Transcript #645 Autoimmunity: How the New AIP Diet Relieves IBD, Hashimoto’s and More With Mickey Trescott

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Autoimmunity: How the New AIP Diet Relieves IBD, Hashimoto’s and More

with Mickey Trescott

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Dr. Wendy Myers

Welcome to the Myers Detox podcast. I’m Doctor Wendy Myers. On this show, we talk about everything related to heavy metals, chemicals, the health issues they cause, and how to detox them. We talk about bioenergetics, emotional trauma, biohacking, and more advanced topics than you’ll hear on other shows. I do not really do the basics so much. I want to talk about more advanced topics in health for people who are a little bit further along on their health journey. 

Today, we have Mickey Trescott on the show, and she is going to be talking about the new autoimmune protocol. And as we know, toxins cause gut dysbiosis, which then leads to leaky gut, which then can lead to autoimmune issues. Autoimmune issues are on the rise for many different reasons, including toxins. But also, our diet can play a big role as well. So Mickey is going to talk to us about her modified autoimmune protocol, which is essentially an elimination diet, but it’s modified based on over a decade of research that she has done.

She’s going to talk about why you don’t want to stay on an elimination diet forever. We talk about the new foods that you can eat on an autoimmune protocol-type diet. We talk about what’s causing autoimmune diseases today. We talked a lot about nutrition, some of the problems with food sensitivity testing, and why they’re not a replacement for elimination diets. It is a lot of really good information that you want to listen to if you are, in fact, dealing with an autoimmune condition. 

Our guest today is Mickey Trescott. She’s an author and nutrition professional, a leading advocate of the autoimmune protocol or AIP. She holds a Master of Science in Human Nutrition and Functional Medicine, and has been practicing as a coach since 2013, helping people personalize diet and lifestyle strategies to support long-term health. She’s also the co-founder of Autoimmune Wellness. Mickey helped grow AIP from a grassroots online experiment into a globally recognized, research-supported protocol used by patients and practitioners around the world. She has collaborated with medical researchers studying the efficacy of AIP for conditions including inflammatory bowel disease, Hashimoto’s, rheumatoid arthritis, and psoriasis. 

In 2017, she co-created the AIP Certified Coach Practitioner Training program, which has since trained more than 1000 healthcare providers worldwide, and best practices for implementing and customizing AIP. She’s the author of four award-winning and bestselling books, including The New Autoimmune Protocol, which introduces the first major update to AIP in over a decade, expanding accessibility while preserving its evidence-based foundation. She lives in the Portland, Oregon area with her husband, Noah. You can learn more about her work at autoimmuneprotocol.com. Mickey, thank you so much for coming on the show.

Mickey Trescott

Thank you for having me, Wendy.

Dr. Wendy Myers

I had you on a long time ago. So why don’t you refresh our memory and tell us a little bit about yourself and why you focus so much on autoimmunity?

Mickey Trescott

I was diagnosed with two autoimmune diseases about 15 years ago. Now, that’s kind of where my whole leadership and work in the space actually started as a patient discovering the autoimmune protocol and recovering my health. Over the past time, I have been working as a cookbook author, a nutritionist, leading the app movement, and actually collaborating now on medical research. At the same time,  I am still working on my own health, working on my own diagnosis journey. I actually recently got diagnosed with another autoimmune condition, psoriatic arthritis, which I started having symptoms of all the way back 15 years ago. It has been very, very mild, I think due to all of the things that I do and have learned to support my health, like AIP, but really at the core, I am very much an autoimmune patient myself and really trying to share information to help other patients, help figure out how to best manage their diet and lifestyle for their chronic condition. That’s where all the passion comes from.

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Dr. Wendy Myers

Talk about how you feel like the autoimmune protocol isn’t just a diet, which a lot of people can get very focused on. It’s more like a structured healing process. Can you talk about what you mean by that?

Mickey Trescott

I love starting here because everybody has heard about it, especially if you’re in the functional or alternative nutrition space. AIP has been around for a while. The thing that people get wrong about it is that it is not a diet. There are different approaches to eating that you may apply, and then you go forward for the rest of your life, because this is a way of eating that works perfectly for you. It is actually a template that you use to determine your ideal diet for chronic illness or autoimmune disease. So it’s actually something that you move through. It’s not something that you do forever. And of course, it does take a commitment to at least three months. I would say a more realistic outlook is actually more on the 6 to 9 month time frame to actually work through the phases.

So there are a few different phases to AIP, which I’m sure we’ll talk about, but I think that’s the biggest misconception. When people hear AIP, they have heard about it, they’ve talked about it, but they might be thinking, this is a diet that you have to eat forever, or maybe a diet you have to eat for prevention. And that’s actually not how it works. It’s more like a tool or a template that you use to actually then design your ideal diet going forward, which is going to look very different from mine. It’s going to look very different for you. Even if we share the same diagnosis or we have the same symptoms, the way that food interacts with our unique biology is just completely different. I’m really an advocate for discovering what works for us, and then carrying that forward to live our healthiest lives.

Dr. Wendy Myers

A lot of people can assume that the IP diet is about lifelong restriction, that they’re not gonna ever be able to eat gluten and dairy and soy and corn and all these things. Can you explain what the real goal is here?

Mickey Trescott

So, from immunology science, elimination diets have been studied since the 60s and they have been used for far longer than that. Elimination diets are not new. And even with all of the research that we have up to this moment, blood tests and all kinds of things that you can do to discover different ways that the immune system is reacting to foods, trial and error in the form of an elimination diet is actually still the gold standard for determining food allergy and sensitivity, because there are just so many different ways that we can show symptoms related to how we’re exposing ourselves to triggers within food.

At this foundation is an elimination diet, and immunology research tells us that we really need three weeks without a trigger in order for our immune system to just calm down. Once that is calmed down, usually that shows up as a measurable improvement in symptoms, which we can talk about later. I really like people to be tracking and honing in on how they feel. But you do have to feel better once you feel measurable improvement, which is not complete healing. That’s another misconception. It is just a measurable improvement. Then you can reintroduce those foods one at a time to figure out which one works for you. So, you’re doing a little bit of a personal science experiment, you know? And that three-week mark is really what research shows as the amount of time you need to be 100% with these triggers.

So that’s where AIP gets the reputation for being really hard and really restrictive, because it is a long list of foods that we are eliminating. But these are foods that science shows are the most likely to be triggers. Now, there’s no guarantee it’s going to be a trigger for you. And I’m hoping that everyone gets a little surprised when they get to the reintroduction phase and they’re like, oh wow, this X, Y, or Z food actually doesn’t affect me. That’s always a win. I would actually say most people have the experience of being able to reintroduce a lot of foods when they get to reintroductions, but it’s those 1 or 2 or maybe if you’re like me, six foods that are actually a problem, then you have that information. You get to move forward with a diet that is truly personalized. And by removing those triggers, then even further, you can even further experience healing.

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Dr. Wendy Myers

Can you talk about some of the medical research behind the autoimmune protocol and what the science actually shows, and which autoimmune conditions have been studied so far?

Mickey Trescott

Starting in 2015, the autoimmune protocol has been used in different groups as an intervention for autoimmune disease. So the first research group that started this all off was at Scripps, the gastroenterology department. They did a study using patients with Crohn’s and ulcerative colitis. IBD collectively is what we refer to as those two conditions. They are digestive autoimmune conditions and the colon that cause ulceration and bleeding.

When people are in flares, they are extremely uncomfortable. So in this pilot study that they did, they ran 17 people with an active flare that had failed on whatever medication, standard treatment, biologic steroids, everything. They were still in a flare. The mean disease duration was 19 years. So these were not people who were newly diagnosed or, you know, were in their first flare. They had been sick for a long time. They had failed conventional treatment. They were in an active flare and the AIP intervention, quite frankly, was amazing at turning around their symptoms. It was a ten-week intervention. At six weeks, they found that 73% of them were in clinical remission. And this is not the researchers saying, how do you feel they actually did colonoscopies?

They were doing blood tests. That clinical remission was defined by the standard of ulcerative colitis and Crohn’s research at the time. So that study got a lot of attention. It got a lot of researchers interested in the autoimmune protocol. From there, there have been two studies on Hashimoto’s thyroiditis. Of course, Hashimoto’s is very different from IBD. It is a hormonal effect. It’s an autoimmune disease that affects the thyroid gland, mostly with Hashimoto’s. The issue is symptom burden. 

I am Hashimoto’s patient myself. I feel so strongly about this when we are treated to conventional, standard, or even functional medicine standard, meaning we are given thyroid hormone replacement, which is the only treatment for Hashimoto’s. Our hormones go back into the normal range. 67% of Hashimoto’s patients continue to report symptoms that affect their daily living. So this is just a feature of Hashimoto’s. It is considered a basic autoimmune condition. It is considered by the medical establishment as such, and they give you some thyroid hormones and send you on your way. But if you know anybody or if you have Hashimoto’s, you know that your experience is so different from that.

We have symptoms that just encompass every organ and body system, and that’s because thyroid hormone is needed everywhere in every cell of your body. So I’m especially excited about this research on Hashimoto’s because it really showed a broad symptom improvement, even when people had normal thyroid hormone levels. And so this was done in a pilot study with a functional medicine doctor. Doctor Abbott was the first one, I think, in 2019, who published a study of 17 women with Hashimoto’s. And then a second group did a longer study. So I think the first one was ten weeks. The second one was 12 weeks. This was a group in Poland, and they did some nutrient density analysis. They did some body composition analysis. 

I won’t go super into the results. But with the Polish team, what they did that was so interesting is they actually measured thyroid volume. And they saw that the inflammation and the thyroid volume decreased throughout those 12 weeks. They also measured body composition. So there was a mean loss of 8 pounds and 10% relative body fat, which is really impressive, especially considering that the study was calorie-controlled. So they took the participants on a standard Polish diet. They assessed their diet; they were eating about 2000 calories, and then their AIP diets had the exact same amount of energy density. But to see that weight loss and that fat loss, while preserving muscle mass with just changing what they were eating, not the energy density of what they were eating, is really important for Hashimoto’s because if you have Hashimoto’s, you know how easy it is to gain weight without eating a lot of food.

That’s part of the inflammation and the hormonal dysregulation. So outside of IBD, Hashimoto’s, there are also studies in rheumatoid arthritis and psoriasis. Both of those are a little bit newer. The psoriasis one hasn’t actually been published yet. So I can’t really talk a lot about the details. But that one, the results are good. Rheumatoid arthritis actually just got published in the last couple of weeks out of New Zealand. So the research is really exciting.

Dr. Wendy Myers

You just released the first major update to AIP in over a decade. What prompted the changes, and how do the core AIP and the modified AIP work? How does that make the protocol more accessible today?

Mickey Trescott

I have a new book out. It’s called the New Autoimmune Protocol. And really, it came out of both that research background. So now we have all these studies of using the autoimmune protocol on real people. We know there are a few different pathways of what’s happening and how people progress through the eliminations. Also, there’s a good history of use within the autoimmune community and clinicians. So there are over 1000 clinicians who are trained to use AIP. They’re all using it in their practices, reporting back to me as the coach of the program. And so we really explored if we were to update AIP based on all of this, anecdotal people’s experiences, based on the evidence from the medical studies, and then based on the experiences that the clinicians are having in their practice

We polled everybody and said what do you guys think? What should we do? We even interviewed the researchers of the AIP studies and were like, hey, if we were kind of playing with some of these levers and the elimination diet, what could we do? And everybody had a little bit of a different idea. But everyone agreed that a less strict approach to the elimination phase would be smart to try out and see if that is something that gets the same results.

So two years ago, we updated the autoimmune protocol unofficially. So it wasn’t published. It was just within the practitioner community. I posted it on my website, with the details on the autoimmune protocol, and we just proposed this modified AIP. We called everything from the research and the historical AIP core AIP. And then the new protocol is modified.

Modified includes a few new foods. So core AIP avoided all grains, all legumes, nuts, seeds, nightshades, dairy, and eggs. That’s the historical protocol that’s been studied in the research. But for modified, we decided to allow rice, any type of rice, but no other grains, pseudo-grains, which include quinoa and buckwheat and things like that, seeds, which include sunflower seeds and flax, and then ghee, but not any other dairy because ghee is clarified and doesn’t have some of those allergenic proteins. The last thing is legumes. So, beans and lentils and that kind of thing. And that’s because of the experience of the researchers and the clinicians.

Of course, people can have sensitivities to these foods, but they are foods that can provide, for some people, a rich source of carbohydrates if they’re somebody who needs more carbohydrates. Some people with IBD need more carbohydrates in order to prevent unnecessary weight loss, while others do not. Maybe they want to do a little more of a lower-meat vegetarian style approach. Having some rice and legumes really rounds out the protein sources. It also has a lot of fiber in the legumes and some nutrient density without really bringing in the potential for some of those sensitive foods. So everybody loves the modified AIP. 

The public AIP audience wrote in, and they were like, well, we’re getting great results with this. The clinicians loved it. So that’s really what led me finally to want to write a book and publish it as an official approach. Hence, the new autoimmune protocol really incorporates that original protocol for the people who want to do it. But then this modified protocol, which I think is the best place to start now for most people, just because it increases accessibility and ease of actually implementing it.

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Dr. Wendy Myers

Yes, because it can just be really difficult to do.  I’m on an elimination diet like that. I mean, it’s very, very restrictive. You have to do it for three weeks or more. If you’re still inflamed and having symptoms, it can be really, really challenging. Do you recommend people do any kind of food sensitivity or food allergy testing at all to maybe bypass the need to do the elimination diet? I know that maybe some people can’t afford to do a bunch of testing, so they’ve just got to tough it out.

Mickey Trescott

Food sensitivity testing is helpful. It only tells a specific way that the food is interacting with the immune system. I love to tell everyone it is information. If you have done one or you have the money to do one, I think it’s great information, but it doesn’t replace the elimination diet because there are just so many other ways that your body could be reacting to those foods.

And back to immunology standards. Even though there is no food sensitivity test, there are like six different methods, which I’m not going to get into here. But they have tested patients with IBS, which is not autoimmune, but IBS. One of the features is that people have a lot of reported food sensitivities, and so there have been studies where they will test all of these IBS patients with all six different ways of food sensitivity testing, and then they will have them do an elimination diet, and they will see what matches up.

Even some of these studies send a camera down like an endoscopy tube, and they apply a little bit of the food that somebody says they’re sensitive to. They see the microscopic inflammation increasing. So they know that something is actually happening. But sometimes it’s like a toss up whether or not it’s going to show up in any of those blood tests, skin tests, or those six different types.

So I always like to tell people, the food sensitivity test does not replace what you learn, but if you do have a food sensitivity test and something comes up, you can layer that on. Now, one caveat is with IgG; sometimes, when somebody has an inflamed gut, and they are just reacting to everything, they can have a food sensitivity test that says that they are reactive to carrots, lettuce, cucumber, and pineapple. That is a really hard situation to then bring that into the elimination phase because these are foods that we are including. And that can be very confusing. So I would say that if you are working with somebody who is well-versed in functional medicine, he or she can kind of help you figure out how to make the best of that.

Sometimes it’s identifying a root cause, sometimes it’s a pathogen or dysbiosis, and treating that, which then allows somebody to move on to something like an elimination diet without having to cut out like a bunch of foods that they’re not truly sensitive to. 

Dr. Wendy Myers

It’s tough because your immune system can react to anything, I mean, anything at all. I personally do bioenergetic testing. I like to do zero testing to find out what foods I’m sensitive to. I do a less robust test called e4 L, and it’s very, very accurate at nine minutes. It’s shockingly accurate in my personal opinion. But again, there’s a lot of complexity, as you mentioned, like cross-reactivity, where you can eat a certain food, like maybe a lot of people eat dairy and gluten together, and you can eat dairy, but then react like it’s gluten. Because of this cross-reactivity, there are a lot of complexities to the immune system.

Mickey Trescott

Oh yeah, I love that you mentioned combinations because alcohol is one that we know causes intestinal permeability in healthy people. Intestinal permeability occurs when those tight junctions in the gut just kind of open up. And 70% of our immune system is in our gut. So of course, we’re eating all these foods. Part of what the immune system is actually doing is saying, yes, this is actually a good thing. We love lettuce and carrots. We’re good. It’s actually saying yes to everything as it’s saying no to the triggers. But when you have alcohol, it just kind of opens everything up a little bit and makes it a little more leaky. So those foods that might be like gray area foods, or foods that maybe don’t affect you all the time, but if you have a lot of them, you have them with alcohol, they will affect you.

This is my experience. I’m kind of in a gray area with eggs and eggs with alcohol. It’s just a full-blown reaction. And it’s just because it’s creating this state where those tight junctions are a little bit open. Intense exercise can be another thing. You know, doing like a high-intensity workout where you’re like doing your hit workout, and then you go have something that’s like, maybe have a dairy whey in a smoothie or something right after, that nervous system state really affects how our gut is functioning.

I don’t want to get anybody like, oh, how am I going to figure all this out? But really doing the experiments and running that trial and error is just so powerful because our states are always changing. When we do tests, it’s like you’re doing it at that moment. So that’s going to give you information about how your body’s reacting at that moment. But it’s hard to bring that into how you navigate the rest of your life. know.

Dr. Wendy Myers

Also, you can have delayed reactions. You can have food sensitivity reactions up to a week, like, yes, even more complexity, for instance. I don’t know what I was thinking. I ate some old tuna fish salad, and I knew that it was the wrong idea, but it just sat in my fridge for a few days, and before that, it had been in the store for a few days. So it was like a week old, and I was like, you know what? I’m just going to roll the dice and hope for the best. And then two days later, you have histamines. The longer the foods sit around you, it develops more histamines. And I thought I was getting the flu. 

It was a couple of days after I had the last portion of it, and I got very, very sick. I have the immune system of a sewer rat. I just have really, really strong immunity, and it just not totally knocked me out. I think a lot of people had food sensitivity reactions. And when they think they’re actually getting sick, I was very surprised by this. I did some bioenergetics testing, and it came up as anaphylaxis. I was having an allergic reaction and a histamine reaction to those foods.

Mickey Trescott

Actually, the study that I was referencing earlier, which, if anybody is a nerd like me, the research group is Fritz Turner, Ravens, et al. But they did the IBS study where they sent the camera, and they applied the allergen, and then they saw what happened with the tight junctions. They took pictures, the person then went on with their life, and then reported when they got symptoms. They found reactions up to 6 to 7 days after they did that whole procedure. So they were like dosing people with something that they know they’re sensitive to. And the people had no symptoms sometimes until that week. So it has been shown in research that food sensitivities can show up in a delayed fashion, which drives a lot of us crazy, but we’re not crazy. It totally can happen. 

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Dr. Wendy Myers

You’ve lived with autoimmune for many, many years, for over a decade. And you’ve recently shared that you’ve experienced a flare or you have that new diagnosis. Can you talk a little about that and walk through what you’re dealing with personally and how you’re addressing that?

Mickey Trescott

I love talking about this because, as an autoimmune patient, there is no cure for autoimmune disease. I really believe that we can manage and we can live well with autoimmune disease. That’s part of why I do what I do. But, with the changing life circumstances and aging, we are bound to have some flare-ups sometimes. I was turning 40 this last year, and I started to notice some hormonal shifts. I had a flare of something that’s new to me, uveitis, which is inflammation in the eye and the iris. I was actually photographing the cookbook. I had been photographing under a lot of stress, cooking a lot of food, and then doing the photography.

So, I was really straining my eyes and my brain a lot. I thought I came down with a headache, and within a week, my vision had changed. I had gone twice to the doctor. Of course, they dismissed it as just using a little bit of the steroid drop. It’s going to go away. You’re going to be fine. But then once I actually was in a true crisis, true emergency, it was like I might have vision loss.

I had to be treated with a whole emergency protocol that included permanently dilating my eye for a week, which was extremely uncomfortable. But I was really lucky that I not only saved my vision, but it led me on the path to doing some genetic testing and following up with rheumatology, which took about eight months, and ultimately getting a diagnosis of psoriatic arthritis, which I had had symptoms of for 15 years. This is not an uncommon experience for autoimmune patients.

It takes an average of five doctors and six years to get a diagnosis of autoimmune disease. So while I got my first two diagnoses right away, within a couple of years I had weird symptoms of some tendon pain and some rashes that even the dermatologist was like, oh, this is nothing. Turns out it’s psoriasis. This uveitis is linked to psoriatic arthritis. And really, it gave me the experience of having to dig back into all of the things that I know help me feel well. So, the nutrition, the lifestyle, the supplements, and taking a step back. I like to call this battening down the hatches.

I really think that this came on because I am starting perimenopause. It kind of coincided with some of the clubs. I know those early perimenopause symptoms, which are like I’m just sleeping a little bit worse. I’m just a little bit more anxious, I’m just a little bit less resilient. And then I felt like my immune system is really just shifting on this monthly cycle, as my hormones are just kind of doing their wacky thing, even after many years of being stable.

So, I like to talk about that just because it is really normal when you have a chronic health condition to go through periods and ebbing and flowing, and then having to learn. I’m really happy that right now I’ve figured out how to find some balance. I found a provider that’s helping me out with some of the perimenopause treatment side of it. I’m just so grateful to be able to have the tools that I learned all those 15 years ago about diet and lifestyle to really lean on in a time like this. But yeah, it is really normal for those of us with autoimmune disease to go through these seasons.

Dr. Wendy Myers

Tell us what the name of your book is, when it’s coming out, and when we can get it.

 

Mickey Trescott

It’s called the New Autoimmune Protocol. It is coming out on May 26th, 2026. It’s the one part that is the guide to the autoimmune protocol. So about half of the book, I talk about all of the research, the studies, why you’d want to try it, and who it’s appropriate for. I walk you through all three phases, whether or not you’re going to do core or modified AIP. That’s transition, elimination, reintroduction, answering questions, and FAQ troubleshooting. And then the second half of the book is a cookbook. It has recipes for core AIP that are kind of collected and then modified AIP that are collected. 

The way that I think about the recipes is, if you’re going to do modified AIP, all the core recipes apply to you. So the whole cookbook is for you. If you’re going to do core, those modified recipes apply once you’ve reintroduced some of those foods. We haven’t really talked about reintroductions, but they happen in the order of foods that are most nutrient-dense and least likely to cause a reaction, of which a lot of those modified foods are early reintroductions. So once you start expanding the diet, all of the recipes are going to be helpful to you, whether or not you’re doing one protocol or the other.

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Dr. Wendy Myers

Well, Mickey, thank you so much for coming on the show. That was super, super informative. I know so many people are dealing with autoimmune. There are so many different doctors in our environment who are destroying our gut microbiome. A leaky gut is a contributing factor to autoimmune. So, autoimmune is the fastest-growing subset of diseases. A lot of people are dealing with that and need solutions. They need therapy. They need to figure out what foods are not working for them. So thanks for providing the step-by-step guide for people to follow.

Mickey Trescott

Thank you, and I appreciate the opportunity to chat about it.

Dr. Wendy Myers

Everyone, I’m Doctor Wendy Myers. Thanks so much for tuning in to the Myers Detox Podcast. I just love bringing all these experts around the world to help you make those distinctions that you need to solve your health problems and upgrade your health, because you deserve that. You deserve to feel good. And that’s why I do this show. Thanks for tuning in.

Disclaimer

The Myers Detox Podcast is created and hosted by Wendy Myers. This podcast is for information purposes only. Statements and views expressed on this podcast are not medical advice. This podcast, including Wendy Myers and the producers, disclaims responsibility for any possible adverse effects from the use of information contained herein. The opinions of guests are their own, and this podcast does not endorse or accept responsibility for statements made by guests. This podcast does not make any representations or warranties about guest qualifications or credibility. Individuals on this podcast may have a direct or indirect financial interest in products or services referred to herein. If you think you have a medical problem, consult a licensed physician.

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