SIBO and Hashimoto's: The Gut-Thyroid Connection

Table of Contents

1. The SIBO and Hashimoto's Connection
2. Why Hashimoto’s Can Increase the Risk of SIBO
3. How SIBO Can Affect Thyroid and Immune Function
4. The 3-Step Approach to Solving SIBO
5. Natural Ways to Support Thyroid Health with Hashimoto’s
6. Heal Your Gut and Restore Digestive Balance
7. FAQs

If you have Hashimoto's and your digestion has never felt quite right, that connection is very real. "The gut is the gateway to health," and in my years of practice, small intestinal bacterial overgrowth, or SIBO, was one of the most common gut issues I saw in my Hashimoto's patients. Research continues to confirm a strong link between the two.

Hashimoto's thyroiditis is the autoimmune form of hypothyroidism, which means it is driven by your immune system, and your immune system largely lives in your gut. Here, I want to show you exactly how SIBO and Hashimoto's feed into each other, how SIBO is treated, and how I approach healing the gut to support the thyroid, all through functional medicine.

The SIBO and Hashimoto's Connection

Your gut and your thyroid are in constant conversation. Roughly 20% of your inactive T4 is converted into active T3 in your gut, so when your gut is out of balance, your thyroid feels it. SIBO occurs when bacteria overgrow in your small intestine, and as I often say, too much of a good thing can be a bad thing.

The relationship is bidirectional, a true chicken-or-egg cycle. Hashimoto's can set the stage for SIBO, and SIBO can worsen Hashimoto's. Because they appear together so often, I recommend looking into SIBO whenever thyroid and digestive symptoms show up side by side. If you are new to this diagnosis, my overview of what your endocrinologist isn't telling you about Hashimoto's is a helpful companion to this piece.

Why Hashimoto’s Can Increase the Risk of SIBO

Hashimoto’s can lead to an underactive thyroid, slowing metabolic processes throughout the body, including digestion and intestinal motility. This can create several conditions that allow bacteria to accumulate in the small intestine:

• Food moves through the digestive tract more slowly, giving bacteria more time to multiply.

• Reduced motility can interfere with the migrating motor complex, the wave-like movement that helps clear bacteria from the small intestine between meals.

• Low stomach acid (HCl), which is common with thyroid dysfunction, can impair digestion and make it easier for bacteria to survive.

Together, these changes help explain why people with Hashimoto’s may be more likely to experience SIBO.

How SIBO Can Affect Thyroid and Immune Function

The connection can work in the opposite direction. An imbalanced gut microbiome may interfere with the conversion of T4 into active T3, potentially contributing to persistent thyroid-related symptoms even when you're taking supplemental thyroid hormone.

SIBO may also contribute to increased intestinal permeability, commonly called leaky gut. When the tight junctions lining the small intestine become compromised, microbes, toxins, and partially digested food particles can enter the bloodstream and activate an inflammatory immune response. This ongoing immune activity may further disrupt thyroid health in people with Hashimoto’s. Understanding what causes autoimmune disease can provide additional context for this connection.

The 3-Step Approach to Solving SIBO

Not everyone with SIBO experiences noticeable symptoms, which is one reason it can go undiagnosed. In fact, an estimated 6% to 15% of healthy, asymptomatic individuals and roughly 50% of people with IBS may also have SIBO. To help support digestive balance and overall gut health, I use a three-step approach that is also included in the SIBO Support Protocol, along with targeted tools and guidance.

Step 1: Starve the overgrown bacteria

• Remove: sugar in all of its simple forms, such as candy, desserts, alcohol, and flours.

• Limit: starchy vegetables, fruit.

Start by removing foods that feed bacteria in the small intestine. This includes sugar, alcohol, and carbohydrates. Bread, cookies, cake, whole grains, and legumes all break down into sugar and fuel bacterial overgrowth.

Also, avoid fermented foods such as sauerkraut, kombucha, kimchi, and kefir. These can worsen symptoms during this phase.

Focus on non-starchy vegetables, leafy greens, lean protein, and healthy fats, with minimal fruit.

Step 2: Disrupt and Prune Back the overgrowth of bacteria

• Biofilm Disruptor is designed to support microbial balance and gut health by disrupting biofilms.

• Microb-Clear® to prune back the overgrowth of bacteria.

Start with Biofilm Disruptor to break down the protective layer that shields bacteria. This step helps antimicrobials work more effectively.

In my practice, I often prescribed Xifaxan and Neomycin to target bacterial overgrowth. Xifaxan is more effective for hydrogen-dominant SIBO, while Neomycin is more effective for methane-dominant cases. These options target harmful bacteria with less disruption to beneficial microbes, but they are generally not covered by insurance and can cost thousands of dollars, and often do not work. For this reason, I had to come up with an alternative for my patients — Microb-Clear® is that!

Microb-Clear®. This blend of magnesium caprylate, berberine, and herbal extracts helps promote bacterial balance. It offers a more gentle approach compared to broad-spectrum antibiotics.

Step 3: Restore and Balance

• Restore with Primal Earth Probiotic supports a healthy gut environment without adding to unwanted bacterial overgrowth.

• Balance with ImmuneIG to add beneficial immunoglobulins and facilitate a healthy inflammatory response.

You can follow the SIBO-fighting steps conveniently with my SIBO Solution Protocol. All of my supplements are physician-formulated and free of gluten, wheat, dairy, corn, soy, GMOs, and yeast.

Natural Ways to Support Thyroid Health with Hashimoto’s

Healing your gut is one of the most powerful steps you can take for Hashimoto's, and it works best as part of a bigger picture. Because Hashimoto's is autoimmune, the goal is to calm the immune attack by addressing its root causes through The Myers Way®. That means removing gluten, one of the most significant triggers of gluten-driven thyroid dysfunction, reducing your toxic burden, and relieving your stress.

Filling the nutrient gaps that so often accompany Hashimoto's matters too. The Hashimoto's Health Bundle brings together targeted support for your thyroid and immune system in one place. For more ways to reclaim your energy, my guide on restoring your health with Hashimoto's walks you through the daily habits that make the biggest difference. Always work with your practitioner to monitor your labs and your supplemental thyroid hormone along the way.

Heal Your Gut and Restore Digestive Balance

I always remind my patients that "If your gut is not healthy, neither are you." When you address SIBO and heal your gut, you remove one of the biggest obstacles standing between you and calmer thyroid autoimmunity. That is the heart of The Myers Way®, and it is exactly what I walk you through in The Thyroid Connection™.

FAQs

• How are SIBO and Hashimoto's connected?
  SIBO and Hashimoto's are connected through a two-way relationship centered on your gut. Hashimoto's slows digestion and gut motility, creating conditions for bacteria to overgrow in your small intestine. In turn, SIBO reduces your gut's ability to convert inactive T4 into active T3 and contributes to leaky gut, a primary trigger of autoimmunity. In Hashimoto's, that leaky gut keeps your immune system attacking your thyroid. Because each condition drives the other, they frequently appear together, which is why I recommend investigating SIBO whenever thyroid and digestive symptoms overlap.
• Can addressing SIBO improve my Hashimoto's?
  Addressing SIBO can meaningfully support your thyroid because a healthier gut improves the conversion of T4 into active T3 and reduces the leaky-gut-driven inflammation that fuels thyroid autoimmunity. Resolving SIBO is not a replacement for working with your practitioner on supplemental thyroid hormone. Instead, healing your gut removes one of the root-cause obstacles standing between you and calmer Hashimoto's, which is exactly what the functional medicine approach is designed to do.
• Should I test for SIBO if I have Hashimoto's?
  Yes, especially if you have digestive symptoms such as bloating, gas, diarrhea, or constipation alongside your thyroid symptoms. Because SIBO and Hashimoto's so frequently occur together, identifying and addressing an overgrowth can be an important part of your recovery. Keep in mind that testing can require more than one sample, and symptoms alone can be a strong signal. Work with a practitioner who understands the gut-thyroid connection so you can address both together, not in isolation.