Can You Heal Your Gut If You're Taking Methimazole or PTU?

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: Can You Heal Your Gut If You're Taking Methimazole (or PTU)?

• Podcast Review: What Happens When Hormones Get Unbalanced?

• Ask Dr. Eric: Are low Akkermansia levels a concern?

Can You Heal Your Gut if You’re Taking Methimazole or PTU?

If you have hyperthyroidism (i.e. Graves’ disease, toxic multinodular goiter) and are taking antithyroid medication like methimazole (MMI) or PTU, you may be wondering: Can I still heal my gut while on these drugs?

The short answer: Yes, but you’ll want to be mindful of how these medications can affect intestinal health and take supportive steps accordingly. Let’s explore the research, the risks, the benefits, and practical strategies.

What the Research Shows: Effects of Antithyroid Drugs on the Gut

Negative Gut and Microbiome Impact. A 2020 study found that antithyroid drugs altered gut microbiota structure and were associated with increased markers of bacterial translocation and liver injury.¹

A 2022 observational study in Graves’ patients treated with methimazole found that after treatment the intestinal flora had significant changes — less bacterial diversity, shifts in genera such as Bifidobacterium, Collinsella, Bacteroides, Prevotella.²

A review on thyroid–microbiome interactions noted that antithyroid drugs (ATDs) “can change the gut microbiota structure” in both animal and human models.³

These findings suggest that taking methimazole or PTU may contribute to gut dysbiosis and possibly to increased intestinal permeability (“leaky gut”). This is relevant because barrier dysfunction, microbial imbalance, and endotoxin (LPS) translocation are factors in thyroid autoimmunity and systemic inflammation.

Evidence of Potential Benefit

A recent paper compared gut microbiota before and after antithyroid drug treatment in Graves’ patients and found that certain microbiome features improved after treatment—suggesting that controlling the hyperthyroid state may in itself help restore microbiome balance.⁴

Another study found that supplementation with the probiotic Bifidobacterium longum alongside methimazole improved thyroid indices in Graves’ patients (reduced TRAb) via the gut–thyroid axis.⁵

In other words: while the medication may impact the gut, controlling hyperthyroidism may itself reduce microbial and immune stress. Plus, taking a probiotic supplement can also provide some great benefits.

Weighing Risks vs. Benefits

The benefits you must keep in mind

Methimazole and PTU are commonly recommended for hyperthyroidism by endocrinologists, and while side effects are common, they usually do a good job of lowering thyroid hormone levels.

When untreated, hyperthyroidism itself causes significant metabolic stress, increased gut motility, malabsorption, weight loss, and decreased bone density.

Therefore, the benefit of normalizing thyroid hormones usually outweighs the potential gut effects — especially when managed proactively.

That being said, there are natural alternatives to consider, such as the herb bugleweed, which is what I took when I personally dealt with Graves' disease. However, not everyone can successfully manage their hyperthyroidism naturally.

The risks you should address

• Altered gut microbiome composition (less beneficial bacteria, more opportunistic bacteria) — potential risk for dysbiosis.

• Possible increase in intestinal permeability (leaky gut) due to drug-induced barrier disruption.

• Secondary nutrient absorption issues (if the gut is compromised), which may further affect thyroid, immune, and metabolic health.

So: Can You Heal Your Gut While Taking Antithyroid Drugs?

Yes — absolutely. Here’s how:

✅ Control the thyroid first. Keeping TSH, free T4 and free T3 within target range helps reduce stress on the body and the gut.

✅ Use gut‑supportive strategies as you go. Think of them as “parallel therapy” to your antithyroid medication.

Implement a gut‑healing protocol while on medication:

✅ Improve microbiome diversity: include a wide variety of fiber‑rich plant foods, fermented foods, and rotate probiotic supplements if tolerated.

✅ Support the intestinal barrier: nutrients such as L‑glutamine, zinc carnosine, N‑acetyl‑glucosamine, aloe vera, deglycyrrhizinated licorice (all of which are in SMT-GI Restore).

✅ Address dysbiosis: if you suspect SIBO, yeast overgrowth, parasites — test or use clinically guided treatment protocols under the guidance of an expert.

✅ Balance diet and lifestyle: reduce refined carbs, sugar and processed foods (which worsen dysbiosis). Manage stress, ensure 7–9 hours of sleep, and exercise moderately.

✅ Monitor nutrients: thyroid medication use plus an impaired gut can reduce the absorption of selenium, iron, vitamin D, and zinc: test periodically and replete as needed.

Practical Scenario & What to Do

If you’ve just started methimazole: It’s a good time to begin gut‑supportive measures concurrently so that the microbiome disruption is minimized rather than treated after the fact.

If you’ve been on antithyroid drugs for some time and have gut symptoms (bloating, irregular stools, food sensitivities): ask for a stool microbiome or comprehensive stool panel (i.e. GI-MAP), test for SIBO if indicated, assess nutrient status, and implement a full gut‑healing plan.

If thyroid hormones are unstable (still hyperthyroid or flip‑flopping): work with your endocrinologist to optimize dose or consider adjunct therapies—and use gut‑support as part of the overall healing strategy. You’ll probably need to work with a natural healthcare practitioner for this.

Conclusion

Taking methimazole or PTU does not mean you have to give up on gut healing. It simply means you need to adopt a smarter, dual‑focused approach: treat the hyperthyroid condition and simultaneously support your gut.

The research shows that antithyroid drugs can alter the microbiome and barrier function—but also that treating hyperthyroidism may allow the gut to recover. With the right nutrition, lifestyle support, and targeted gut‑healing interventions, you can work toward restoring your gut health even while on medication.

If you’re navigating hyperthyroidism, thyroid autoimmunity, or gut dysfunction, consider reaching out for integrative support — and know that healing your gut and your thyroid can go hand in hand.

Graves’ Disease Survival Roadmap Training

Recently I released a new training called "The Graves' Disease Survival Roadmap", which you can find in my new Healing Graves' Naturally Skool Community. It is completely free, and includes eight modules.

 Click Here to access the free training

As for the community, if you have Graves’ disease you’ll want to check out this community, as includes the following:

🚀 A community for those with Graves' disease and other types of hyperthyroidism looking to regain their health and avoid RAI and surgery.

💥 When someone is diagnosed with Graves' disease by an endocrinologist, the three options given are 1) antithyroid medication, 2) radioactive iodine, and 3) thyroid surgery.

While there is a time and place for conventional treatment, since 2009 I've been helping people with Graves' disease regain their health naturally and avoid RAI and surgery

Join to access the following:

✅ FREE Graves' Survival Roadmap Training

✅ FREE Monthly Hyperthyroid Healing Diet Q & A call

✅ 24/7 Community Access

 Click Here to join the community access the free training

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 episode I chatted with Bria Gadd, also known as "The Period Whisperer", about hormone imbalances. In this conversation, Bria shares her own perimenopause journey and the lessons that shaped her work from understanding health debt to managing stress and supporting gut health. We also discuss metabolic typing, including the concept of “oxidizers” how your body’s rate of turning food into fuel can influence whether you thrive on higher-protein or higher-carbohydrate foods.

Tune in now for clear, compassionate guidance that can help you feel stronger and more balanced at any age.

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: ARE LOW AKKERMANSIA LEVELS A CONCERN?

Dr. Eric, I did a GI-MAP which showed very low Akkermansia muciniphila levels, and I was wondering if this could prevent my gut from healing?

Thanks for your question! Although I don’t run a comprehensive stool panel on every patient, I’ve reviewed many GI-MAP results over the years. It’s quite common to see less-than-detectable or low levels of Akkermansia muciniphila, even in people who aren’t experiencing severe gut symptoms.

So, is this something to worry about? And more specifically, could low Akkermansia levels stand in the way of gut healing?

What is Akkermansia muciniphila and Why Does It Matter?

Akkermansia muciniphila is a mucin-degrading bacterium that belongs to the phylum Verrucomicrobia.⁶ It plays a critical role in maintaining the intestinal mucus layer, which serves as a physical barrier protecting the gut lining from harmful substances. This mucus-degrading activity may sound counterintuitive, but Akkermansia also stimulates mucin production, effectively helping to maintain the integrity of the intestinal barrier.

Its presence has been associated with:

• Improved gut barrier function

• Reduced intestinal permeability ("leaky gut")

• Better metabolic and immune regulation

Given that increased intestinal permeability is part of the triad of autoimmunity I've discussed in the past, it’s reasonable to conclude that low Akkermansia levels may contribute to—or make it more difficult to reverse—a leaky gut.

Should You Take an Akkermansia Supplement?

The next logical question is: If my Akkermansia is low, should I take a supplement to raise it?

That depends on who you ask. Some practitioners recommend supplementing right away, especially if the levels are undetectable. Others (myself included) prefer to first try natural, diet-based strategies to promote the growth of this beneficial bacterium—especially since the body often responds more favorably to food-based inputs when it comes to microbiome diversity and resilience.

A review article entitled “Strategies to Promote the Abundance of Akkermansia muciniphila” outlined a few research-backed ways to boost its levels naturally:⁷

✅ Prebiotic fiber supplementation (e.g., inulin, fructooligosaccharides)

🍓 Polyphenol-rich foods (especially berries, cranberries, pomegranate, and green tea)

🥗 Intermittent fasting or caloric restriction in some cases

❌ Avoiding ultra-low-fiber diets like long-term strict low-FODMAP or carnivore diets

When to Consider Supplementing

If you’ve already optimized your diet to include fiber and polyphenol-rich foods, and your gut symptoms are still present—or you re-test and Akkermansia levels are still low—then supplementation might be worth considering. While more research is needed on long-term supplementation, early studies show that taking Akkermansia may have benefits for gut barrier integrity and metabolic health.

That said, supplementation should always be part of a comprehensive plan that includes dietary and lifestyle changes—not a replacement for them.

Additional Thyroid-Related Resources

Click Here for What Happens When Hormones Get Unbalanced? (episode 218)

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

References:

Click Here to access the references

That’s a wrap