IBS vs. IBD: Key Differences, Thyroid Connection, and Natural Solutions

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: IBS vs. IBD: Key Differences, Thyroid Connection, and Natural Solutions

• Podcast Review: What Does Trauma Have to do With Thyroid Health?

• Ask Dr. Eric: Can I eat fermented foods instead of taking a probiotic supplement?

IBS vs. IBD: Key Differences, Thyroid Connection, and Natural Solutions

Many people with thyroid and autoimmune thyroid conditions experience digestive challenges. While I’ve previously written about gut imbalances like leaky gut and dysbiosis, in this edition of the newsletter I want to focus on two often-overlooked conditions that frequently intersect with thyroid autoimmunity: Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD)—which includes Crohn’s disease and ulcerative colitis.

What Is Irritable Bowel Syndrome (IBS)?

IBS is a functional gastrointestinal disorder affecting an estimated 11% of people worldwide.¹ It’s characterized by chronic abdominal discomfort, bloating, gas, and changes in bowel habits—ranging from constipation to diarrhea, or a mix of both. Most individuals with IBS report lower abdominal pain, a hallmark symptom of the condition.

IBS Subtypes:

• IBS-D: Diarrhea-predominant

• IBS-C: Constipation-predominant

• IBS-M: Mixed type

Common Triggers:

✔️ Gut infections

✔️ Antibiotic use

✔️ Stress

✔️ Food sensitivities

✔️ Dysbiosis and small intestinal bacterial overgrowth (SIBO)

Conventional treatment includes antispasmodics, laxatives, SSRIs, and newer agents targeting serotonin and chloride channels. However, these don’t address the underlying imbalances contributing to the condition.

The IBS-SIBO Connection

SIBO is a major contributor to IBS symptoms. I’ve discussed SIBO in a previous newsletter, as in this condition excessive bacteria populate the small intestine where they don’t belong—leading to fermentation, gas, bloating, and irregular stools. Research shows a strong association between IBS and SIBO, particularly in those with IBS-D.

The gold standard for diagnosis is a hydrogen/methane breath test. Once confirmed, treatments may include:

✅ Antibiotics like rifaximin

✅ Herbal antimicrobials (e.g., berberine, oregano oil)

✅ Motility agents such as ginger, 5-HTP, or Iberogast

✅ Support for digestion (enzymes, HCl) and gut barrier integrity

Without addressing motility, many people relapse—so prokinetic support is often key to long-term healing.

Breakthrough in IBS Testing: CdtB and Vinculin Antibodies Emerging research has linked post-infectious IBS to autoimmune responses triggered by acute food poisoning or gastroenteritis. This results in antibodies forming against:

➤ CdtB (Cytolethal Distending Toxin B)

➤ Vinculin, a protein involved in gut motility

These antibodies damage the interstitial cells of Cajal (which regulate peristalsis), contributing to poor motility and SIBO. Fortunately, blood tests now exist to measure CdtB and anti-vinculin antibodies, helping to definitively confirm IBS as an autoimmune gut motility disorder.

What Is Inflammatory Bowel Disease (IBD)?

Unlike IBS, IBD is an inflammatory and often autoimmune condition affecting the GI tract lining. The two primary forms include:

• Crohn’s Disease (can affect any part of the GI tract)

• Ulcerative Colitis (affects only the colon)

Over 1.5 million Americans live with IBD, and incidence is rising globally. Symptoms often include:

• Persistent diarrhea

• Abdominal cramping

• Weight loss

• Fatigue

• Extraintestinal symptoms (joint pain, skin rashes, eye inflammation)

The exact cause remains unclear, but contributors include:

✅ Genetic predisposition

✅ Gut microbiome imbalances

✅ Immune dysregulation

✅ Environmental triggers

Markers of Inflammation: IBS vs. IBD

IBS is a non-inflammatory condition, while IBD involves significant intestinal inflammation. Blood tests like CRP and ESR are general inflammation markers, but stool-based markers provide more gut-specific insight:

If calprotectin and lactoferrin are normal, IBD is unlikely. If elevated, further investigation (e.g., colonoscopy) may be warranted.

The Thyroid-IBD Autoimmunity Link

Research shows a potential association between autoimmune thyroid disease and IBD.

Some studies suggest:^2,3

✔️ Increased prevalence of thyroid autoantibodies in those with IBD

✔️ Case reports of simultaneous Hashimoto’s and ulcerative colitis

✔️ Higher rates of hypothyroidism in Crohn’s patients

However, larger studies have shown inconsistent results. In contrast, the link between thyroid disease—especially hypothyroidism—and IBS/SIBO is much stronger.

Why? Hypothyroidism slows GI motility, making SIBO more likely. And since SIBO contributes to IBS, the connection becomes clearer. That said, I’ve also seen Graves’ disease patients struggle with SIBO, even though they typically have accelerated gut transit.

Natural Approach to IBS and IBD

Both IBS and IBD benefit from a personalized, gut-focused approach. I commonly use a 5R Framework I’ve discussed in previous newsletters, which includes:

1. Remove: Inflammatory foods (gluten, dairy, processed oils), infections (H. pylori, parasites), toxins that disrupt the gut

2. Replace: Digestive enzymes, HCl or bile salts (if needed), missing nutrients

3. Reinoculate: Probiotics (if tolerated) , prebiotic foods (as tolerated, especially for IBS)

4. Repair: Gut-healing nutrients (L-glutamine, zinc, vitamin A), bone broth, cabbage juice, deglycyrrhizinated licorice

5. Rebalance: Stress reduction, improved sleep, nervous system support (vagus nerve stimulation, breathwork)

Final Thoughts

IBS and IBD are distinct, but both can impact thyroid health and vice versa. If you have an autoimmune thyroid condition and unexplained GI symptoms, consider:

• Testing for SIBO

• Evaluating inflammatory markers

• Exploring food sensitivities

• Supporting gut function with a structured, step-by-step approach

And if you’ve already been diagnosed with IBS or IBD, addressing gut health and autoimmunity together may help uncover overlooked triggers—and lead to better outcomes.

Which Hyperthyroid Healing Diet Should You Follow?

There’s no single diet that everyone with hyperthyroidism should follow. Diet selection is a highly personal choice that must consider individual health conditions, lifestyle, and preferences.

In my book, The Hyperthyroid Healing Diet, I explore three different diets in detail, explaining what each involves and how you can start implementing the right one for you. This book will benefit those with Graves' disease, toxic multinodular goiter, and subclinical hyperthyroidism.

There is a lot of confusion when it comes to the foods people with hyperthyroidism should eat and which ones they should avoid, and the truth is that there isn’t a single diet that fits everyone perfectly. That’s why The Hyperthyroid Healing Diet doesn’t just focus on one diet, but instead gives multiple diet options, while at the same time guiding you towards the one most suitable for your situation and condition.

Note: those who purchase The Hyperthyroid Healing Diet will also gain access to the online resources, which includes dozens of recipes, checklists related to the different diet options, and a few bonus chapters not included in the book.

By reading this book you will discover the following:

✅ The ideal diet for Graves’ disease, toxic multinodular goiter, subacute thyroiditis, and subclinical hyperthyroidism

✅ Hidden sources of common allergens and other ingredients to avoid 3 ways to detect specific food triggers

✅ How much protein those with hyperthyroidism should consume on a daily basis

✅ The truth about food sources of iodine

✅ How to increase muscle mass and bone density

✅ What diet you should follow if you’re a vegan or vegetarian

✅ Addressing weight loss and weight gain concerns

✅ What you need to do to achieve optimal adrenal health How to optimize your adrenals, improve sleep quality and duration, and heal your gut

✅ And much, much more!

Click Here to Order the Hyperthyroid Healing Diet

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 the relationship between trauma and thyroid health. Some, if not many, roadblocks behind thyroid healing have a covert driver that only a few doctors ask about: unresolved trauma.

Trauma can keep the nervous system in a constant state of high alert, which may cause the immune system to remain overactive and antibodies to stay elevated. Even if you’re eating well, supporting your gut, and managing stress today, past trauma can still influence how your body responds.

This doesn’t mean trauma is always the root cause and the answer, but it’s often overlooked in both conventional and functional medicine. In this episode, I share how trauma may affect thyroid health and why addressing it could open new doors for healing when efforts seem to no avail.

Tune in to discover how processing old trauma may be the answer in lowering thyroid antibodies and moving your healing forward.

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: CAN I EAT FERMENTED FOODS INSTEAD OF TAKING A PROBIOTIC SUPPLEMENT?

Dr. Eric, I see that you recommend probiotic supplements, but what are your thoughts about eating fermented foods instead?

Thank you for your question! While I personally take and recommend high-quality probiotic supplements like SMT-Probio, I also encourage incorporating probiotic-rich foods into your diet. But a common question I receive is: Can fermented foods offer the same benefits as probiotic supplements?

To help explain this, I often compare it to the question of whether someone can rely on Brazil nuts for selenium instead of taking a supplement. Brazil nuts are a great whole food source of selenium, and I enjoy eating them myself. However, when working with patients, I usually recommend a selenium supplement—because the selenium content in Brazil nuts can vary widely.

One nut might contain 20 mcg of selenium, while another might contain 80 mcg. So if you're eating three nuts a day, you might be getting 60 mcg—or as much as 240 mcg. Supplements, on the other hand, provide a consistent and reliable dose.

If You’re Planning to Rely on Fermented Foods…

I understand that probiotic supplements—especially high-quality ones—can be costly. And I generally advise rotating probiotics to expose the gut to a variety of beneficial strains. If you're consuming a diverse array of fermented foods daily, you may be able to rely less on supplements.

The challenge is that most people don’t eat enough fermented foods, or they eat the same type repeatedly (e.g., only sauerkraut). Many also don’t consume them on a consistent, daily basis. We now understand that a high diversity of gut bacteria is essential for optimal health. If you plan to rely on food-based sources, it's critical to include a variety of fermented foods in your daily routine.

Here are a few examples to consider:

• Sauerkraut

• White kimchi (a nightshade-free option)

• Pickled vegetables (raw and unpasteurized)

• Unsweetened coconut yogurt

Whenever possible, homemade fermented foods are ideal, as they typically contain higher levels of live cultures. If you’re buying them, look for raw, unpasteurized options kept in the refrigerated section—these are more likely to contain active probiotics.

Why Not Do Both?

You don’t necessarily need to choose either fermented foods or supplements—you can do both. While I personally take a daily probiotic with well-researched strains, I understand not everyone can commit to this daily expense. In such cases, you might consider taking a probiotic three or four times per week, and rely on a variety of fermented foods the other days.

Ultimately, I’ve been consistently taking probiotics for years—but if you enjoy fermented foods, I absolutely encourage including them in your diet. They can be a powerful part of a gut-healing lifestyle, especially when consumed regularly and with variety.

Additional Thyroid-Related Resources

Click Here for What Does Trauma Have To Do With Thyroid Health? (episode 217)

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