Eczema and Gut Health - How Does the Gut Microbiome Affect Your Skin?
Written by Madeline Spawton - 4th May, 2025
If your child struggles with eczema, you’re probably familiar with the cycle: relentless itching, cracked and weeping skin, steroid creams, and then fleeting relief. Many parents are experiencing frustration with endless cycles of temporary improvement after using topical creams, then a change in weather or a trip to the swimming pool and voila - another flare!
A growing question that we get in the clinic is: is there a link between eczema and gut health? And the answer is yes! Research increasingly highlights the connection between gut health and skin, which we call the “gut-skin axis”. By understanding how the gut influences the skin, we can shift our focus to proactive, nourishing choices that support your child’s body as a whole, not just their symptoms, and build healthier foundations long-term.
What is Eczema?
Eczema, also called atopic dermatitis, is an inflammatory skin condition commonly occurring in childhood, often in babies and young children. It is characterised by dry, red, itchy patches on the skin, which can sometimes crack, ooze, become infected, or scaly.
Flare-ups can be set off by a mix of things. Common triggers include certain foods, environmental irritants, and even emotional stress. At its core, eczema is often driven by an overactive immune system, influenced by both genetic and environmental factors (2). It’s also more common in children who have a family history of allergies, asthma, or hayfever. If you’d like a deeper dive into these underlying causes, we covered them in more detail in our earlier eczema article here.
While eczema might seem like just a skin problem, there’s usually much more going on beneath the surface! It can be tough to manage, and many parents find that topical treatments alone don’t fully address their child’s symptoms completely. This is where gut health comes into play!
What is the link between eczema and gut health?
So, how does gut health affect skin? The answer lies in the gut-skin axis—the connection between our skin and gastrointestinal system (1). The health of our gut is essential for digestion, immune balance, and controlling inflammation. The key components of the gut that influence skin health include:
The stomach, with its production of stomach acid, is essential for breaking down food and releasing key nutrients that support skin health and reduce inflammation linked to eczema.
The pancreas and liver contribute digestive enzymes and bile acids that our body needs for optimal nutrient absorption.
The gut lining acts as a protective barrier that prevents harmful substances from leaking into the bloodstream and triggering systemic inflammation that can manifest in the skin.
The small intestine is important in absorbing nutrients critical for skin health
And most importantly, the large intestine houses our microbiome, which is made up of trillions of bacteria, fungi, and other microorganisms that influence our immune system and inflammation (3).
How does gut health affect skin?
So, how exactly does a healthy gut and all these individual parts of our digestive system help the skin?
When the gut is healthy, it helps regulate the immune system by creating a balanced (and appropriate!) response to environmental triggers. The gut lining acts as a semi-permeable barrier, allowing beneficial nutrients to pass through while keeping harmful substances, like undigested food particles, toxins, and infections, out of the bloodstream. A protective mucus layer coats the gut, preventing irritation and inflammation, and providing a home for beneficial bacteria that produce anti-inflammatory substances that help calm the immune system and reduce overall inflammation. Additionally, the gut communicates directly with immune cells, helping them recognise the difference between harmless substances (like food and pollen) and real threats (like viruses and harmful bacteria).
The gut microbiome - the collection of microbes, such as bacteria and fungi, that naturally live in our gut - is also important in a balanced immune response. Within a healthy gut, the beneficial bacteria outnumber the harmful bacteria, helping to maintain a balanced immune response and keep inflammation in check. These beneficial bacteria not only help digest food but also produce substances called short-chain fatty acids (SCFAs) - anti-inflammatory compounds that support the integrity of the gut lining and balance immune function (14).
When all these parts are working well, the immune response stays balanced, reducing the risk of overreactions that can contribute to conditions like eczema.
What Happens When the Gut Is Unhealthy?
When the gut is out of balance, it can struggle to regulate the immune system effectively, leading to overactivity and hypersensitivity to environmental triggers. Instead of acting as a strong protective barrier, a weakened gut lining (aka leaky gut) allows undigested food particles, toxins, and harmful bacteria to pass into the bloodstream, triggering inflammation and immune system overreactions. The mucus layer that normally supports beneficial bacteria may become disrupted, reducing the production of anti-inflammatory substances like SCFA that help keep immune responses in check.
One of the key factors contributing to an unhealthy gut is dysbiosis, an imbalance between the beneficial (aka “good”) bacteria and the pathogenic or inflammatory (aka “bad”) bacteria in the microbiome. When dysbiosis occurs, due to factors like poor diet, antibiotics, or chronic stress, the balance shifts, and bad bacteria can start to thrive. These inflammatory species produce toxins and other substances that irritate the gut lining, weaken the immune system, and promote systemic inflammation.
Additionally, this heightened immune response may mistake harmless substances (like food or environmental allergens) as threats, increasing allergic reactions - hello eczema!
What Causes Gut Imbalance and Skin Dysbiosis?
So, what throws this delicate gut system off track? Understanding the common factors that lead to gut and skin dysbiosis can make a big difference for parents supporting children with eczema. From diet and lifestyle to environmental exposures, many everyday factors can disturb gut health and contribute to eczema flare-ups. Let’s take a closer look at some of the key ones.
Dietary Imbalances: A diet high in sugar and low in fibre is one of the biggest disruptors of a healthy gut. Sugar feeds harmful bacteria and yeast, while fibre nourishes beneficial microbes that produce anti-inflammatory compounds and help maintain the gut lining. Without enough fibre and wholefoods, the diversity and resilience of good bacteria drop, making the gut more prone to irritation and imbalance. Add in processed foods and preservatives, and you reduce microbial diversity even further, weakening the gut's protective functions and fuelling inflammation that can show up on the skin.
Antibiotics and Medications: While sometimes necessary, antibiotics don’t discriminate—they wipe out beneficial bacteria along with the harmful ones. Research shows that antibiotic use in childhood can significantly affect the diversity and proper development of the microbiome (6). Even a single course can alter the microbial balance, and repeated use may lead to persistent imbalances. Other medications, such as steroids, NSAIDs, and antacids, can also impair digestion, reduce protective stomach acid, or damage the gut lining, making it harder for the gut ecosystem to recover.
Environmental Toxins: Exposure to environmental toxins—from air pollution and pesticides to cleaning products and synthetic personal care items—can compromise the gut in several ways. These substances may alter the gut microbial composition, damage the mucosal lining, increase oxidative stress, and impair detoxification pathways. The resulting imbalance and inflammation can affect immune response and skin barrier function, contributing to flare-ups in children predisposed to eczema.
Mould and Fungal Exposure: Mould and the mycotoxins it produces can significantly compromise gut health. These toxins can weaken the gut lining, increase intestinal permeability (7). and create an environment where harmful microbes like Candida thrive. This not only contributes to dysbiosis but also places added pressure on the immune and detoxification systems, triggering inflammation and hypersensitivity reactions that can worsen eczema (7).
Chronic Stress and Lack of Sleep: Stress activates the release of cortisol and other stress hormones that can suppress digestive function and shift the microbial balance toward more harmful species. It also increases gut permeability and can reduce secretory IgA, the gut’s first line of immune defence (8). Sleep deprivation further disrupts circadian rhythms that regulate gut repair and microbial cycles, compounding inflammation and increasing the likelihood of eczema flares.
Food Sensitivities and Allergies: Reactions to certain foods—particularly common triggers like dairy, gluten, soy, or eggs—can drive immune overactivity and inflammation in the gut and skin. In susceptible children, these foods can irritate the gut lining or fuel the growth of pro-inflammatory bacteria. On top of that, preservatives, artificial colours, and flavour enhancers can impair gut barrier integrity and stress the liver’s detoxification capacity, both of which may contribute to worsening skin symptoms in sensitive children..
8 Simple Ways to Improve Gut Health for Eczema in Children
Now that we’ve looked at how the gut can be disrupted by things like diet, antibiotics, environmental toxins, and stress (oh so many things!)—you might be wondering: What can I actually do to support my child’s skin and gut health?
The good news is that the gut microbiome is responsive and adaptable. With the right support, it’s possible to restore balance, reduce inflammation, and strengthen the gut-skin connection. While every child is different, and there’s no one-size-fits-all solution, there are many simple, evidence-informed steps parents can take to support gut health and eczema at home. And because the gut plays such a central role in immune function and skin health, even small changes can make a meaningful difference.
Here are some key areas to focus on:
1. Nourish with the Right Foods
What your child eats plays a huge role in shaping their gut microbiome. Making small changes to their diet can help reduce inflammation, feed beneficial bacteria, and calm eczema flares.
Focus on Whole, Unprocessed Foods: Include a wide variety of whole foods—such as vegetables, fruits, whole grains, legumes, nuts, seeds, and quality proteins. Colourful fruits and vegetables, especially leafy greens and berries, are rich in antioxidants and vitamins A & C that help regulate inflammation and support the immune system. Whole grains and legumes provide fibre to nourish beneficial gut bacteria, while nuts and seeds offer zinc, vitamin E, and healthy fats that strengthen the gut and skin. Oily fish such as salmon, sardines, and mackerel supply anti-inflammatory omega-3 fatty acids, and extra virgin olive oil offers healthy fats and polyphenols that support immune and gut health. Prioritising these kinds of whole foods and limiting ultra-processed or sugary options creates a gut environment that can help reduce inflammation and support clearer, healthier skin.
Choose Organic When Possible: We know that long-term exposure to low levels of pesticides (common in conventionally grown produce) has been shown to alter the gut microbiome (9). Where possible, opt for organic or spray-free options, or grow your own—kids often love helping in the garden! But if organic isn’t accessible (because let’s be honest—have you seen the price of groceries lately?), you can still reduce exposure without blowing the budget by prioritising organic choices based on the Environmental Working Group's "Dirty Dozen" and "Clean Fifteen" lists. These guides highlight which fruits and vegetables tend to carry the most pesticide residue (the Dirty Dozen) and which are typically lower in residues (the Clean Fifteen). This way, you can make informed choices about where going organic will give you the biggest benefit for your buck.
Boost Fibre Intake: Fibre is essential food for your child’s gut bugs! When kids eat fibre, it feeds the good bacteria in their gut, allowing them to thrive and produce those important compounds called short-chain fatty acids. These help reduce inflammation and repair the gut lining—both important in managing eczema. Try including fibre-rich foods like oats, lentils, apples, carrots, and chia seeds regularly. Research shows that a low-fibre diet can lead to an imbalanced gut microbiome (13), so even small daily swaps can make a big difference to your child’s skin and overall health.
Add Prebiotic Foods: These are specific types of fibre that act as fuel for healthy gut bacteria. Try garlic, onion, leek, asparagus, banana, and cooked and then cooled oats or rice.
Introduce Fermented Foods (if tolerated): Yogurt with live cultures, kefir, kimchi, miso, and sauerkraut can all help increase probiotic diversity. Start small and observe how your child responds.
2. Consider Probiotics
Unless you’ve been living under a rock (in which case, welcome back!), you’ve probably heard about probiotics and eczema, and maybe even tried them for your child! These are live, beneficial bacteria that help support a healthy gut microbiome—and they’re especially worth considering when it comes to kids with eczema. But there are a few important things to know before grabbing a random product from the supermarket.
Choose the Right Strains: Not all probiotics are created equal. Research supports the use of certain strains, like Lactobacillus salivarius LS01, for improving eczema symptoms in children (15).
Work with a Qualified Practitioner: A tailored probiotic plan—based on your child’s age, symptoms, and history—will give the best results. Too much or the wrong strain can sometimes worsen symptoms, especially in sensitive children.
Remember—probiotics are just one piece of the puzzle. They work best alongside dietary and lifestyle changes.
3. Support Stress Regulation
Stress has a powerful impact on both the gut and skin. When children are stressed, their body produces hormones like cortisol, which can upset the balance of gut bacteria and increase inflammation.
Emotional Connection Comes First: Time with loving adults, calm moments together, and consistent routines help children feel safe and regulated.
Encourage Movement & Play: Physical activity supports both stress relief and gut health. Let them run, jump, swim, dance—or do whatever brings joy to their body.
Outdoor Play & Soil Exposure: Contact with nature and soil has been shown to support gut microbial diversity (11). Gardening, getting messy, and simply playing in nature are great ways to nurture both mood and microbiome.
Mindfulness for Kids: Age-appropriate breathwork, yoga, story meditations, or even singing can help calm an overstimulated nervous system.
4. Prioritise Quality Sleep
Sleep is when the body restores and repairs, and this includes the skin, the gut lining and the immune system. Lack of sleep can increase inflammation and reduce the diversity of good bacteria in the gut (12).
Create a Predictable Bedtime Routine: Keeping wake-up and sleep times consistent helps regulate circadian rhythms, which are linked to microbiome health.
Avoid Screens Before Bed: Blue light suppresses melatonin production, making it harder for kids to wind down.
Use Soothing Rituals: Warm baths, gentle music, a cup of chamomile tea (if age-appropriate), and calming books can all help signal bedtime to the body.
5. Reduce Environmental Irritants
While this isn’t strictly gut-related, it’s worth reminding parents of other common triggers that can add to the eczema load:
Use low-tox, fragrance-free products for laundry, body, and cleaning
Avoid synthetic clothing that doesn’t breathe well
Be mindful of over-bathing or using hot water, which strips natural oils from the skin
This reinforces a holistic, inside-out and outside-in approach.
6. Identify Food Sensitivities and Triggers
Some foods can irritate the gut lining or trigger immune responses in sensitive children, worsening both gut and skin inflammation. These are different from full-blown allergies and can be harder to detect.
Common Culprits Include: Dairy, gluten, soy, eggs, citrus, and food additives like preservatives and artificial colours.
Elimination Diets Can Be Helpful: Temporarily removing and reintroducing certain foods (under guidance) can help pinpoint triggers. Keep a food and symptom diary to notice patterns.
Consider Functional Testing: IgG food sensitivity testing or other functional pathology can sometimes offer additional insight into what might be driving symptoms. This should always be interpreted in the context of your child’s full picture by a qualified practitioner.
7. Consider Gut Testing
In more complex or chronic eczema cases, comprehensive gut microbiome testing can be helpful to assess for:
Gut inflammation
Imbalances in microbial species
Overgrowths of yeast or pathogenic bacteria
Digestive insufficiencies (like low enzymes or bile acids)
These results can help tailor treatment more specifically, especially when progress is slow or symptoms are severe.
8. Address Nutrient Deficiencies
Nutrients like zinc, vitamin D, omega-3 fatty acids, and vitamin A are crucial for both skin and immune health—and deficiencies in these are commonly seen in children with eczema.
Zinc supports wound healing, immune regulation, and gut lining integrity. Low levels are linked with poor skin barrier function.
Vitamin D plays a key role in regulating immune responses and inflammation. Kids with eczema are often low.
Omega-3s (from oily fish, flaxseeds, or supplements) have anti-inflammatory effects and support skin hydration and healing.
Consider testing or supplementing under the guidance of a practitioner to ensure your child isn’t missing anything critical for healing.
Understanding the connection between gut health and eczema opens up new possibilities for supporting your child’s skin health. Supporting gut health doesn’t mean aiming for perfection. It’s about making small, consistent changes over time that add up to a more balanced internal environment.
If you’re not sure where to start or need help creating a plan tailored to your child, working with a paediatric naturopathic experienced in children’s gut and skin health can make all the difference.
Disclaimer: This article is for educational purposes and does not constitute individual health advice. It is important to seek the advice of your primary health practitioner to assess what is right for you and your child. If you have questions of an individual nature, you are welcome to book a free chat here.
More about Children’s Naturopath Maddie Spawton:
Maddie is a dedicated naturopath and certified postpartum doula with a focus on supporting infants, children, and families. She holds a Bachelor of Health Science from Torrens University and brings additional expertise in maternal and infant health. She is passionate about preventative care during pregnancy and preconception, helping families lay the foundation for lifelong wellness.
Practising via telehealth, Maddie’s clinical work covers a range of conditions, including eczema, asthma, digestive issues, anxiety, autism and ADHD.
If you want to get in touch or have any more questions about the above, you are welcome to get in touch here or make an time for a free chat here.
If you want to keep learning, you can keep reading the research here:
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