Immune Tolerance: The Overlooked Key to Preventing and Reversing Thyroid Autoimmunity

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: Immune Tolerance: The Overlooked Key to Preventing and Reversing Thyroid Autoimmunity

• Podcast Review: The Overlooked Link Between Brain Healing and Thyroid Health

• Ask Dr. Eric: What Should I Do if I Can’t Tolerate Probiotic Supplements?

Immune Tolerance: The Overlooked Key to Preventing and Reversing Thyroid Autoimmunity

In the previous newsletter, I spoke about food allergies, sensitivities, and intolerances. I briefly mentioned how a loss of oral tolerance can be a factor in the development of food sensitivities.

But it goes beyond this. A loss of oral tolerance can also set the stage for an autoimmune condition such as Graves' disease or Hashimoto's. While the term “oral tolerance” might not be as popular as “leaky gut,” a loss of oral tolerance is one pathway that can ultimately contribute to the development of a leaky gut.

Why Avoiding Foods Isn’t Enough

When someone has a food allergy or sensitivity, they usually just avoid the food they’re reacting to and don’t do anything else. If someone is working with a natural healthcare practitioner, there’s a good chance they will also take steps to improve the health of their gut microbiome, which can definitely help increase oral tolerance.

Getting back to simply avoiding foods — the reason this alone isn’t enough is because it doesn’t address the root cause of the oral tolerance issue. If a loss of oral tolerance is driving food sensitivities, then avoiding certain foods while ignoring the underlying immune imbalance doesn’t make much sense.

What Is Oral Tolerance?

Oral tolerance is defined as a state of systemic unresponsiveness that is the default response to food antigens in the gastrointestinal tract.¹ So what does that actually mean?

Every day we eat food, and you don’t want your immune system treating food particles as foreign invaders. Instead, your immune system “learns” that food is safe — and that learned response is known as oral tolerance.

Here’s how it works: When you eat food, it enters the stomach and intestines. Food particles are sampled by immune cells in the gut called dendritic cells, which are a type of antigen-presenting cell. These cells present the food particles to T cells and essentially send a message that says, “This is safe.” As a result, the immune system does not mount an attack.

When someone loses oral tolerance, the immune system may begin reacting to food proteins — or even to beneficial microbes — which can lead to food allergies, food sensitivities, and other immune-related issues. In fact, if oral tolerance is functioning optimally, you are far less likely to develop food sensitivities in the first place.

What Causes a Loss of Oral Tolerance?

There are several factors that can contribute to a loss of oral tolerance.

Low Regulatory T Cells. Regulatory T cells (Tregs) act as “peacekeepers” in the immune system. They prevent other immune cells from overreacting to harmless substances like food proteins.

I’ve mentioned Tregs in previous newsletters because having adequate levels helps keep autoimmunity in check. A decrease in Tregs is one factor that can contribute to a loss of oral tolerance.

Low Secretory IgA. Secretory IgA (SIgA) serves as the first line of defense in protecting the intestinal lining from toxins and pathogenic microorganisms.²

In other words, SIgA plays a major protective role in the gut. Both the adrenal saliva test and comprehensive stool panels I commonly recommend assess SIgA levels — and it’s very common to see these levels low.

When I was diagnosed with Graves' disease, my saliva test revealed low SIgA. It took some time before my levels normalized, which we confirmed through retesting.

Low SIgA can absolutely contribute to a loss of oral tolerance.

Gut Dysbiosis. An imbalance in the gut microbiome can also impair oral tolerance. Correcting dysbiosis and increasing microbial diversity can help restore immune balance.

Increased Toxic Burden. An elevated toxic load can overstimulate immune cells in the liver (Kupffer cells), making them more reactive. Reducing toxic burden and supporting detoxification pathways can therefore support immune tolerance.

Of course, this is always a work in progress because we live in a toxic world.

Other Types of Immune Tolerance

I first learned about immune tolerance from Dr. Datis Kharrazian. He explains that in addition to oral tolerance, there is also chemical tolerance and self-tolerance.

We are constantly exposed to environmental toxicants. While our bodies are resilient, everyone has a different threshold. Some people develop a loss of chemical tolerance.

Dr. Kharrazian suggests that those with autoimmune conditions have some degree of loss of oral tolerance and chemical tolerance, which ultimately contributes to a loss of self-tolerance — meaning the immune system begins attacking the body’s own tissues.

So yes, reversing autoimmunity involves finding and removing triggers and healing the gut. But restoring immune tolerance may also require addressing nutrient deficiencies, detoxification capacity, immune regulation, and more.

How to Increase Oral Tolerance

Here are some key strategies:

Properly Break Down the Food You Eat. This means chewing thoroughly, having adequate stomach acid, and producing sufficient digestive enzymes.

If food proteins are not properly digested, larger fragments can stimulate the immune system and contribute to a loss of oral tolerance.

Increase SIgA Levels. Ways to support SIgA include:

✅ Eating a whole-food, nutrient-dense diet

✅ Managing stress

✅ Addressing gut infections

✅ Taking probiotics

✅ Supporting with nutrients such as zinc, vitamin A, and L-glutamine

Increase Tregs. Tregs can be supported through diet and lifestyle changes. Certain nutrients may also help, including:³

✅ Vitamin D

✅ Vitamin A

✅ Omega-3 fatty acids

✅ Zinc

✅ Selenium

Optimize Liver Health. You can’t eliminate all toxin exposure, but you can reduce it. Supporting detoxification pathways through diet, lifestyle, and targeted supplementation can help improve immune tolerance.

Correct Intestinal Dysbiosis. A diverse, plant-rich diet can improve microbiome diversity. But in some cases, additional steps are necessary.

If infections are present, they need to be addressed. Environmental toxicants such as glyphosate and microplastics can also disrupt the microbiome — another reason to reduce toxic burden as much as possible.

Final Thoughts

Oral tolerance isn’t a trendy term like “leaky gut,” but it plays a foundational role in immune health.

If oral tolerance is impaired, the immune system may overreact to foods, microbes, and eventually even self-tissues. Restoring immune tolerance isn’t just about avoiding trigger foods — it’s about improving gut integrity, supporting Tregs and SIgA, reducing toxic burden, and strengthening overall immune balance.

When immune tolerance is functioning properly, the risk of thyroid autoimmunity decreases significantly.

Find Your Hashimoto’s Triggers

If you have Hashimoto’s thyroiditis, visiting an endocrinologist is likely to result in a prescription for thyroid hormone replacement. And while there is a time and place for thyroid hormone, the problem is that it doesn’t do anything for the autoimmune component of Hashimoto’s.

And so what happens is that many people will take thyroid hormone without doing anything to improve the health of their immune system, which means that over time further damage to their thyroid gland will take place.

The good news is that you can do things to reverse the autoimmune component of Hashimoto’s. And the best way to accomplish this is by finding and removing your triggers.

My book “Hashimoto’s Triggers” will show you how to do this. By reading this book you will discover the following:

• More than one dozen triggers of Hashimoto’s thyroiditis

• The different diet options, and how to detect your specific food triggers

• Everything you need to know to heal your gut

• How to reduce fatigue, brain fog, hair loss, lose weight, and address other common symptoms

• Strategies to lower thyroid antibodies when nothing else has worked

• Nutritional supplements and herbs for Hashimoto’s

• A comprehensive list of the blood tests you should get, along with other specific tests that can help detect your triggers

• What you need to do to achieve optimal adrenal health

• Natural treatment options for viruses, pathogenic bacteria, parasites, Candida, and SIBO

Click Here to order the book “Hashimoto’s Triggers”

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 chatted with Dr. Louise Swartswalter, as we had a conversation about The Overlooked Link Between Brain Healing and Thyroid Health.

Healing doesn’t always stall because the body lacks the right nutrients or protocol. Sometimes it’s because the brain and nervous system are still holding unresolved trauma. In the episode Dr. Louise Swartswalter explains how neurobiofeedback and trauma release work can influence regulation, resilience, and the body’s ability to heal.

This conversation helps connect the dots between brain health, emotional patterns, and chronic symptoms, especially when standard approaches haven’t gone far enough. It also helps explain why some people don’t respond as expected to supplements, diet, or even well-designed functional plans.

So If you’re open to exploring how brain health and trauma resolution might fit into a root-cause thyroid healing approach, this episode will give you a thoughtful 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: WHAT SHOULD I DO IF I CAN’T TOLERATE PROBIOTIC SUPPLEMENTS?

Dr. Eric, whenever I take probiotic supplements I experience a lot of bloating and gas. Should I stop taking them, or should I just “grin and bear it?”

Thanks for your question! I’m a big advocate of probiotic supplements, and the reason for this is because we are constantly being exposed to toxins and toxicants that can disrupt the gut microbiome. This includes microplastics, glyphosate, mycotoxins, and other environmental toxins.

Because of this, I personally have been taking probiotic supplements on a daily basis since being in remission from Graves’ disease, and I commonly recommend probiotics to my patients as well.

That said, it’s important to listen to your body. If someone experiences digestive symptoms when taking probiotic supplements, it usually means there is an underlying imbalance that needs to be addressed. For example, some people might have small intestinal bacterial overgrowth (SIBO), while others might have a histamine intolerance.

Either way, the goal should be to identify and address the root cause. For example, if someone has SIBO that is causing gas and bloating, it is perfectly fine to focus on addressing the SIBO and take a temporary break from probiotic supplements.

Another option is to use probiotics that tend to be better tolerated in those with SIBO, although when working with someone who has significant symptoms, I think it’s perfectly reasonable to stop probiotics temporarily. Once the SIBO or other imbalance has been addressed, you can then reintroduce probiotics and see how you respond.

As a side note, I find that people with SIBO often have more difficulty tolerating prebiotics than probiotics. So if you are dealing with SIBO and are taking a probiotic supplement without any worsening of symptoms, there usually isn’t a need to stop it—unless the practitioner you are working with specifically recommends doing so.

Final Thoughts

While probiotic supplements can be extremely beneficial for supporting gut health, they aren’t tolerated by everyone—especially when there is an underlying imbalance such as SIBO or histamine intolerance. If probiotics worsen your symptoms, don’t force yourself to continue taking them. Instead, focus on identifying and correcting the underlying issue. Once your gut environment improves, many people find they are able to reintroduce probiotics without any problems.

Additional Thyroid-Related Resources

Click Here The Overlooked Link Between Brain Healing and Thyroid Health (episode 230)

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:

(1) https://pmc.ncbi.nlm.nih.gov/articles/PMC6110983/
(2) https://pmc.ncbi.nlm.nih.gov/articles/PMC3774538/
(3) https://pmc.ncbi.nlm.nih.gov/articles/PMC9067578/

That’s a wrap