The Gut-Thyroid Connection: Uncovering the Root Causes of Intestinal Permeability

Thyroid Pharmacist - Dr. Izabella Wentz
In this episode of Thyroid Pharmacist Healing Conversations, Dr. Izabella Wentz explores the science behind intestinal permeability (leaky gut), a critical factor in both Hashimoto’s and irritable bowel syndrome. Drawing from her own story and over a decade of clinical research, she shares how healing the gut can lower thyroid antibodies, improve symptoms, and even bring autoimmune conditions into remission.
What you’ll learn in this episode:
✅Why intestinal permeability is central to autoimmunity. Dr. Alessio Fasano’s “three-legged stool” theory shows that while we can’t change our genes and don’t always know our exact triggers, we can heal intestinal permeability – often reducing inflammation and lowering thyroid antibodies. Dr. Wentz shares steps that can strengthen your gut lining and calm immune reactivity.
✅Leaky gut often shows up before an autoimmune diagnosis. IBS symptoms frequently appear 5 to 15 years before Hashimoto’s or other autoimmune conditions. Digestive pain, reflux, or bloating may be early warning signs, but intestinal permeability can also exist without gut symptoms. Discover how to recognize these early patterns and begin restoring balance before autoimmunity progresses.
✅Food sensitivities play a big role. Gluten and dairy are the most common culprits, but soy, eggs, nuts, grains, and nightshades can also trigger leaky gut. Dr. Wentz shares her tips on short-term elimination plans, tracking symptom responses, and safely reintroducing foods.
✅Nutrient deficiencies can prevent gut healing. Zinc and glutamine are two of the most critical nutrients for repairing the gut lining, yet they’re often depleted in people with autoimmune disease, chronic stress, or poor digestion. Discover how to assess your nutrient status and use targeted supplementation or food-based support to rebuild your gut barrier.
✅Gut infections and imbalances are hidden drivers. SIBO, Candida, mold colonization, and parasites like Blastocystis hominis all contribute to intestinal permeability. Discover how functional tests such as breath tests, organic acid testing, GI-MAP, or mycotoxin panels can uncover these hidden infections, and how to work with your practitioner to treat them effectively.
✅Healing your gut transforms overall health. Restoring gut integrity can lead to remission of Hashimoto’s and IBS, and even improve conditions like migraines, asthma, and allergies. Discover how strategies like mindful eating, stress reduction, and using key nutrients can help your intestinal lining thrive.
Be sure to subscribe to the Thyroid Pharmacist Healing Conversations podcast so you don’t miss an episode!
✅Dr. Wentz’s new book, IBS: Finding and Treating the Root Cause of Irritable Bowel Syndrome, will be out on March 17, 2026. Many people with Hashimoto’s have irritable bowel syndrome, which can be both a root cause and symptom of autoimmunity. This comprehensive guide reveals how irritable bowel syndrome is often a catch-all diagnosis that overlooks treatable root causes. It offers a step-by-step approach to help readers understand what’s really driving gut symptoms, and how to create a personalized plan to restore gut health and overall wellness.
🔗Order your copy of IBS: Finding and Treating the Root Cause of Irritable Bowel Syndrome here: https://thyroidpharmacist.com/ibs-book-preorders/
🔗Sign up for the Thyroid Pharmacist Weekly Thyroid Solutions Newsletter here: https://thyroidpharmacist.com/gift/
🔗For the full list of resources and products mentioned in this episode, and to get the full episode transcript, see complete show notes here: https://thyroidpharmacist.com/articles/podcast/
Full Transcript
Introduction to leaky gut and autoimmunity 0:00
So you've removed gluten. Maybe you have removed dairy, maybe you tried more progressive elimination diets. You're eating clean, but your symptoms are still remaining. Could the mesing piece actually be intestinal permeability, which is shown to be a factor in most cases of autoimmune disease like Hashimoto's, in many cases, of irritable bowel syndrome, and a lot of chronic health conditions? Hi, welcome to today's episode of Thyroid Pharmacists Healing Conversations with Dr. Isabella Wentz, your thyroid pharmacist.
That's me. Today, we're going to be diving into some of the root causes of intestinal permeability, also commonly called leaky gut. But if you were to do a search online for leakey gut, people might say it doesn't exist. And when you actually search for intestional permeabilty, you will see thousands of published medical research supporting the fact that intestinal permeability does exist and it does play a role in autoimmune disease, IBS, Hashimoto's and a whole host of other chronic health conditions.
There's a connection between the gut and the thyroid and immune system. This connection was, I believe, made popular by a researcher named Dr. Alessio Fasano, and he talked about the three-legged stool of autoimmunity, where we need to have a genetic predisposition for a health condition. We need a trigger, so something that brings on the condition, then for the third factor that needs to be present in order for autoimmunity to develop is known as intestinal permeability or leaky gut. Now here's the thing, it can be quite challenging to figure out what your triggers are, right?
So is your trigger excess iodine, is you trigger a deficiency, your is trigger an infection, so on and so forth, we don't always know what our triggers
The gut-thyroid connection and the three-legged stool 1:56
The other part of the three-legged stool is genetic predisposition. In this day and age, we can't really change or choose our genes, like we're kind of going to get what we are going get. But the third factor, the intestinal permeability factor. We can always work on that and we find some really relevant root causes that when treated, you can actually get this three-legged stool to fall by treating the the leg of intestinal permeability and then the autoimmune condition stops expressing itself. So what does that mean for a person with Hashimoto's or irritable bowel syndrome or other conditions is your symptoms start improving.
The inflammation improves in your body and then if you have markers of autoimmunity such as thyroid peroxidase antibodies or thyroglabulin antibodies, those will start reducing themselves and eventually get into our remission range. So today I want to talk to you about some common drivers of intestinal permeability that I have seen in people with Hashimoto's and also spoiler alert irritable bowel syndrome. I have to share with you that before I got diagnosed with Hashimoto's, I had an irritable bowel syndrome diagnosis.
Not the most glamorous diagnosis to have, definitely not fun, and I treated that pretty much with over-the-counter medications. I found that eating less red meat seemed to help, but I never really got like a really good handle on it. And then eventually I started to have more and more progressive symptoms. Now, by the time I was in my late 20s, Iwas diagnosed with Hashimoto's thyroiditis and Istarted to try to figure out if there was anything I can do to make myself feel better. If there is anything that brought on the condition and if I could get the conditions into remission.
This is when I came across Dr. Alessio Fasano's work. This was when came I across the Institute of Functional Medicine and functional medicine training and I learned that in many cases a person will have a
Personal Hashimoto's journey and IBS history 4:17
diagnosis such as irritable bowel syndrome or symptoms of irritable bowel syndrome for 5, 10, or 15 years before they get an autoimmune diagnosis. And the timeline really fit with me. I was in my early 20s when I started to have irritative bowel symptoms. And then as time went on, I started to have more and more symptoms to the point that I was diagnosed with Hashimoto's. And what scientists and researchers believe is that there is this intestinal permeability component that essentially prevents the immune system from working properly.
So instead of your immune being managed properly, a lot of that immune is in the gut, you go on to attack benign things such as foods, and you can go on to attack your own physiology. In my case, my immune system decided that my thyroid gland was a threat and so it marked my Thyroid gland for destruction. And this is what happens in people who have Hashimoto's most common cause of hypothyroidism in the developed world. So what does it mean to have intestinal permeability and what are the symptoms?
Well for about 50% of people it's actually an asymptomatic condition so they may not have any symptoms of it but they might have autoimmune markers that suggest this is an issue for them, they Might have markers such as elevations in zonulin if they were to do a test for this, This is something that you can order through functional medicine practitioners. I'll also put a link to RUPO where you self order that and give you more information on how to get access to that type of testing. There's also a test known as lactulose mannitol test that can also test to see if you have intestinal permeability or leaky gut.
So some people may attribute symptoms like autoimmunity or inflammation or joint pain to intestino permeabilty. And this is oftentimes the case where people will present with various symptoms and you can probably connect a whole host of symptoms to intestinal permeability just because we know that autoimmune conditions have hundreds of systems. The most classical symptoms, however, of intestino permeabilty are going to be digestive symptoms. So irritable bowel syndrome that might present like diarrhea, constipation, bloating, stomach pain, sometimes acid reflux, and a lot of times people with intestinal permeability are going to be diagnosed with irritable bowel syndrome, but in many cases they're not.
So they might just be having some quote unquote occasional digestive symptoms and sometimes they may have zero digestive. Symptoms so just because you don't have necessarily digestive, symptoms doesn't mean you have intestino permeabilty. However, if you have an autoimmune condition like Hashimoto's, there's a good chance that you do have intestinal permeability.
Symptoms and testing for intestinal permeability 7:22
If you Have IBS, There's A very, very good Chance that You have Intestinal Permeability as well. So the gut is oftentimes a super, super important target for you to treat. When I first started to learn about intestinal permeability, I learned about the role of foods in triggering inflammation and triggering that leaky gut in our bodies. And this makes sense, right? Because what we're eating is going to really impact our digestive function. One of the first studies I came across on my healing journey with Hashimoto's was in people who had celiac disease and Hashimoto's.
Their celia disease were newly diagnosed and once they got off of gluten, a lot of them were able to improve their thyroid function. Some of then actually just being gluten-free were actually able shed their Hashimao's diagnosis. And so I wondered to myself, oh, Could I have a condition like celiac disease that's causing my Hashimoto's? And of course, my doctor at the time was like, oh, you don't have celia disease. Gluten is not something you need to worry about. But looking at different patient experiences and working with integrative practitioners, going through functional medicine training, I decided to give the gluten-free diet a try.
And lo and behold, i felt significantly better just a few days. A lot of my symptoms like acid reflux, and IBS symptoms and pain, fatigue started improving. A lot of things got really better when I went gluten free. And I was like, okay, so maybe it was the gluten causing my intestinal permeability. Then I got into deeper about different foods. So there's other food sensitivities that can actually cause intestinal permeability, gluten and dairy being the most common ones, but also soy. And in some people it could be a whole host of different food sensitivity, typically managed by the IgG branch of the immune system.
What I've noticed initially with my own health and studying people with Hashimoto's and going to functional medicine trainings is that there tended to be a cluster of foods that were more likely to problematic in addition to gluten, dairy, and soy, also eggs, nuts, grains, nightshades. For a while, elimination diets were, I found, to very, very helpful for a lot of people. There were also dietary protocols like Paleo and Autoimmune Paleio that I have found to be very helpful for many of my clients.
However, I will say in some cases people would get stuck.
Food triggers and elimination diets 10:03
So they would eliminate a whole bunch of foods. They'd start to feel better, but then they'd reach a plateau and some of their symptoms would start creeping back, right? And this actually happened to me. I had been on the GAPS diet, which is an elimination diet. and all of a sudden I stopped making progress where my symptoms just were not getting better and actually some of the bloating started to come back and I did another food sensitivity test and it turned out that I was sensitive to more foods.
Now, food sensitivity tests out there on the market, there's a lot of them. Some of the are completely disconnected from what's actually happening in the body. some of do have a long track record of showing the correct results. So if a test says that you are pineapple sensitive, by golly, if we take pineapple out of your diet, you're going to feel better. This is very relevant too, if you're thinking about doing a food sensitivity test, I only recommend all the tests. In my experience of over 10 years, this has been the one that's been reliable.
If you've done other food-sensitivity tests, there's a chance that you might have false negatives and false positives. But I digress. So I was talking about how, in some cases, you can eliminate all the foods and feel better. In some case, as you could eliminate just a few foods, and fuel better, if 90 days goes by and you've eliminated foods. And you're still not 100% better there's something deeper going on underneath the surface. So it could be a nutrient deficiency. For example, glutamine and zinc are the two most common nutrients that can be depleted in people with digestive issues and digestive distress and autoimmune disease.
They are critical for gut lining repair. There are various things that could really set them off and deplete them. So if you're under a lot of stress, If you have low stomach acid, if you had low protein intake, there's a really good chance that you might be deficient in these nutrients. In my experience, people who are runners tend to deplete themselves of glutamine. People who're chronically sick with colds and things of that nature and viruses. They might be zinc deficient. People who are have a poor appetite are oftentimes going to be Zinc deficiant.
Some people are genetically predisposed to have less zinc absorption from their foods. So these are some additional considerations to Have. Generally speaking, you can support gut health and intestinal permeability with supplementing with zinc and L-glutamine. L glutamine might be up to five grams a day, sometimes upto 15. You definitely want to start low and go slow. It can make you quite constipated if you've had diarrhea. And zinc, I usually like to recommend the zinc picolinate version or zinc carnosine version and with with regard to the picolinate you don't want to go above 30 milligrams per day or any kind of elemental zinc unless you're working with a practitioner because that can deplete some other nutrients as well.
So these are two potential reasons why you might still have intestinal permeability and or leaky gut even if you've eliminated some foods.
Nutrient deficiencies and gut lining repair 13:18
The other potential root cause might be small intestinal bacterial overgrowth. So our small intestine is supposed to be sterile and not have any kind of bacteria growing in it. And when we have an over growth of Bacteria there, sometimes this happens from food poisoning. Sometimes it happens because our digestion is slow or we Have low stomach acid or We might have H. pylori. This can actually contribute to intestinal permeability. In fact, Dr. Alessio Fasano mentioned that SIBO, or Small Intestinal Bacterial Overgrowth, makes the gut more permeable, and if for many people, then gluten does.
With gluten, you can have a variety of reactions anywhere from months after one exposure to gluten where you have intestino permeabilty for a long time, if you had celiac disease, for minutes for other people that might not be sensitive, With SIBO, it's going to be an ongoing thing. Like as long as those bacteria are all in your small intestine, they're going be causing intestinal permeability. We can test for these with a breath test. It's relevant to note that people with hypothyroidism tend to more susceptible to SIBo.
One study mentioned, very tiny, tiny studied about 50% of people, with hypothyroidist actually had SIbo. So this is something that is very relevant for a lot of people with Hashimoto's. Some of the symptoms to watch out for would be bloating, reflux, reactions to high fiber foods, reaction to probiotics and fermented foods. Cebo bacteria can be very powerful histamine producers. And so this something you might need to treat with herbals, medications such as Rifaximin and even a targeted elemental diet.
Again, I do recommend breath testing to figure out if this is a root cause for you. And for many people, this has actually been tied to irritable bowel syndrome. About 70% of the time, people with irritative bowel will have this as a potential contributing factor.
SIBO as a major driver of leaky gut 15:30
Now, beyond that, you can also have an overgrowth of various other microbes in your body. One of them could be candida, one of the could mold. I oftentimes will recommend testing with an organic acid test and a mycotoxins test to see if that colonization is relevant for you. Typically, I see this with people who have urinary issues, oxalate issues. they might have a weird kind of food cravings, especially for sugar. They might be sensitive to carbs, they may have blood sugar issues, mood changes.
These are some things that can be very much relevant to an autoimmune journey. Again, these things do need to be treated accordingly. A lot of times I might recommend anti fungal meds or anti-fungal herbals. And then another very underappreciated root cause is actually parasites. which can be powerful drivers for intestinal permeability. In Hashimoto's, about 30% of people have the protozoal parasite Blastocystis hominis in my experience. And this parasite can actually make people shift their immune system to be more of attack my thyroid variety.
People oftentimes do go into remission when that protozoa is treated. The research is now showing they've done case studies and very small clinical trials of patients that do going to remissions with Hashimoto's when they have this parasite and a parasite is properly treated, oftentimes I recommend something like a gut GI map or gut zoomer test to figure out if you have this. If this is relevant for you, there's also a test called para wellness research test that looks for different types of protozoa.
Some people have, this some people, have others and I also really love to utilize the beneficial yeast sarcomyces boulardii to clear that proto zoa Some people might do like parasite cleanses that are very popular that, are on the market but it's important to note that not every parasite is susceptible to every cleanse to, every herb and to. Every medication so for this particular one the medication Alinea tends to work best.
Other microbes, parasites, and chronic gut issues 17:58
there are other medications that have been used historically that has led to resistance such as metronidazole for example might not work so well for this particular protozoa. The other really interesting thing about this proto zoa is that it also has been found to cause chronic hives, chronic urticaria, and irritable bowel syndrome. So even in greater percentages than what I'm finding in Hashimoto's, Hashimoto's was about 30%, but more people with chronic Hives and more People with Irritable Bowel Syndrome are actually being found to have protozoa such as blastocystis hominis, sometimes giardia, and sometimes others that are in their system and nobody's really detecting them, nobody is really finding them.
Sometimes the proto zoa make them sensitive to a whole bunch of foods, Sometimes, the protozoa predispose them to sebo. and really prevent them from properly managing their gut integrity leading to that intestinal permeability and leading the expression of IBS symptoms as well as to the expressions of autoimmunity. So I've kind of done a really big deep dive on gut health because a lot of the information on the market was, if you have leaky gut, then you need to have, eliminate some foods, maybe have some bone broth, have a few probiotics, and then, you'll heal your gut.
And clinically, like, there were some people with Hashimoto's that got better this way, but then other people, with HashiMoto's, did all those things and they still weren't better. So, I really had to do a deep dive into figuring out what was driving that intestinal permeability with people. And through that process, I've worked with a lot of clients who had both Hashimoto's and irritable bowel syndrome. A lot the factors do overlap. One of the things I'm super excited to share with you is I have been working on this book, about the root causes of irritable bowel syndrome.
This is coming out on March 17th, but it could be pre-ordered on Amazon and Barnes & Noble and wherever fine books are sold right now. And this book really gets into finding and treating the Root Cause of Irritable Bowel Syndrome. I've gone down the rabbit hole. So if there is a cause or a driver of your gut issues, of you're autoimmune issues that's going to be in there. A lot of times we say that disease begins in the gut. I truly do believe that. For a lot people who are chronically ill, they have Hashimoto's.
fibromyalgia, irritable bowel syndrome, there are just so many connections to the intestinal permeability and I've created this book for you guys so that
New IBS book announcement and closing thoughts 20:48
you can take charge of your own health and that You can figure out what's really behind all of Your gut challenges. I hope that you'll check it out. Again, it is available now for pre-order. This is kind of my official first announcement for letting you know that it's out in the world. I have to say it took about 12 years to write. It is something that has the knowledge base has been really growing for me. I felt a little bit of imposter syndrome when I was writing it because I'm like, hey, I am a thyroid specialist.
This is where I've been focusing up my energy. But again, i've had so many people with irritable bowel syndrome that I had to help to get their thyroid balance and get there. Autoimmunity balance was really a big focus. on their gut health. And then about seven years ago, my husband was actually diagnosed with inflammatory bowel disease and ulcerative colitis. So we had to figure out how to get that into remission. That really streamlined my understanding of gut-health. I have helped Thousands of people at this point recover their gut health and recover, their health.
So getting IBS into remission, Hashimoto's into emission, even inflammatory bowel disease into admission. A lot of times other things shift and symptoms improve when you heal your gut. I saw a meme many moons ago. It was like, I have 99 problems, but healing my gut solved like 97 of them. And I think that is very, very relevant to what I've been seeing. in my own health, in family's health and in the health of the clients that I've worked with. Like migraines go away, asthma symptoms go, away allergies go.
All kinds of things that every now and then I'll still be surprised at the symptoms that do go when a person has intestinal permeability and we figure out what's driving it and treat it properly. So I'm super excited to share this with you. If you know somebody that might be helped, by a root cause approach to irritable bowel syndrome, please share this information with them. If you know somebody who's dealing with autoimmunity and intestinal permeability or Hashimoto's, Please do share with him.
I hope this conversation has been healing on your healing journey. Until next time.
Comments