What your digestive health reveals about your skin and what you can do about it.

Introduction

If you have been living with eczema, you already know how frustrating it can be. The relentless itch, the inflamed patches of skin, the sleepless nights, all while trying product after product with little lasting relief. What most people do not know is that the answer to their eczema may not start with their skin at all. It may start in their gut.

Over the past decade, a growing body of research has revealed a powerful connection between gut health and skin health, a relationship scientists call the gut-skin axis. This axis describes the two-way communication network between your digestive system and your skin. When the gut microbiome is out of balance, it can trigger and worsen inflammatory skin conditions like eczema. Conversely, supporting your gut can lead to measurable improvements in skin health.

Gut microbiome tests are now making it possible to look inside that connection and personalize eczema treatment in ways that simply were not possible before. This article explores how gut health testing works, what it reveals, and how it can become a cornerstone of effective eczema skin care.

What Is Eczema and Why Don't Topical Treatments Always Work?

Eczema, also known as atopic dermatitis, is a chronic inflammatory skin condition affecting more than 31 million Americans. It is characterized by dry, itchy, inflamed skin that can appear anywhere on the body but most commonly affects the face, hands, elbows, and behind the knees. While it is often thought of as a skin problem, eczema is fundamentally an immune system disorder.

 

The skin's outer layer, a.k.a., the “skin barrier”, normally acts as the body’s protective shield, keeping allergens and irritants out and moisture in. For people suffering with eczema, this skin barrier is impaired, making skin more vulnerable to environmental triggers. But here is the important question: why is the immune system misfiring in the first place?

For many patients, topical steroids and moisturizers address the symptom, i.e., the inflamed skin part, but not the “root” cause. This is why so many people cycle through treatments that work temporarily but never fully manage the condition. It should be noted that in worst case scenarios, regular use of topical steroids for eczema relief can lead to a devastating condition known as topical steroid withdrawal (TSW). However, a closer look into various “internal factors” such as gut health, hormones, and nutrition, often tells a very different story.

The Gut-Skin Axis: How Your Digestive Health Drives Skin Inflammation

The gut-skin axis refers to the bi-directional relationship between the gastrointestinal tract and the skin. Your gut is home to trillions of microorganisms, i.e., bacteria, fungi, and viruses collectively known as the “gut microbiome”. These microbes play a central role in regulating immune function within the body, managing inflammation, and producing signaling molecules that influence the entire body, including the skin.

When the gut microbiome is balanced, it helps train the immune system to respond appropriately to threats without overreacting. But when the microbiome becomes disrupted/unbalanced, a condition known as dysbiosis, immune regulation breaks down. The immune system becomes hyperreactive, releasing pro-inflammatory signals that can manifest as eczema flares, hives, or other skin conditions.

Research has shown that infants with lower gut microbial diversity are significantly more likely to develop atopic dermatitis. [1] Studies in adults have also found that people with eczema tend to have measurably different gut microbiome compositions than those without, particularly lower levels of beneficial bacteria like Lactobacillus and Bifidobacterium. [2]

The gut-skin axis is also influenced by intestinal permeability a.k.a. 'leaky gut.' When the gut lining becomes permeable, bacteria and toxins can enter the bloodstream, triggering systemic inflammation that worsens skin conditions like eczema.

The Role of Hormones and Other Internal Triggers [3]

Many eczema sufferers notice that their skin flares appear to be tied to stress, menstrual cycles, or other hormonal shifts. This is not a coincidence. The connection between itchy skin and hormone imbalance is well established in dermatology. Cortisol, the body's primary stress hormone, can impair the skin barrier and trigger inflammatory immune responses when chronically elevated. Stress is one of the most common triggers for adult eczema, with studies showing that 57% of females (compared to 41% of males) report that stress makes their eczema worse. [6]

Estrogen and progesterone fluctuations, particularly around the menstrual cycle, pregnancy, or menopause, can also influence skin hydration, skin barrier function, and immune sensitivity. Some women find that their eczema worsens significantly in the week before their period, pointing to a hormonal factor that conventional eczema skin care products simply cannot effectively address. 

What many people fail to realize is how deeply intertwined the gut microbiome is with hormonal balance. The gut produces and regulates neurotransmitters, including serotonin, and modulates hormone metabolism. An imbalanced gut can amplify hormonal disruptions, creating a cascade of inflammatory signals that reach the skin. Studies have shown the negative impact menstrual cycles have on those suffering from eczema. Testing the gut microbiome can help uncover whether hormonal dysregulation is being driven, or made worse, by gut dysfunction. [7]

What Is a Gut Microbiome Test and What Does It Show? [4]

A gut microbiome test, sometimes called a stool microbiome analysis, is a diagnostic tool that analyzes the composition and diversity of bacteria and other microorganisms in your digestive tract. Modern tests use advanced DNA sequencing to identify the species present in your gut and compare them to healthy reference populations.

A comprehensive gut microbiome test can reveal:

•       The overall diversity of your gut microbiome (low diversity is associated with inflammation and disease)

•       Levels of beneficial bacteria like Lactobacillus and Bifidobacterium that support immune regulation

•       Presence of harmful or pro-inflammatory bacteria that may be driving skin reactions

•       Presence of parasites (protozoa or worms) or H.pylori infection

•       Markers of intestinal permeability (leaky gut) or inflammation of the mucus layer (sIgA) that allow inflammatory particles to enter the bloodstream

•       Short-chain fatty acid production, which helps regulate immune function and skin barrier integrity

•       Fungal overgrowth (such as Candida) that can trigger immune hypersensitivity

Unlike a generic skin allergy test, a gut microbiome test gives your healthcare provider a window into the internal immune and inflammatory environment that may be perpetuating your eczema. It moves treatment from reactive to proactive, from managing flares to addressing root causes.

Symptoms That Suggest Your Gut and Skin Are Connected

Not everyone with eczema has obvious digestive symptoms. But many do without even realizing that these symptoms may be related to their skin condition. Common signs that your gut health may be contributing to your eczema include:

•       Bloating, gas, or abdominal discomfort, especially after eating

•       Irregular bowel movements, constipation, or loose stools

•       Food sensitivities or reactions after eating certain foods

•       Fatigue and brain fog, which can indicate systemic inflammation

•       Eczema flares following antibiotic use, which disrupts the microbiome

•       Skin symptoms that worsen during periods of high stress or digestive upset

If any of these patterns sound familiar, a gut microbiome test may be a valuable next step in understanding, and finally resolving, your eczema.

How to Repair Your Gut Microbiome for Healthier Skin [5]

Once a gut microbiome test identifies specific imbalances, a targeted protocol can be developed. Understanding how to repair gut microbiome health is not a one-size-fits-all process, but rather, depends on what the test actually finds. That said, several evidence-based strategies form the backbone of most gut repair protocols for eczema.

Dietary Changes

A gut-friendly diet rich in fiber, fermented foods, and polyphenols (antioxidants) feeds beneficial bacteria while supporting microbial diversity. Eliminating common gut irritants like processed sugar, ultra-processed foods, refined oils, and alcohol, reduces the inflammatory load on both the gut and the skin. Identifying and removing specific food triggers, as guided by testing, can accelerate recovery.

Probiotics and Prebiotics

Targeted probiotic supplementation, particularly strains of Lactobacillus rhamnosus and Bifidobacterium longum, has been shown in clinical trials to reduce eczema severity, particularly in children but also in adults. Prebiotics (fiber-rich foods and supplements that feed good bacteria) are equally important for sustaining microbiome diversity improvements.

Addressing Intestinal Permeability

Healing a leaky gut involves the use (consumption) of targeted nutrients such as L-glutamine (an amino acid that supports gut lining integrity), zinc, and collagen. Reducing gut inflammation via the consumption of omega-3 fatty acids and curcumin can also help restore barrier function over time.

Stress and Sleep Management

The gut-brain-skin axis means that chronic psychological stress directly harms the gut microbiome. Prioritizing quality sleep, incorporating mindfulness or stress reduction practices, and supporting one’s nervous system through regular movement are all evidence-supported strategies for improving both gut and skin health.

What to Expect from a Gut-Centered Eczema Treatment Plan

A gut-centered (inside) approach to eczema treatment does not replace topical (outside) eczema skin care, but instead, enhances it. Think of it as addressing the fire at its source rather than just cooling the surface. Most patients who follow a gut repair protocol alongside their dermatological care, i.e., an inside-outside approach, report a reduction in flare frequency and intensity within 8 to 12 weeks, though individual timelines vary based on the severity of dysbiosis.

The process typically begins with a gut microbiome test, followed by a consultation with a functional medicine practitioner, integrative dermatologist, or naturopath who can interpret results and develop a personalized plan. Repeat testing at three-to-six-month intervals can confirm whether the microbiome is shifting in the right direction, thereby allowing the protocol to be refined accordingly.

It is important to set realistic expectations since healing the gut is a gradual process. But unlike topical treatments that require daily application indefinitely, improving gut health can create lasting changes in immune regulation, thereby potentially reducing eczema severity for the long term.

Myths and Facts About Gut Health and Eczema

Myth: Eczema is purely a skin condition and cannot be treated from the inside.

Fact: Eczema is an immune-mediated condition with strong roots in internal health, including gut microbiome balance, hormonal function, and nutritional status. Internal interventions have significant, evidence-backed effects on eczema outcomes.

Myth: Gut microbiome tests are only for people with digestive disorders.

Fact: Gut microbiome imbalances can occur without obvious digestive symptoms. People with eczema, psoriasis, rosacea, and other inflammatory skin conditions frequently show measurable microbiome disruptions even without gastrointestinal complaints.

Myth: Probiotics are all the same.

Fact: Probiotic strains differ significantly in their effects. The specific strains shown to benefit eczema in clinical research include Lactobacillus rhamnosus GG and Bifidobacterium longum. Choosing an appropriate strain based on testing results yields far better outcomes than a generic supplement.

Myth: Diet changes alone can cure eczema.

Fact: Diet is a powerful tool, but it is one component of a comprehensive protocol. For many patients, lasting improvement requires a combination of dietary changes, targeted supplementation, stress management, and consistent eczema skin care.

Frequently Asked Questions (FAQ)

What are the gastrointestinal symptoms of eczema?

Many people with eczema experience digestive symptoms including bloating, abdominal cramping, loose stools, constipation, and nausea, especially after eating “trigger” foods. This occurs because eczema and gastrointestinal issues often share the same underlying driver: immune dysregulation rooted in gut microbiome imbalance. Research has found that children and adults with atopic dermatitis are significantly more likely to also have irritable bowel syndrome (IBS) and other functional gastrointestinal disorders. If your skin flares and your digestive discomfort tend to worsen together, this is a strong signal that the gut-skin axis is at play.

What is the gut protocol for eczema?

A gut protocol for eczema typically follows a structured approach: (1) Test — use a gut microbiome test to identify specific imbalances, dysbiosis, or intestinal permeability; (2) Remove — eliminate dietary triggers, inflammatory foods, and any harmful bacterial overgrowth; (3) Repair — use targeted nutrients like L-glutamine, zinc, and collagen to restore gut lining integrity; (4) Reinoculate — introduce beneficial bacteria through strain-specific probiotics and fermented foods; and (5) Rebalance — support long-term gut diversity through a high-fiber, anti-inflammatory diet and lifestyle changes. This five-step approach, often used by functional medicine practitioners, addresses the internal drivers of eczema alongside conventional eczema skin care.

What testing should be done for eczema?

A comprehensive evaluation for eczema should include:

·      a gut microbiome test (stool analysis) to assess microbial diversity and dysbiosis;

·      allergy skin prick testing (IgE-mediated) for environmental allergens;

·      organic acid testing (OAT) to provide a metabolic snapshot of overall health, evaluate intestinal microbial overgrowth (yeast/bacteria), mitochondrial function, neurotransmitter levels, and nutrient deficiencies;

·      blood tests including vitamin D, zinc, essential fatty acid levels, and complete blood count; and

·      hormone panels if hormonal triggers are suspected, given the link between itchy skin and hormone imbalance.

·      Patch testing may also be recommended by a dermatologist to identify contact allergens. Together, these tests provide a full picture of the internal and external factors driving your eczema.

Is eczema a liver or gut issue?

Eczema has connections to both liver and gut function, but research points most strongly to the gut as the primary internal driver. The gut microbiome directly regulates immune responses and inflammatory pathways central to eczema. The liver, meanwhile, plays a supporting role: it filters toxins from the bloodstream and processes inflammatory compounds. When the gut is permeable (leaky gut), the liver is exposed to a higher toxic load, which can amplify systemic inflammation and worsen skin conditions. So, while the gut is the more directly implicated organ in eczema, supporting liver detoxification pathways can also be a useful component of a comprehensive internal treatment protocol.

What vitamin deficiency causes eczema?

Several nutritional deficiencies are strongly associated with eczema. Vitamin D deficiency is among the most significant since vitamin D plays a critical role in immune regulation and skin barrier function, and low levels are consistently associated with higher eczema severity. Zinc deficiency impairs wound healing and weakens the skin barrier, making flares more frequent and harder to resolve. Omega-3 fatty acid deficiency reduces the skin's ability to maintain hydration and suppress inflammatory signals. Vitamin E and vitamin C both support antioxidant defense and skin repair. Deficiencies in these nutrients can often be identified through blood testing and correcting them through diet or supplementation is an important part of a holistic approach to how to repair gut microbiome and skin health simultaneously.

Conclusion

Eczema is a complex, multifactorial condition such that for many people, no amount of topical treatment will fully resolve it because the root cause lies deeper. The gut-skin axis is one of the most compelling frameworks in modern integrative medicine, offering a scientifically grounded explanation for why gut health so powerfully shapes the health of our skin.

A gut microbiome test is not just a diagnostic tool, but rather, it is a map. It shows you exactly where the imbalances lie and points you toward targeted, personalized strategies for improvement. Combined with evidence-based approaches on to how to repair gut microbiome health; dietary changes; use of certain types of probiotics; and alignment with thoughtful eczema skin care, a gut-centered approach represents the frontier of eczema treatment.

If you have been struggling with eczema and feel like you have tried everything, consider that you may not yet have looked in the right place. Talk to a healthcare provider experienced in functional or integrative dermatology about gut microbiome testing. Your skin may be trying to tell you something your gut already knows.

Call to Action

Have you tried a gut health approach to managing your eczema? If not, then you’ve definitely come to the right place because here at Codex Labs we’ve taken gut microbiome testing, consultation, and treatment to the next level.

Our recently launched dermatology-focused telehealth platform, DECODE.ME, represents a paradigm shift in chronic skin disorder treatment and management. By identifying the root cause(s) of chronic skin disorders like eczema and acne, followed by establishing an inside-out treatment regimen recommended by a member of our esteemed roster of tele-dermatology health professionals, both your gut and skin will thank you based on how they feel, and how good your skin looks!

Available via this platform is a series of testing kits including DECODE.MYGUT which, in addition to assessing the diversity and balance of a person’s gut microbiome, also tests for the presence of certain biomarkers which are indicative of leaky gut and intestinal inflammation. Because “knowledge is power” as the saying goes, this type of genetic testing can yield “powerful” insight/data into the condition (diversity) of an individual’s gut microbiome. With this critical information, more precise and effective treatment strategies can be developed to help rebalance the gut microbiome, fill-in any gaps in the gut’s intestinal lining, and give your body and skin the much needed relief it has been needing all along.

One specific test worth highlighting is the DECODE.MYHEALTH Organic Acids Test (OAT). It is a comprehensive, at-home urine assessment that analyzes 76 metabolites to provide a detailed "snapshot" of your metabolic and nutritional health. By measuring these chemical by-products, the test evaluates how effectively your body’s pathways are functioning, particularly within the skin-gut-brain-biome axis.

The OAT test provides the following:

·       Comprehensive Insight: It goes beyond basic blood work to assess mitochondrial function (energy), neurotransmitter balance (mood/stress), and microbial overgrowth (gut health).

·       Root Cause Discovery: The test identifies underlying genetic or lifestyle contributors to symptoms by highlighting nutrient deficiencies and toxic exposures.

·       Actionable Data: Results provide a roadmap for personalized diet modifications, detoxification strategies, and targeted supplementation to optimize your overall well-being.

Essentially, it’s a deep dive into your internal chemistry that translates complex biological data into a clear plan for feeling—and looking—better.

Once the necessary data has been obtained, and an appropriate treatment regimen identified, Codex is there to help you achieve your goal of keeping your gut healthy, balanced, and happy as can be seen by how great your skin looks and feels. To that end, Codex Labs has developed several dietary supplements meant to rebalance and restore the gut. These include:

-              BIA GUT BARRIER SUPPORT SET: a prebiotic + probiotic supplement set designed to improve skin barrier health by fortifying the gut barrier and supporting the immune system.  

-              BIA GUTBUILDER: a comprehensive prebiotic formulation of naturally derived prebiotic fibers, amino acids, antioxidants and superfoods to help digestion, increase immunity, support beneficial gut bacteria, fortify the intestinal barrier, increase collagen production, and soothe the lining of the gut.

 

While microbiome testing provides data, targeted products help support gut balance. Codex Labs develops science-backed formulations designed to support the gut-skin axis and overall barrier health. So, if you suspect that you may be experiencing some sort of “gut”-related issues impacting your skin health/appearance and overall well-being, or if you’re just curious, then Codex Labs has just the diagnostic tools to help you gain valuable insight into your gut’s condition. These diagnostic tools, coupled with easy access to dermatological consultations via the DECODE.ME platform, plus instant access to various innovative science-based treatment options, will help get your gut microbiome and barrier back to its happy place. How can we be so sure? Because we have the clinical data to prove it!

 

Visit the Codex Labs website: https://codexlabscorp.com

Explore their eczema-specific product line: https://www.codexlabscorp.com/collections/eczema

If you found this article helpful, subscribe to our blog for more evidence-based insights on skin health, the gut-skin axis, and integrative approaches to common skin conditions. And if you are ready to take the next step, visit Codex Labs to explore products formulated to support your skin from the inside-out.

 

References:

1.    https://pubmed.ncbi.nlm.nih.gov/22831283/

2.    https://pmc.ncbi.nlm.nih.gov/articles/PMC8070932/#:~:text=7.,)%20is%20stimulated%20%5B41%5D.

3.    https://nationaleczema.org/blog/eczema-teen-hormones/

4.    https://www.medparkhospital.com/en-US/disease-and-treatment/gut-microbiome-test

5.    https://pmc.ncbi.nlm.nih.gov/articles/PMC10741029/

6.    https://pmc.ncbi.nlm.nih.gov/articles/PMC10970750/

7.    https://pmc.ncbi.nlm.nih.gov/articles/PMC11107838/