Why Your Eczema Isn’t Just a Skin Problem: The Hidden Gut Imbalances You Need to Heal

By Diane Angela Fong. ND & Tori Taggart, MS, CNS, LDN

If you’ve been living with eczema, you already know how frustrating it can be. The itching, the flares, the cracked or inflamed skin and the endless creams and steroid prescriptions that never seem to offer more than temporary relief. But what if the real issue isn’t the skin at all?

What if the root of eczema is happening underneath the surface, deep inside the gut?

More and more research is revealing that eczema is not just a skin disorder - it’s a reflection of internal imbalance. Specifically, imbalances in the gut microbiome, fungal or bacterial overgrowth, parasitic infections, and a compromised intestinal barrier directly influence inflammation in the skin. Eczema is actually a signal that something deeper inside the body needs attention.

This explains why topical treatments offer only short-term improvement. They don’t address the underlying causes -the microbial imbalances, immune dysregulation, and gut permeability that continually feed inflammation. When you repair and rebalance the gut, however, the skin often begins to heal in ways people never thought possible. 

Why the Gut Matters So Much in Eczema

Your gut is home to trillions of microorganisms - bacteria, fungi, viruses, and even microscopic parasites. Together, they form the gut microbiome, a living ecosystem that affects digestion, immunity, detoxification, hormone regulation, and your skin.

When this ecosystem is healthy and balanced, it produces metabolites such as short-chain fatty acids that strengthen the gut lining, regulate immune responses, support the skin barrier, and reduce inflammation. Beneficial species like Bifidobacteria and Lactobacilli help keep the immune system healthy and balanced.

But modern life affects our gut with endless exposures. Antibiotics, stress, pesticides, medications like NSAIDs or PPIs, high-sugar diets, alcohol, poor sleep, highly processed foods, and environmental toxins can shift the microbiome into dysbiosis -an imbalance where harmful species overgrow and beneficial species get crowded out. Our bodies just can’t keep up with the funneling of all of these exposures. This overflowing funnel is evidenced as eczema.

Dysbiosis → Leaky Gut → Immune Activation → Skin Inflammation

When dysbiosis takes hold, the lining in the intestinal tract becomes weakened. Tight junctions between gut cells begin to loosen, allowing fragments of bacteria, toxins, and undigested food molecules to leak into the bloodstream. The immune system responds to these fragments causing internal inflammation and the skin expresses itself externally as eczema. This process doesn’t look the same in every person. For some, it’s driven mainly by bacterial overgrowth. For others, chronic fungal overgrowth or parasitic infections are major contributors. In many cases, it’s a mix of all three.

Candida, Bacterial Overgrowth, and Parasites: The Hidden Triggers Nobody Talks About

When it’s time to begin solid foods, babies with eczema often benefit from a slightly slower, more intentional approach. Instead of jumping straight into a wide variety of foods or early allergens, the focus shifts first to gut support, skin healing, and inflammation reduction. This creates the foundation they need to tolerate foods- especially common allergens.

Candida and Fungal Overgrowth

Candida albicans is a type of yeast that normally lives harmlessly in the gut. But stress, antibiotics, steroids, and sugar-heavy diets can cause it to overgrow. When Candida becomes excessive, it produces toxins that irritate the gut lining and increase intestinal permeability. These toxins enter the bloodstream, creating inflammation that can worsen eczema. Candida is a common type of fungal overgrowth but there are others as well.  People with fungal overgrowth will often experience digestive symptoms, sugar cravings, fatigue, brain fog, and/or skin rashes especially on areas like folds on the skin, elbow creases, behind the knees, and the scalp. Yeast overgrowth in the gut is a common culprit for eczema. In addition, malassezia is a type of fungus that lives externally on the skin. When the gut is imbalanced and the skin barrier is weak, malassezia can overgrow externally as well.  Learn more about fungal overgrowth and eczema in our past blog post.

Bacterial Imbalances and Skin Symptoms

Gut bacteria have a powerful influence on the skin. Low levels of beneficial species and overgrowth of opportunistic or pathogenic bacteria can contribute to skin inflammation. Some bacteria produce toxins called endotoxins and some can also produce a histamine response, both of which can worsen itching.

We also know that people with eczema often struggle with Staphylococcus aureus colonization on the skin. Dysbiosis in the gut can make the skin more susceptible to this type of overgrowth and infection. 

Parasites: The Overlooked Cause of Chronic Rashes

Parasites are far more common than most people think even in the United States. Exposure happens through food, water, soil, pets, travel, swimming in lakes or rivers, or simply touching contaminated surfaces and then touching your mouth.  

A strong gut ecosystem typically keeps parasites in check. But if your microbiome is imbalanced, your immune system weakened, or your stomach acid low, parasites can take hold more easily.

Parasites can worsen eczema by:

• Triggering chronic immune activation

• Releasing toxins that damage the gut lining

• Disrupting the microbiome

• Worsening histamine responses

• Creating nutrient deficiencies

  
  

Some people with parasitic infection have obvious digestive symptoms but many do not. For others, the only sign of a parasitic infection is chronic skin flares, itching (especially at night), hives, worsening food sensitivities, or cycling eczema flares that don’t respond well to treatment.

How We Identify Gut Imbalances: GI-MAP, GI Effects & Comprehensive Testing

Because gut imbalances can vary so widely from person to person, the most important step is proper testing. At Cleanbody, we use advanced functional stool tests that reveal the full picture of gut health.  We utilize a few different types of stool tests to evaluate the health of the microbiome. 

GI-MAP (Diagnostic Solutions)

The GI Map is a comprehensive stool test that relies on quantitative polymerase chain reaction (qPCR) technology to detect parasites, bacteria, H. pylori, fungi, and more by targeting the specific DNA of the organisms tested. 

It provides a highly sensitive and detailed look at:

• Pathogenic bacteria, viruses, and parasites (DNA-level detection)

• Candida and fungal species

• Beneficial flora levels

• Dysbiosis patterns

• H. pylori

• Zonulin (a key marker of leaky gut)

• Pancreatic elastase (digestion capacity)

• Beta-glucuronidase (detox function)

• Secretory IgA (immune strength)

• Inflammatory markers like calprotectin

With a GI Map, we can evaluate the health of the microbiome, assess for leaky gut, and determine if there is any inflammation in the gut.  

GI Effects (Genova Diagnostics)

The GI Effects by Genova looks at the 3 key functions of gut health arranged in the "DIG" format: Digestion/Absorption, Inflammation/Immunology, and the Gut Microbiome:

This comprehensive test offers:

• Microbiome diversity scoring

• SCFA production

• Yeast and bacterial overgrowth

• Parasitology (3-day or PCR-enhanced options)

• Inflammation and immune markers

• Steatocrit (fat malabsorption)

• Digestion and absorption indicators

• Dysbiosis index

• Gut barrier markers

  
  

In addition, this test offers a culture of the stool that looks at what bacteria or yeast grows to establish possible infections/pathogens. 

The GI Map is a great start for gut testing and the GI Effects is a very comprehensive test evaluating many aspects of gut health.  Both of these tests can help us to understand exactly what’s happening inside your gut ecosystem -what needs to be removed, what needs to be repaired, and what needs support.  Some people discover severe fungal overgrowth or some uncover parasites that were completely missed by conventional testing. Others find deep dysbiosis or a weakened gut barrier they never knew existed. 

In addition to stool testing, we also use testing such as food sensitivity panels, organic acids testing, histamine or DAO levels, and targeted blood work especially  when symptoms or the stool results suggest deeper issues. This approach gives a full spectrum of understanding to what is going on internally in the body and allows us to find the root cause and work on healing from the inside out. 

How We Heal the Gut to Heal the Skin: The Cleanbody Method

Once we understand the exact imbalances contributing to your eczema, we build a personalized healing plan using the Cleanbody Method -our comprehensive framework that supports the body from multiple angles.  This involves a process of Evaluating, Optimizing and Supporting the body. 

We develop a plan to heal the gut by cleaning up the nutrition, removing any pathogens, reducing inflammation and repairing the gut lining, restoring and rebuilding the microbiome, supporting proper detox and supporting the nervous system. 

Nutrition: CleanFOOD

A nutrient-dense, anti-inflammatory, microbiome-supportive diet is essential. We often use a CleanFOOD approach that emphasizes whole foods, fiber-rich fruits and vegetables, lean proteins, healthy fats, and minimal processed foods. Many people also benefit from short-term elimination of their specific trigger foods while the gut heals.

Removing Pathogens When Necessary

If stool testing reveals Candida, parasites, or bacterial overgrowth, we use targeted herbal protocols, gentle antimicrobials, and sometimes homeopathic remedies to rebalance the gut — always in a personalized, stepwise manner to prevent flares.

This may include herbs like wormwood, black walnut, clove, neem, or professional-grade blends designed to be effective yet safe. We never recommend treating parasites or fungal overgrowth blindly — doing so can create more inflammation and worsen eczema. Testing guides the process.

Repairing the Gut Lining

This is where gut-healing nutrients shine.

Many people benefit from:

• L-glutamine

• DGL licorice

• Slippery elm

• Aloe vera

• N-acetyl-glucosamine

• Zinc carnosine

• Gut Mend (our comprehensive formula)

These nutrients help tighten the gut barrier, soothe inflammation, and restore mucosal integrity, which directly supports skin healing.

Restoring the Microbiome

Probiotics, prebiotics, and postbiotics — when used properly and at the right stage of healing — can transform the gut ecosystem. SCFA-supporting fibers, fermented foods, and targeted strains help shift the microbiome toward balance and reduce inflammation.

Detox & Liver Support

Since toxin overload can worsen eczema, we support detox pathways with tools like milk thistle, dandelion root, antioxidants, hydration strategies, proper bowel motility, and sometimes epsom salt baths.

Lifestyle + Nervous System Support

Chronic stress increases intestinal permeability and suppresses digestive function — and eczema flares often follow. Practices like meditation, breathwork, adequate sleep, grounding routines, CleanMIND tools, and movement patterns from our CleanFIT approach help restore nervous system balance so the gut can heal fully.

Why Working With a Practitioner Makes All the Difference

Gut healing is powerful — but it’s rarely linear. Treating the wrong imbalance at the wrong time can make symptoms worse. Killing pathogens when the gut lining is still highly permeable can trigger more flares. Taking probiotics while fungal overgrowth is active may feed the wrong species.

This is why working with experienced practitioners matters. At Cleanbody, we don’t guess.We test.We interpret.We personalize every plan.We monitor symptoms, adjust doses, and support your system at every step.

Many people with eczema finally find relief only when someone looks at the full picture — the microbiome, the immune system, digestion, detox pathways, toxins, infections, food reactions, lifestyle factors, and stress patterns.

Final Thoughts: Your Skin Reflects Your Internal Terrain

Eczema is not a sign that your skin is broken. It’s a sign that your body is communicating — and the message is often coming from the gut.

Gut imbalances such as dysbiosis, Candida overgrowth, parasites, bacterial pathogens, and weakened intestinal barrier function are some of the most common (and most overlooked) drivers of chronic eczema. When you identify and address these root causes, the skin can finally begin to repair itself, sometimes faster than you ever imagined.

If you’ve tried everything and are still struggling, it may be time to look inward — literally.

Our team is here to guide you through testing, interpretation, personalized nutrition plans, gut healing protocols, and the Cleanbody Method so you can transform your health from the inside out.

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If you’re ready to go beyond diet changes and uncover the root gut issues that may be driving inflammation, make sure to check out our Holiday Eczema Healing Bundle — designed to give you clarity, answers, and a personalized path forward.

🎁 Holiday Eczema Healing Bundle — $497

Includes:✨ GI-MAP Gut Test✨ 40-minute Eczema Evaluation Visit✨ 1 Month of Eczema Essentials Support (Total value $667 - Save $170)

Whether you’re a parent, someone living with eczema, or looking for a meaningful gift for a loved one — this bundle provides clarity, answers, and a personalized path toward healing.

👉 Learn more or purchase the Holiday Bundle here

We're Going Live!

We are going live to discuss this topic on Thursday, December 18 at 12:00 pm PST! Watch the live or check out the replay here:

About the Authors:

Tori Taggart, MS, CNS, LDN is a Cleanbody Practitioner specializing in meeting people in their health journeys by digging into the root causes of various chronic diseases and conditions. Through the use of healthy food along with aspects of the natural world around us (sunshine, nature, clean water, stress management, relationships, etc), she helps to empower her clients to take charge of their own health and trust their bodies to thrive and heal.

Dr. Diane Angela Fong, ND, is the CEO and founder of Cleanbody, a wellness company dedicated to treating and preventing chronic disease. She is the creator of the Cleanbody Method, which follows a three-step process: Evaluate (digging into the root causes of chronic disease using lab testing and other evaluation tools), Optimize (enhancing health foundations by addressing nutrition, lifestyle, and toxic exposures), and Support (optimizing organ functions through healing protocols).

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Medical Disclaimer: The information provided in this blog post is for educational and informational purposes only. It is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the advice of your physician or other qualified healthcare provider with any questions you may have regarding a medical condition or treatment and before undertaking a new health care regimen. Never disregard professional medical advice or delay in seeking it because of something you have read on this website.