduced number of good bacteria - we can often see side effects. This imbalance is known as dysbiosis. If your child is suffering from any of the below symptoms it might be worth considering if it's down to poor gut health, and speaking to a doctor if symptoms persist:

  • Diarrhoea
  • Constipation
  • Low energy/fatigue & poor concentration
  • Low mood
  • Constant colds & flu
  • Bloating
  • Eczema & allergies
Dysbiosis can be responsible for a number of health concerns in children, including colds and flu

Causes for gut dysbiosis in kids


Stress can impact the gut microbiome and can also result in inflammation in the body if experienced on a long-term basis. There are a lot more reasons these days why children might feel stressed. They are under more pressure to perform at school and many do lots of extra-curricular activities on top of homework and school tests. There are also more social pressures to navigate today.

Encourage your child to take a break occasionally, to go outside and play or read a book. Find ways to manage their stress, even if it’s something as simple as a day out with the family or a cuddle with mum or dad.


Antibiotics are the most commonly prescribed medication given to children12. Unfortunately, they can be extremely damaging to the gut microbiome. Antibiotics are not always selective and instead of targeting the bug causing the infection, they wipe all the good and bad gut bacteria entirely! This can cause dysbiosis, which explains why your child might develop diarrhoea or thrush from their course of antibiotics.

Repeat prescriptions of antibiotics can be especially damaging to the microbiome and can result in health problems in later life. If your child needs antibiotics then they should take them, but you might consider giving them a probiotic supplement too, to help top up their levels of good gut bacteria again.


Another cause of dysbiosis could be diet. It’s not always easy for busy parents to provide five portions of fruit and vegetables daily, but these foods can really enrich the microbiome and enhance gut health.

Lots of fruits and vegetables contain fibre, which encourages a balanced gut microbiome filled with lots of friendly bacteria. Aside from occasional treats, also try to steer clear of sugar. Unfortunately, bad gut bugs love it as much as we do! We recommend swapping to wholegrain pasta or bread, and snacking on homemade cereal bars to lower sugar consumption in quick, easy ways your little ones will hardly notice.

Eating healthily is important for your child's gut, and making food together can be a great family activity


Like toddlers at nursery, children’s immune systems are challenged at school. Although it’s good to get a little bit of exposure, as discussed earlier, you also want your children to have the best defence system in place. Friendly bacteria form a strong barrier along the gut lining, making it difficult for bad bugs to enter. That’s one reason why cultivating healthy gut bacteria aids immunity.

With dysbiosis though, friendly bacteria decreases, weakening this barrier and exposing parts of the gut lining. This creates a perfect opportunity for bad bacteria to enter and cause problems. A weakened immune system may not be as prepared to fight infections, meaning your child might take longer to recover from a school bug or illness.

Never fear, probiotics are here! One study showed children aged 3-7 who took a daily probiotic had a 25% reduction in risk of illness, compared to those who didn’t take a probiotic. There was a 40% risk reduction of missing school in the group taking probiotics compared to placebo. If you'd like to support your child's gut health at school, try adding high-quality probiotic strains to their daily routine.

You might also be interested in Dr Kate's Baby Probiotics and Probiotics and Pregnancy articles.


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2. Sanchez-Valverde F et a., (2009). The impact of caesarean delivery and type of feeding on cows milk allergy in infants and subsequent development of allergic march in childhood. Allergy. 64: 884-889

3. Huang L et al., (2015). Is elective caesarean section associated with a higher risk of asthma? A meta-analysis. Journal of asthma. 52: 16-25.

4. Liu S et al., (2013). The impact of caesarean section on offspring overweight and obesity: a systematic review and meta-analysis. International Journal Obesity. 37: 893-899.

5. Wu T et al., (2018). Infant and adult inhalation exposure to resuspended biological particulate matter. Environ. Sci. Technol. 52(1): 237-247.  

6. S Lynch et al., (2014). Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children. Journal of Allergy and Clinical Immunology. DOI: 10.1016/j.jaci.2014.04.018

7. Carroll F et al., (2016). Factors influencing parents decision- making when sending children with respiratory tract infections to nursery. Journal of Public Health. 38(2): 281-288

8. Ownby D et al., (2002). Exposure to dogs and cats in the first year of life and risk of allergic sensitisation at 6 to 7 years of age. JAMA. 288 (8): 963-972.

9. Cheema G et al., (2017). Effect of prenatal dog exposure on eczema development in early and late childhood. Annals of Asthma, Allergy and Immunology. 119 (5): S14

10. Laynaert B et al., (2001). Does living on a farm during childhood protect against asthma, allergic rhinitis and atopy in adulthood?. AJRCCM. 164(10):

11. Christian LM et al., (2015). Gut microbiome composition is associated with temperament during early childhood. Brain Behav Immun. 45: 118-127

12. Nicolini G et al., (2014). Combating the rise of antibiotic resistance in children. Minerva Pediatr. 66(1):31–9