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Understanding Atopic Eczema 3.1: Gut Microbiome and Its Causes

  • Writer: Marcelline Goyen
    Marcelline Goyen
  • Mar 13
  • 6 min read

Updated: Mar 16

Worldwide, about 2.6% of the population suffers from atopic eczema, which amounts to over 200 million people. And that is not even counting all other forms of eczema. This is therefore a skin condition that we should take seriously, especially given the severe consequences that can significantly negatively impact daily life (ADL) [ Source


In this three-part series on (atopic) eczema, various aspects of (atopic) eczema in relation to the skin-gut axis are discussed: 3.1 deals with eczema and its relationship to gut-related causes. 3.2 deals with eczema in relation to diet, such as dairy, grains, and gluten, and 3.3 deals with eczema and the use of prebiotics, probiotics, and a healthy diet.


Atopic eczema and the skin-gut axis: a complex interaction model


Table of Contents



Introduction


Atopic eczema is a chronic skin condition that affects millions worldwide, causing redness, itching, and inflammation. Recent research highlights a strong connection between eczema and the gut microbiome, the community of microorganisms living in our digestive tract. Understanding the eczema gut microbiome is essential to recognizing the root causes of eczema and finding effective ways to manage it. This post explores how the gut microbiome influences eczema, identifies common causes, and offers practical advice to support both gut and skin health.



What Is the (Atopic) Eczema Gut Microbiome?


The gut microbiome consists of trillions of bacteria, viruses, fungi, and other microbes living in the intestines. These microorganisms play a crucial role in digestion, immune system regulation, and even skin health. When the balance of this microbial community is disrupted, it can lead to inflammation and immune responses that may trigger or worsen (atopic) eczema symptoms.


In people with atopic eczema, studies have found differences in the diversity and composition of gut bacteria compared to those without the condition. This imbalance, often called dysbiosis, can affect the skin’s barrier function and immune responses, making the skin more vulnerable to irritation and allergic reactions.



How the Gut Microbiome Influences Eczema


The gut and skin communicate through what is known as the gut-skin axis. This connection means that changes in the gut microbiome can directly impact skin health. Here’s how:


  • The method of birth: Normal birth via vaginal birth canal versus cesarean section. With a normal birth, the baby comes into contact with the mother's vaginal, anal, and skin microbiome during delivery. With a cesarean section, the baby misses this encounter with the vaginal and anal microbiome, resulting in less developed microbiome and a higher risk of developing eczema.

  • Immune System Modulation: The gut microbiome trains the immune system to respond appropriately to threats. Dysbiosis can cause the immune system to overreact, leading to inflammation seen in eczema.

  • Barrier Function: A healthy gut supports the production of molecules that strengthen the skin barrier. When the gut is unhealthy, the skin barrier weakens, allowing irritants and allergens to penetrate more easily.

  • Inflammatory Signals: Harmful bacteria in the gut can release toxins and inflammatory molecules that travel through the bloodstream to the skin, triggering eczema flare-ups.


Research published in journals such as Frontiers in Immunology and The Journal of Allergy and Clinical Immunology supports these mechanisms, showing that improving gut health can reduce (atopic) eczema severity.




Skin-gut axis books by Marcelline Goyen BSc Skin Therapy and author



Recognizing the Causes of (Atopic) Eczema Linked to the Gut


Identifying what disrupts the gut microbiome is key to managing eczema effectively. Several factors can contribute to gut imbalance and eczema development:


1. Diet and Food Sensitivities


Certain foods can irritate the gut or trigger immune responses that worsen eczema. Common offenders include:


  • Dairy products,

  • Gluten-containing grains,

  • Processed foods high in sugar and additives,

  • Foods causing allergic reactions, such as nuts or shellfish.


Food sensitivities vary by individual, so keeping a food diary and working with a healthcare provider can help identify triggers.


Severe eczema due to gluten and wheat. A case study
Severe eczema due to gluten and wheat. A case study on the skin-gut treatment of severe eczema in which wheat/gluten proved to be the main cause. This case is described in my second book (NL 2023, EN 2024, DE 2025).

2. Antibiotic Use


Antibiotics can kill both harmful and beneficial gut bacteria, leading to dysbiosis. Frequent or prolonged antibiotic use may increase the risk of eczema flare-ups by disrupting the gut microbiome balance.


3. Stress and Lifestyle Factors


Chronic stress affects gut health by altering the microbiome and increasing intestinal permeability (leaky gut). Poor sleep, lack of exercise, and smoking also negatively impact gut and skin health.


4. Environmental Exposures


Pollutants, harsh soaps, and chemicals can affect the skin barrier and gut microbiome indirectly by increasing inflammation and immune system activation.



Common Triggers That Affect the Gut and Skin


Understanding triggers that influence both gut and skin health helps in recognizing eczema causes:


  • Infections: Gut infections can disrupt microbial balance and provoke immune responses linked to eczema.


Seborrhoic eczema & gut parasites: A case study
Seborrhoic eczema & gut parasites: A case study on the treatment of severe seborrhoic eczema in which gut parasites proved to be the main cause. This case is described in my second book (NL 2023, EN 2024, DE 2025).
  • Low Fiber Intake: Fiber feeds beneficial gut bacteria. A diet low in fiber can reduce good bacteria, increasing inflammation.

  • High Sugar Consumption: Excess sugar promotes growth of harmful bacteria and yeast, worsening gut imbalance.

  • Lack of Prebiotics and Probiotics: Prebiotics are food fibers for healthy bacteria. Probiotics are healthy bacteria that help to restore the gut microbiome and may improve eczema symptoms.



Practical Steps to Support a Healthy Gut Microbiome


Improving gut health can help manage eczema by reducing inflammation and strengthening the skin barrier. Here are practical tips:


  • Eat a Balanced Diet: Focus on whole foods rich in fiber, such as fruits, vegetables, legumes, and whole grains. These feed beneficial gut bacteria.

  • Include Probiotics: Foods like yogurt, kefir, sauerkraut, and kimchi contain live bacteria that support gut balance. Probiotic supplements may also help but consult a healthcare provider first.

  • Avoid Known Food Triggers: Identify and eliminate foods that worsen eczema symptoms.

  • Limit Antibiotic Use: Use antibiotics only when necessary and follow medical advice to protect gut flora.

  • Manage Stress: Practice relaxation techniques such as meditation, yoga, or deep breathing to reduce stress-related gut disruption.

  • Stay Hydrated: Drinking enough (warm or hot) water supports digestion and skin hydration. Start and end your day with hot water.

  • Exercise Regularly: Physical activity promotes a healthy gut microbiome and reduces inflammation.



Thank you for reading my blog post. If you'd like to learn more about the skin-gut-microbiome connection and its relationship to skin problems like acne, rosacea, and eczema, check out my books. Now available in Dutch, English, and German!



Marcelline Goyen BSc Skin Therapy and author in the Netherlands


Marcelline Goyen BSc Skin Therapy and author in the Netherlands



Frequently Asked Questions (FAQ)


What is the eczema gut microbiome?

The eczema gut microbiome refers to the community of microorganisms in the gut that influence eczema development and severity by affecting immune responses and skin health.


Can changing my diet improve eczema?

Yes, adjusting your diet to include more fiber and probiotics while avoiding trigger foods can support gut health and reduce eczema symptoms.


How does stress affect eczema and the gut?

Stress disrupts the gut microbiome and increases intestinal permeability, leading to inflammation that can worsen eczema flare-ups.


Are probiotics effective for eczema?

Some studies suggest probiotics can help balance gut bacteria and reduce eczema severity, but results vary. Consult a healthcare provider before starting supplements.


Why do antibiotics worsen eczema?

Antibiotics can kill beneficial gut bacteria, causing dysbiosis that may trigger immune responses linked to eczema.



Conclusion and Next Steps


Understanding the eczema gut microbiome reveals how deeply connected gut health is to skin conditions like eczema. Recognizing causes such as diet, antibiotic use, stress, and environmental factors empowers you to take control of your health. By supporting a balanced gut microbiome through mindful eating, stress management, and lifestyle changes, you can reduce eczema flare-ups and improve your overall well-being.


Start by tracking your diet and symptoms, then explore gut-friendly habits. For personalized advice, consult a healthcare professional specializing in gut and skin health. Your journey to healthier skin begins with nurturing your gut.



Skin-gut axis book (2024) by Marcelline Goyen BSc skin therapy and author


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