Understanding the Brain-Gut-Thyroid Axis

New Book on IBS and IBD!

I’m super excited to let you know that my friend Dr. Izabella Wentz will be releasing her new book: IBS: Finding and Treating the Root Cause of Irritable Bowel Syndrome

I got an advanced copy of the book and it is packed with some great information! You can get her book on Amazon, Barnes & Noble, and other places where books are sold.

Her book is available for pre-order, and the release date is on Tuesday March 17th 2026

Also be on the lookout for my interview with Dr. Izabella on the Save My Thyroid podcast, which will be released on Tuesday March 24th.

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: Understanding the Brain-Gut-Thyroid Axis

• Podcast Review: Methylene Blue for Thyroid, Low Energy and Chronic Health Conditions

• Ask Dr. Eric: Is there a link between ulcerative colitis and thyroid autoimmunity?

Understanding the Brain-Gut-Thyroid Axis

Many people with Graves’ disease or Hashimoto’s have been told some version of:
“Your TSH is off… take this medication… see you in a few months.”

But you can’t fully understand thyroid health by looking at the thyroid alone. The thyroid is part of a bigger communication network—and two of the most important “communication hubs” are:

✅ The brain (especially the hypothalamus and pituitary)

✅ The gut (including the microbiome and digestive function)

As you know, the focus of the "Healthy Gut Healthy Thyroid" newsletter is on how having a healthy gut microbiome is necessary for a healthy thyroid. But we don't want to overlook the importance of the brain.

Let’s break this down in a way that’s easy to understand and practical.

The Brain Controls the Thyroid (Through the HPT Axis)

The hypothalamus is like the “master regulator”, as it tells the pituitary gland what to do. The pituitary is considered to be the "master gland", and it sends TSH (thyroid-stimulating hormone) to the thyroid.

This entire system is called the HPT axis (Hypothalamus–Pituitary–Thyroid axis). It’s a core part of how your body maintains balance and adapts to stress, temperature changes, and metabolic needs.

So if the signal from the brain is off, the thyroid may respond accordingly—even if the thyroid gland itself isn’t the original “problem.”

Neurotransmitters Can Influence Thyroid Signaling

On the Save My Thyroid podcast I interviewed Dr. Shane Steadman, and he talked about how serotonin and dopamine help regulate the hypothalamus.

Why does this matter?

Because many people with thyroid and autoimmune thyroid conditions also deal with symptoms like:

✔️ Low mood or anxiety

✔️ Low motivation

✔️ Sleep disruption

✔️ Chronic stress patterns

Research supports that there’s real biological overlap between brain signaling (including dopamine pathways) and thyroid axis regulation.

Does that mean “it’s all in your head”? Of course not.

It means the brain is part of the physiology—and it’s often a missing piece.

The Brain, Stress Response, and the Gut: Enter the Vagus Nerve

In previous newsletters I discussed the parasympathetic nervous system, and how it's our “rest and digest” system. And the main nerve that helps make that happen is the vagus nerve, which runs from the brainstem down to the digestive organs.

When vagal tone is low (often seen with chronic stress, trauma patterns, or neurological dysfunction), you can see:

✅ Slower motility (constipation)

✅ Poor digestion and absorption

✅ Increased gut-related symptoms

This fits with what the science calls the gut–brain axis—a bidirectional communication network where the vagus nerve plays a major role in regulating digestive function and inflammation.

During our interview Dr. Steadman also shared that in his clinic, they evaluate vagus nerve function in essentially every patient—because sometimes what looks like “a gut problem” is actually a brain–vagus–gut signaling problem. And so while there is a time and place for diet changes and supplementation, you don't want to overlook the importance of the nervous system when it comes to healthy digestion.

The Gut Also Helps Convert Thyroid Hormone

This is a key point that many thyroid patients never hear. Your thyroid primarily produces T4, which is the inactive form of thyroid hormone. Your body then converts T4 into the active hormone T3 in peripheral tissues.

A meaningful portion of thyroid hormone metabolism involves the gut, including the influence of gut microbes and deconjugation enzymes (like Beta-glucuronidase), which are part of thyroid hormone’s normal cycling and metabolism. Research shows that the gut microbiome can influence thyroid hormone homeostasis and metabolism in multiple ways.

This is one reason why someone can have persistent hypothyroid-type symptoms even when they’re “doing all the thyroid things,” because the gut piece is still compromised, thus affecting the conversion of T4 to T3.

And it's a bit of a catch-22 situation, as sometimes hypothyroidism can also contribute to gut sluggishness—so it becomes a chicken-or-egg scenario.

That’s why a combined approach often works better than chasing one single target.

“Leaky Gut” and “Leaky Brain”: The Barrier Connection

Many readers are familiar with increased intestinal permeability (leaky gut). I discussed this in detail in Newsletter #47.

Just like the intestinal barrier, the blood–brain barrier (BBB) is also built with tight-junction structures that limit what can pass between cells. Tight junctions are foundational to BBB integrity.

And when it comes to intestinal permeability, zonulin is one of the best-known regulators of tight junction function in the gut. And while there are tests to determine if someone has a "leaky brain", it's not as commonly discussed as having a leaky gut.

But clinically, when people work on inflammation and gut barrier support, they often report improvements in things like:

✔️ Brain fog

✔️ Focus

✔️ Mood

✔️ Headaches

At minimum, it’s a reminder that inflammation can affect both gut and brain function.

Constipation Can Be a Gut Issue… or a Brain–Vagus Issue

This was another standout moment in the interview I had with Dr. Shane Steadman.

We often think constipation as being caused by a magnesium deficiency, low fiber, not enough water, or gut dysbiosis. And without question these can all be factors.

But Dr. Steadman emphasized that sometimes constipation persists even when someone “checks all the boxes,” and that’s when you have to consider:

✔️ Vagus nerve function

✔️ Brainstem signaling

✔️ Past concussion/trauma history

✔️ Neurological patterns that suppress motility

The point isn’t that constipation means Parkinson’s or Alzheimer’s (it usually doesn’t). It’s that the nervous system has a real influence on motility, and sometimes the brain piece is overlooked.

I should also mention that one of Dr. Steadman's mentors was Dr. Datis Kharrazian, who I have also learned a great deal about the gut-brain connection. In fact, Dr. Kharrazian has a very comprehensive book called "Why Isn't My Brain Working?" that you might want to check out if you find this topic to be fascinating like I do.

Blood Sugar and Oxygen: Two “Brain Basics” That Affect Everything

During our interview Dr. Steadman shared a simple framework from neurology: the brain needs glucose, oxygen, and stimulation. From a practical perspective, two of the most overlooked issues that can contribute to fatigue, brain fog, mood changes, and even stress physiology are:

➤ Blood sugar rollercoasters

➤ Low oxygen delivery (anemia, sleep-disordered breathing, shallow breathing patterns)

Even if someone is eating “healthy,” if they’re skipping meals, under-eating protein, living on caffeine, or constantly stressed, blood sugar instability can show up quickly—and the brain doesn’t like it.

So… Where Do You Start?

Dr. Steadman said something I completely agree with: complex cases can look like a tangled fishing line. You don’t fix it by yanking harder—you fix it by finding the right thread. In his practice, their approach often includes three overlapping “arms”:

1. Neurological support (brain function, vagus nerve, stimulation strategies)

2. Metabolic support (sleep, blood sugar, nutrients, thyroid, adrenals)

3. Immune/inflammation support (autoimmunity drivers, barrier integrity, inflammation load)

Not everyone needs all three at full intensity—but many people do need more than one.

Practical Takeaways You Can Start Applying

Here are a few simple, thyroid-friendly “brain–gut–thyroid axis” supports:

✔️ Support vagal tone (rest-and-digest)

✔️ Slow nasal breathing (especially longer exhales)

✔️ Humming/singing/gargling (simple vagus stimulators)

✔️ Daily walks (gentle nervous system regulation)

✔️ Support gut–thyroid conversion and metabolism

✔️ Prioritize regular bowel movements (motility matters)

✔️ Emphasize whole, anti-inflammatory foods

✔️ Address dysbiosis/SIBO/constipation patterns when present

✔️ Support brain basics

✔️ Stabilize blood sugar (protein + fiber + healthy fats per meal)

✔️ Address iron deficiency/anemia and sleep quality if relevant

Final Thoughts

When someone is diagnosed with Graves’ disease or Hashimoto’s, the focus is almost always on the thyroid gland itself. But as you learned from this discussion, the thyroid doesn’t function in isolation. It responds to signals from the brain, and it depends on the gut to properly activate thyroid hormone and regulate immune function.

This helps explain why some people continue to struggle with symptoms even when their thyroid hormone levels appear “normal.” If there are imbalances involving the nervous system, vagus nerve, gut microbiome, or immune system, simply addressing the thyroid alone may not be enough.

The good news is that these systems are interconnected in a positive way as well. Supporting gut health, improving stress resilience, stabilizing blood sugar, and calming the nervous system can all help restore proper communication within the brain-gut-thyroid axis.

In other words, healing the thyroid often involves supporting the entire network—not just the gland itself.

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 chatted with Dr. Scott Sherr about Methylene Blue for Thyroid, Low Energy and Chronic Health Conditions. When fatigue lingers, it can be a sign that the body’s ability to produce energy isn’t functioning the way it should. Could that be what’s happening in your case?.

In this episode Dr. Scott Sherr explains why energy dysfunction is so common in chronic illness, and how methylene blue is being used clinically to support mitochondrial function, oxidative stress balance, and detoxification.

I also explain why this topic is especially relevant for people with thyroid and autoimmune conditions, based on what I see regularly in practice. We finish by discussing nervous system regulation, GABA support, and why calming the stress response is often necessary before energy can truly improve.

If you’ve been feeling worn down despite “doing all the right things,” this episode will help you think differently about what your body may actually need.

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 THERE A LINK BETWEEN ULCERATIVE COLITIS AND THYROID AUTOIMMUNITY?

Dr. Eric, I have ulcerative colitis and I was wondering if there is any relationship between this and Graves' disease?

Thanks for your question! The two most common inflammatory bowel diseases (IBD) are Crohn’s disease and ulcerative colitis. IBD affects an estimated 1.5 million Americans, 2.2 million people in Europe, and several hundred thousand more worldwide.¹ The incidence of these inflammatory bowel disorders continues to rise, and there is still no single clear cause.

Common symptoms of ulcerative colitis include abdominal pain, diarrhea, rectal bleeding, and weight loss. The cause is believed to be multifactorial, involving a combination of genetic susceptibility and environmental triggers. Gut dysbiosis appears to play a key role in initiating and maintaining inflammation in IBD.²

How Do These Conditions Relate to Thyroid Health?

In the scientific literature, there have been case reports suggesting a possible association between thyroid autoimmunity and inflammatory bowel disease.^3,4,5 However, a cohort study of 162 patients with ulcerative colitis found thyroid dysfunction in only four patients (three with hypothyroidism and one with hyperthyroidism).⁶

So based strictly on prevalence data, the association doesn’t appear overwhelmingly strong.

That said, there are shared immune mechanisms that make the connection biologically plausible.

Shared Immune Pathways

Both ulcerative colitis and Graves’ disease are immune-mediated conditions involving dysregulation of T cells and inflammatory cytokines.

For example:

Th17 cells play a significant role in inflammatory bowel disease and have also been implicated in thyroid autoimmunity.⁷ in addition, both thyroid autoimmunity and IBD involve a breakdown in immune tolerance and regulatory T cell (Treg) dysfunction.⁸

Finally, pro-inflammatory cytokines such as IL-6, IL-17, and TNF-alpha are elevated in IBD and are also involved in autoimmune thyroid conditions.

The Gut-Permeability Connection

Another important link is increased intestinal permeability (“leaky gut”).

Both Crohn’s disease and ulcerative colitis are associated with increased gut permeability.⁹ And as I’ve discussed many times before, a leaky gut is one of the three components of the triad of autoimmunity.

So if someone already has IBD — and therefore ongoing gut inflammation and increased permeability — and they also have a genetic predisposition to Graves’ disease or Hashimoto’s, this could potentially increase their risk of developing thyroid autoimmunity.

What This Means Practically

Over the years, I’ve worked with some patients who had both thyroid autoimmunity and IBD. However, I wouldn’t say that I’ve seen a high percentage of my Graves’ or Hashimoto’s patients also dealing with ulcerative colitis.

Still, if someone has IBD, it makes sense to be proactive about:

• Supporting gut healing

• Improving microbiome diversity

• Reducing systemic inflammation

• Supporting regulatory T cell function

Addressing these factors can benefit both gut and thyroid health.

Note: Dr. Izabella Wentz discusses inflammatory bowel disease in her new book on IBS, including her husband’s experience with ulcerative colitis.

Additional Thyroid-Related Resources

Click Here for Methylene Blue for Thyroid, Low Energy and Chronic Health Conditions (episode 232)

Click Here to preorder Dr. Izabella Wentz’ book on IBS

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