3 Gut Tests That Could Unlock Your Healing

Welcome to Healthy Gut Healthy Thyroid!

This is your weekly roundup of the BEST actionable steps for those people with thyroid and autoimmune thyroid conditions who want to restore their health…by healing their gut. Whether you have hyperthyroidism or Hashimoto’s you will benefit from the content in this newsletter.

In today's issue:

• Main Topic: 3 Gut Tests That Could Unlock Your Healing

• Podcast Review: Never Eat These Foods with Hyperthyroidism

• Ask Dr. Eric: Is Itchy Skin Common In Thyroid Autoimmunity?

Three Gut Tests That Can Unlock Your Healing

When I dealt with Graves’ disease back in 2008–2009, I didn’t do any specific functional medicine testing for the gut. While I've since recommended a number of gut-related tests to many of my patients over the years, this isn’t something I recommend for every single person with a thyroid or autoimmune thyroid condition.

For instance, if someone is experiencing digestive symptoms but is also consuming a highly processed, nutrient-deficient diet, the priority should be to clean up the diet first. There's no point in investing in testing if foundational dietary habits haven’t been addressed.

That said, even in the absence of digestive symptoms, underlying gut imbalances may still exist—but that doesn’t mean every patient needs testing right away.

When Should You Consider Gut Testing?

While not every patient needs advanced gut testing, there are specific situations where it can be incredibly helpful:

✅ Persistent Digestive Symptoms. This can include ongoing bloating, gas, diarrhea, constipation, abdominal pain, or reflux that doesn’t resolve with dietary and lifestyle changes.

✅ Suspected SIBO (Small Intestinal Bacterial Overgrowth). This often presents as significant bloating, particularly after eating carbs or fiber, along with IBS-like symptoms. A history of food poisoning, abdominal surgery, or prolonged PPI use are also risk factors.

✅ Chronic or Unexplained Conditions Potentially Linked to the Gut. These include skin issues (e.g., eczema, psoriasis, acne), joint pain, fatigue, brain fog, or nutrient deficiencies like B12, iron, or vitamin D—despite supplementation.

✅ Thyroid Antibodies That Won’t Normalize. If someone has cleaned up their diet, managed stress, optimized adrenal function, and reduced toxic exposure but their antibodies remain high, then it’s time to look deeper into gut health.

✅ Clear Standard GI Testing but Ongoing Symptoms. If tests like colonoscopy, endoscopy, abdominal imaging, or celiac panels are normal—but symptoms persist—functional gut testing is often the next best step.

✅ Poor Response to Standard Interventions. When diets like low FODMAP or strategies like fiber modulation and probiotics don’t lead to improvements, gut testing can uncover hidden imbalances.

The 3 Best Functional Medicine Gut Tests

Test #1: Comprehensive Stool Analysis (e.g., GI-MAP, GI Effects)

What It Measures:

• Digestive markers (e.g., elastase, steatocrit)

• Gut microbiome diversity and balance

• Pathogens (e.g., H. pylori, parasites, viruses)

• Inflammatory markers (e.g., calprotectin, secretory IgA)

Why It’s Valuable:

This is my go-to test for detecting hidden infections, gut inflammation, and microbial imbalances. It provides insight into digestive function, immune activation in the gut, and how well the microbiome is functioning overall.

Test #2: SIBO Breath Test

What It Measures:

Hydrogen and methane gas production after consuming a sugar solution (usually lactulose or glucose)

Why It’s Valuable:

SIBO is a common underlying cause of gas, bloating, and post-meal discomfort—especially after FODMAP-rich foods. It can also increase intestinal permeability (leaky gut), contribute to nutrient deficiencies, and drive inflammation.

Test #3: Organic Acids Test (OAT)

What It Measures:

• Metabolic byproducts from bacteria and yeast

• Mitochondrial function

• B-vitamin status

• Detox and oxidative stress markers

Why It’s Valuable:

The OAT is one of the best tools for detecting yeast overgrowth, including Candida, which can sometimes be missed on stool testing. It also assesses for Clostridia species, which can be a treatment priority if present, and gives insight into systemic metabolic health beyond just the gut.

What About Leaky Gut Testing?

Some people ask about testing for intestinal permeability, such as:

✔️ Cyrex Labs’ Array #2

✔️ Lactulose/Mannitol test

✔️ Zonulin levels

While these tests can help determine whether a leaky gut is present, they don’t tell us why it’s happening. And in clinical practice, I typically assume a compromised gut barrier in most autoimmune patients and move forward with supportive protocols. However, if a patient strongly prefers confirmation through testing, I’m happy to order it.

Conclusion

Functional medicine gut testing isn’t for everyone—but it can be a powerful tool for those with persistent symptoms, autoimmune conditions, or unexplained health concerns. Tests like the GI-MAP, SIBO breath test, and OAT can reveal what conventional labs often miss and provide a roadmap to healing.

If you’ve been doing everything “right” but still aren’t improving—or if your thyroid antibodies won’t budge—it might be time to look deeper into your gut.

Save My Thyroid Podcast Review

I have a podcast called "Save My Thyroid", where I discuss how people with hyperthyroidism and Hashimoto's can save their thyroid and regain their health. And during each edition of this newsletter I'll briefly discuss a recent podcast episode.

In a recent podcast episode I discussed which foods you should avoid if you have hyperthyroidism. This episode lays out a foundational overview of foods that are best avoided when healing from hyperthyroidism or Graves’ disease. I cover the “big ones” like gluten, dairy, refined sugar, alcohol, and grains, as well as the less obvious culprits. I also explain the reasoning behind these recommendations, including gut permeability, immune reactivity, and long-term thyroid stability. You’ll leave with a clearer sense of which foods might be interfering with healing, even if they don’t cause obvious symptoms.

Click Here if you’re overwhelmed with conflicting diet advice and want a grounded place to start.

Ask Dr. Eric

During every issue I'll answer a question or two that I think can benefit most people with a thyroid or autoimmune thyroid condition. If you'd like for me to consider your question for a future edition of this newsletter email your question to [email protected].

QUESTION: IS ITCHY SKIN COMMON IN THYROID AUTOIMMUNITY?

Has anyone been diagnosed with Graves' disease had super itchy skin as a symptom? My legs get extremely itchy each night.

This question came up in my Graves' Disease and Hashimoto's Natural Solutions Support Group, and while it was asked specifically in relation to Graves' disease, skin issues—particularly itching—are common among people with both Graves’ disease and Hashimoto’s thyroiditis.

Understanding the underlying cause of itchy skin is essential for addressing it effectively. Although many assume it’s always due to histamine, the reality is that itching can stem from multiple root causes—many of which are highly relevant to those with thyroid autoimmunity.

Common Causes of Itchy Skin

Some of the most common causes of itching include:

• Dry skin

• Diabetes

• Impaired bile flow

• Medication side effects

For those with hyperthyroidism, medications like methimazole can sometimes cause skin rashes or itching. If you're on antithyroid medication and notice persistent itching, speak with your healthcare provider.

The Role of Histamine in Itching

Histamine is one of the best-known mediators of itching. It acts on H1 receptors found on sensory nerve fibers in the skin. While histamine plays a major role in conditions such as urticaria (hives), other biochemical mediators can also be involved, including:

• Acetylcholine

• Pro-inflammatory cytokines

• Endogenous opioids

• Prostaglandins

This means itching isn’t always a “histamine problem,” so blindly following a low histamine diet or taking antihistamines may not address the root cause.

Gut Health and Itchy Skin

A compromised gut is often at the root of chronic skin issues, including itching. Dysbiosis, intestinal permeability (“leaky gut”), and food sensitivities can all trigger immune responses that show up on the skin.

If you’re eating inflammatory foods like gluten, or if you’re dealing with unresolved gut infections or imbalances, healing the gut could be the missing link to resolving your skin symptoms.

Strategies to Help Relieve Itchy Skin

Here are a few steps you can take to reduce or eliminate itchy skin:

✅ Follow an Elimination Diet

An autoimmune Paleo (AIP) diet is often helpful for those with thyroid autoimmunity, as it removes many common food triggers. This can help lower systemic inflammation and reduce immune reactivity.

✅ Consider a Low Histamine Diet

If histamine is a suspected contributor, try eliminating high-histamine foods like:

• Fermented foods (e.g., sauerkraut, pickles)

• Shellfish

• Smoked meats

• Aged cheeses

• Alcohol

✅ Reduce Inflammation

Since inflammatory cytokines and prostaglandins can trigger itching, reducing systemic inflammation is essential. This includes addressing chronic infections, removing food sensitivities, and supporting detoxification pathways.

✅ Heal the Gut and Support Immune Balance

Both Graves’ disease and Hashimoto’s are autoimmune conditions, and since 70–80% of the immune system resides in the gut, restoring gut integrity is critical to calming immune-related skin symptoms.

✅ Address Dry Skin

Dry skin doesn’t always lead to itching, but it can be a contributing factor. Causes of dry skin can include:

• Low thyroid hormone levels (especially in Hashimoto’s)

• Nutrient deficiencies (e.g., omega-3 fatty acids, zinc, vitamin A)

Make sure thyroid levels are properly managed and that nutrient needs are met through diet or supplementation.

✅ Support Liver and Kidney Detoxification

The liver and kidneys play a central role in detoxification. When overburdened, skin issues like itching may occur. Support these organs through:

• A diet rich in vegetables and filtered water

• Herbal support such as milk thistle, dandelion, and NAC

• Glutathione or glutathione precursors to support detoxification

✅ Consider Natural Antihistamine Support

Natural compounds that may help reduce histamine load include:

• Quercetin

• Vitamin C

• DAO (diamine oxidase) enzymes (help degrade dietary histamine)

Additional Thyroid-Related Resources

Click Here for Never Eat These Foods With Hyperthyroidism (episode 211)

Click Here to access hundreds of thyroid-related articles and blog posts

Click Here to join the Graves’ disease and Hashimoto’s community

Click Here to purchase one of Dr. Eric’s thyroid-related books

Click Here to work with Dr. Eric and his team

That’s a wrap