Mickey: When most people start the Autoimmune Protocol, they understandably focus on the food, what foods you’re removing, which foods to include, and how to do all of the meal planning. But one of the most important things happening during AIP is often something that you can’t actually see: changes in your gut environment itself.Because AIP isn’t just designed to remove potential food triggers, it’s also designed to support some of the systems that are commonly affected in autoimmune disease, including the gut lining, the microbiome, nutrient status, and immune regulation.And changes in these areas don’t always happen quickly or in a perfectly straight line. For a lot of people, healing happens gradually and over time. Maybe digestion becomes more stable, maybe energy improves, or maybe certain foods that cause symptoms early on become tolerable much later in the process, which is always a delightful surprise.This was definitely true for me. When I first started AIP, my gut health was clearly struggling. I had celiac disease, years of nutritional deficiencies from both autoimmunity and a very depleted vegan diet, and my digestion itself was just not functioning well. My bowel habits weren’t regular, I dealt with bloating frequently, and even though I experienced progress in the elimination phase, my early reintroductions honestly did not go very well.And I remember feeling at the time just so disappointed. But looking back now, I can see that my body simply needed more time, more nourishment, and more support before it was ready for some of those foods once again. And over the years, as I consistently focused on nutrient density, lifestyle, and supporting my gut health, my tolerance changed dramatically. Foods that once felt completely off the table for me, like certain nightshades, and eventually even dairy, became tolerable much, much later in my healing journey.And even now, I can usually tell when my gut health is starting to trend in the wrong direction. For me, that often looks like bloating after meals or changes in digestion or bowel regularity. Those are signs that I need to just go back and refocus on the basics, the things that we have honestly talked about over and over on this podcast. More fermented foods, more fiber, more nutrient-dense meals, and better overall recovery habits.So today we’re going to talk about what is actually happening in the gut during AIP, including things like intestinal permeability, the microbiome, nutrient density, and why healing often continues well beyond the elimination phase itself.Because understanding gut healing on AIP can help you approach healing with just a little more clarity, patience, and confidence.​Welcome back to the Autoimmune Wellness Podcast. I’m your host, Mickey Trescott, and this is another installment in our AIP Deep Dive series. So far in this series, we’ve covered the full framework of the Autoimmune Protocol from transition to elimination to reintroduction, along with the foundational role of nutrient density and lifestyle practices that support healing throughout the entire process.If you’re new here, make sure you start with episodes 51 and listen through 55 for a complete overview of every single phase of the Autoimmune Protocol.Today, we’re diving into one of the biggest questions underneath all of it. What is actually happening in the gut while somebody is doing AIP? Because while most people focus on those food lists, the real story is what those dietary and lifestyle changes might be supporting behind the scenes , or more specifically, inside your gut.We are going to talk about the gut lining, the microbiome, immune regulation, nutrient status, and why so many people notice that their tolerance to food changes over time. So if you are somebody who has some experience with elimination, maybe you are feeling frustrated that your reintroductions haven’t gone well, this episode is for you.And before we get started, just a reminder that this podcast is intended for educational and informational purposes only. It’s definitely not medical advice, and always work with your qualified healthcare provider when making changes to your diet, supplements, or treatment plan. Okay, let’s jump into it.

[00:04:35] Why The Gut Matters in Autoimmune Disease

Mickey: So before we talk about gut healing itself, we first need to understand why the gut matters so much in autoimmune disease in the first place. Because the gut is not just responsible for digesting food, it’s also deeply connected to the immune system. In fact, a large portion of the body’s immune activity is associated with the gut and the tissues surrounding it.The digestive tract is constantly interacting with the outside world through everything that we eat, drink, and are exposed to, so the immune system has to stay in very close communication with it at all times. And one of the gut’s biggest jobs is deciding what is safe, what is harmful, and what should be actually absorbed into our body, and what should we keep out.So the gut is functioning both as a barrier and a communication center. On one hand, it needs to allow nutrients from food to pass through so that your body can use them for energy, repair, hormone production, immune regulation, and all of the other things that keep you alive and functioning well. But at the same time, it also has to prevent unwanted things from crossing into the bloodstream unnecessarily, things like pathogens, toxins, and partially digested food particles.And that balance is so important because when the gut environment becomes disrupted, whether that is from chronic inflammation, infections, medications, stress, poor diet, lack of sleep, or a combination of all of the above, the immune system can become more activated and more reactive over time. Think about how that affects people with autoimmune disease, right? And this is where we start hearing terms like intestinal permeability, immune dysregulation, systemic inflammation, and microbiome imbalance.Now, I want to be really careful here because there is a lot of misinformation online about gut health. The gut is not the only driver of autoimmune disease, and we don’t want to oversimplify something that is actually very complex. Autoimmune disease involves genetics, environment, immune function, infections, stress, hormones, and many other overlapping factors. But what we do know is that the gut plays an important role in immune regulation, and intestinal permeability is associated with autoimmune disease in the scientific literature. In fact, every autoimmune disease that has been studied has been associated with this condition.We also know that many people with autoimmune disease experience digestive symptoms or signs of impaired gut function, whether that is bloating, reflux, constipation, food reactivity, or irregular bowel habits. And even beyond digestion itself, the gut can influence things like your energy levels, your mood, your skin health, inflammation, nutrient absorption. That last part is especially important because if your digestion and absorption are compromised, it becomes much harder for the body to get the nutrients that it needs for repair and immune regulation.And honestly, this is again a really big piece of my own story. I already mentioned that before AIP I had been dealing with undiagnosed celiac disease, along with being super depleted from a vegan diet that left me with multiple nutrient deficiencies. I was low in nutrients that are incredibly important for immune health and tissue repair, things like B12 and iron, my digestion itself was clearly not functioning optimally.And at the time, I didn’t fully understand how connected all of these things were, but looking back, it makes a lot of sense that my body needed time and consistent nourishment before it could tolerate a wider variety of foods again.This is one of the reasons why AIP is structured the way it is. People often just think that it’s a long list of foods to remove, but the protocol is really trying to do a couple things at once. Reduce that inflammatory burden, support nutrient density, create a more stable and nourishing gut environment, and give the immune system an opportunity to calm down.All of these things don’t happen perfectly or instantly, but gradually over time, and it doesn’t just happen during elimination. This is a key theme of this episode, and what I want everybody to take away today. For many people, gut healing and improved tolerance continue long after reintroductions begin, and sometimes even for years afterwards.

[00:09:10] Intestinal Permeability (aka “Leaky Gut”)

Mickey: So with that foundation and idea in mind, let’s talk more specifically about one of the concepts people hear about most often when discussing gut health and autoimmune disease, intestinal permeability, sometimes called “leaky gut”. Now, this phrase can sound dramatic, and honestly, it sometimes gets used in ways that are oversimplified or exaggerated, but the underlying concept itself is very real and well-established in the scientific literature.Your intestinal lining is designed to function as a selective barrier. You can think of it as almost like a finely woven filter. Its job is to allow helpful things through, like nutrients, water, vitamins, minerals, amino acids, fatty acids, while keeping larger particles, pathogens, and unwanted substances from crossing too easily into the bloodstream.And one of the ways it does this is through structures called tight junctions. These are tiny protein connections between the cells lining the intestinal wall that help regulate what passes through and what stays out. And under healthy conditions, those tight junctions open and close in a very controlled way.They’re dynamic, they’re responsive, and they are a part of your normal physiology. But when the gut environment is under stress for a long period of time, those barriers can become less regulated, and when that happens, larger particles might pass through more easily than they should. The immune system definitely notices that, and because the immune system is constantly monitoring what crosses this barrier, it might respond with increased immune activity and inflammation.That’s essentially what we mean when we talk about increased intestinal permeability. Now importantly, this isn’t something unique to autoimmune disease alone. Intestinal permeability can be influenced by many different factors, including chronic inflammation, infections, certain medications, disruptions to your sleep, stress, dietary factors, alcohol, and other changes in the microbiome.And stress is a really big one here. People often think of stress as purely emotional, but the body experiences stress physically, too. Lack of sleep, over-training, illness, under-eating, blood sugar instability all cause chronic physiological stress, and they all influence gut function and barrier integrity.This is one of the reasons I always emphasize that healing on AIP isn’t just about food, because you can theoretically eat this perfect elimination diet, but if your nervous system is constantly overwhelmed and your body never gets a chance to shift into repair mode, healing becomes so much harder. And this is also where I think people sometimes misunderstand what AIP is actually doing.The elimination phase is not magically healing the gut overnight. What it’s really doing is helping reduce some of the ongoing inputs that might be contributing to inflammation or barrier stress for each person while simultaneously increasing nutrient density and creating conditions that better support repair. That distinction is important. Removing triggers alone isn’t enough. The body also needs adequate nutrients, enough calories, protein, micronutrients, sleep, stress regulation, and time. And for many people, quite a bit of time.I think my own experience really reflects this. When I first started AIP, again, my digestion was really struggling. I was super bloated every time I ate. I had really irregular bowel habits. I had all these nutrient deficiencies, and I just had very little resilience when it came to reintroducing foods, even though I had been in the elimination phase long enough to experience some solid improvements. And early on, I interpreted those failed reintroductions as proof that my gut was perhaps permanently dysfunctional, and that I would likely need to eat this super restricted diet long term.And I know many of you might be in this exact same situation. Now I see those reactions differently. For me, they were signs that my gut environment and immune system still needed more support and more time for healing. And over the years, that turned out to be the case. As my nutrient status improved, my digestion became more stable, and my overall health became more resilient, my tolerance to foods gradually expanded, too, slowly and steadily over time.And I think that’s an incredibly important message for everybody to hear because early reactions during reintroductions do not necessarily mean never again. Sometimes they just mean not yet, and that can be really hard to trust when you’re in the middle of the process. Healing is often less about flipping a switch and more about gradually rebuilding capacity over time.

[00:14:10] The Microbiome Shift

Mickey: So now that we’ve talked about the gut lining itself, let’s move into another major piece of the gut-healing conversation, the microbiome, and what tends to shift there during AIP.The microbiome refers to the community of bacteria and other microorganisms living primarily in the digestive tract. And while there’s still a lot we’re learning about it, we know that the microbiome plays important roles in digestion, immune regulation, inflammation, and even things like metabolism and mood.And importantly, your microbiome is not static. It changes in response to diet, stress, sleep, medications, illness, environment, and lifestyle factors. It is so responsive. This is one of the reasons why AIP can create such significant shifts for some people, especially if their diet beforehand was low in nutrient density or heavily reliant on ultra-processed foods.When somebody starts AIP, they’re often reducing many of the things associated with microbiome disruption, including those processed foods, those additives, excess sugar, and foods that may be increasing inflammation or digestive symptoms for that individual. And then at the same time, they’re usually increasing foods that help support microbial diversity and gut health. Fiber-rich vegetables, colorful plant foods, fermented foods, seafood, healthy fats, and a much wider range of micronutrients and phytonutrients.And those shifts can influence the gut environment pretty significantly over time. One of the things researchers are especially interested in is the production of compounds called short-chain fatty acids, including one called butyrate. These compounds are produced when the gut bacteria ferment certain types of fiber, and they help support the cells lining the colon and play a role in maintaining gut barrier health and regulating inflammation.Now, I don’t think you need to memorize terms like short-chain fatty acids, unless you’re a nerd like me, but I do think it’s helpful to understand that the foods we eat are constantly influencing the environment inside the gut and the organisms that are living there and that keep us healthy. And sometimes when that environment starts changing, people actually feel a little bit worse before they feel better.This is something I like to normalize because it can be unsettling if you’re not expecting it. So as you are increasing your fiber, your vegetables, your fermented foods, or maybe you’re just starting with shifting away from highly processed foods, you might temporarily notice some more bloating, some gas, some changes in your digestion, or just your gut feeling a little bit different than usual.And while ongoing severe symptoms should absolutely be addressed right away, some temporary adjustment during major dietary changes can be a normal part of adaptation. The microbiome is responding to a completely different food environment than it might have been used to before, and sometimes the gut just needs a little bit of time to adapt to new routines, more fiber, different foods, and a changing microbial environment.And interestingly, some of the AIP research has suggested that changes in symptoms and quality of life might be related to, at least in part, the effects on the gut environment and microbiome-mediated immune regulation. Again, this is still a very much evolving area of research. I don’t want to oversimplify it, but it does support the broader idea that foods and lifestyle patterns we repeat consistently can influence the gut ecosystem in meaningful ways over time.

[00:17:55] Nutrient Density = Repair Mode

Mickey: And that brings us to a really important part of the conversation, the role of nutrient density in repair and rebuilding. You’ve heard me say this before. One of the biggest misconceptions people have about AIP is that a lot of people think the benefit just comes from the removals, but you guys, if you’ve been listening to any of these episodes, you know that one of the most therapeutic parts of AIP is often what gets added in.Because gut healing and immune regulation require raw materials. The body cannot repair tissue, produce enzymes, regulate inflammation, maintain that gut lining, or support the immune system without adequate nutrition. And this is especially important in autoimmune disease, where nutrient deficiencies are incredibly common. Years of inflammation, digestive dysfunction, restrictive diet, chronic stress, medication use, or malabsorption can all deplete the body over time, and that depletion is significant because nutrients are not optional extras when it comes to healing.This is one of the reasons why nutrient density is such a central principle of the Autoimmune Protocol, why I wrote the book The Nutrient Dense Kitchen. We are trying to increase the concentration of vitamins, minerals, amino acids, healthy fats, and phytonutrients that support all of these things that we want to happen.And this is where some of the hallmark AIP foods really do the heavy lifting. Things like bone broth, collagen-rich foods, organ meats, seafood, colorful vegetables, healthy fats, fermented foods, and high-quality proteins. These foods provide nutrients that are deeply involved in repair processes. For example, amino acids like glycine, glutamine, and proline are important for connective tissue and gut lining support.Zinc and vitamin A are involved in maintaining the integrity of the intestinal barrier and supporting immune function. Omega-3 fats help regulate inflammation and are just so helpful to maintaining a healthy microbiome. Iron and B vitamins are essential for energy production and oxygen transport.And many colorful plant foods provide fiber and phytonutrients that help support both the microbiome and the immune system. This is also one of the reasons that the updated AIP framework puts such a strong emphasis on inclusion and abundance, not just restriction. The question isn’t only what are we removing, it is also are we consistently nourishing the body enough to support healing?Because those are two different things. And honestly, this was a major lesson for me personally. When I started AIP, it wasn’t just about removing foods. It was about finally giving my body nutrients it had been missing for a very long time. And I noticed over many years, you guys, I’ve been doing this now for 15 years, the more consistent I am with nutrient-dense foods, the more stable my digestion and resilience have become.And the research on AIP reflects this as well. Some of the researchers studying AIP have proposed that at least part of the positive changes that people experience may be related to improvements in nutrient status, effects on the gut environment, and changes involving the microbiome and immune regulation.And in studies involving autoimmune disease and inflammatory bowel disease, participants often showed improvements not just in symptoms and quality of life, but also in their digestive symptoms, energy, and well-being.

[00:21:30] Why Lifestyle Still Matters

Mickey: Now, of course, nutrition isn’t just the entire picture, which brings us to the next equally important piece of gut healing, lifestyle. Because even the most nutrient-dense diet can’t fully compensate for chronic stress, poor sleep, and nervous system overload.Here is something that I think people really need permission to hear. Healing doesn’t happen in isolation from the rest of your life. Your body is constantly taking in information from your environment. How much stress you’re under, whether you feel safe, whether you’re resting, whether you’re sleeping, whether you’re overextended, whether your nervous system ever gets a chance to settle.All of that influences digestion and immune function, and we actually know from research that stress itself can directly affect the gut. Stress can influence intestinal permeability, digestive function, inflammation, motility, and even that composition of the microbiome. Which means you can be eating an incredibly nutrient-dense food, but if your body is constantly stuck in a high-alert state, healing just becomes that much more difficult.And sleep can be a huge part of this. Sleep is when the body carries out so much of its repair work. Immune regulation, tissue repair, nervous system recovery. All of those processes are deeply connected to sleep quality. I think people often underestimate how much poor sleep can affect their digestion and their inflammation.And then there’s stress management. Now, I want to be really clear here because this conversation can easily become frustrating for people living with chronic illness. Stress management doesn’t just mean relax or meditate, and it doesn’t mean that your illness is your fault because you’re stressed.Honestly, we are under much more stress than a normal, healthy person. But what it means is recognizing that chronic stress changes physiology, and if we can support the nervous system more consistently, we often create a better environment for healing. That might look like better boundaries, more rest, therapy, breathing practices, spending more time outside, reducing overcommitment, asking for help, or simply creating more consistency and predictability in daily life.And importantly, it does not have to look perfect to matter. Movement is another important piece here, too. Not extreme exercise or punishing workouts, but gentle, supportive movement can improve circulation, support motility and digestion, regulate stress hormones, and positively influence the microbiome.Things like walking, mobility work, some strength training, yoga, stretching. Literally whatever is appropriate and accessible for you to move your body in a way that brings you joy and helps grease everything up a little bit. These things are going to help the body and the gut function better overall.And I think one of the biggest mindset shifts people experience over time with AIP is realizing that healing is much broader than just food. In the beginning, a lot of us focus just on elimination. I was definitely here myself. And that makes sense because the food piece feels really tangible and measurable. But over time, you might realize that these other factors matter a lot too.I know for me personally, when my gut health starts trending in the wrong direction, it’s usually not just about food. Yes, I probably need some more fermented foods or some more fiber or some more nutrient-dense meals, right? But when I step back and look honestly, I also often realize I’ve been stressed, I’ve been sleeping less, I’ve been doing too much, or I have been disconnected from the routines that help me feel grounded and regulated.And that’s important because it reminds us that gut health is dynamic. It’s not something that you fix once and you never think about again, but it’s something that responds to the overall conditions of your life.

[00:25:31] Why Healing Isn’t Linear

Mickey: So now that we’ve talked about food, nutrients, the microbiome, and lifestyle, let’s move into another incredibly important part of this conversation, and that’s why healing so often feels nonlinear and why ups and downs during the process are completely normal.So when you look at long-term healing, symptoms can shift, tolerance can change, and the body can become more resilient in some ways while still struggling in others. And honestly, this is a completely normal phenomenon when you’re talking about rebuilding systems that might have been under stress for years or even decades.I’ve said this before, healing is not like flipping a switch. It’s rebuilding capacity and resilience, and that rebuilding takes time. This is especially important when it comes to gut health and reintroducing foods. I think sometimes people assume that the goal of reintroductions is just to pass or get these “yes” foods back into their diet immediately.But reintroductions are really giving you information about where your body is right now, and sometimes that information is, “This food is okay,” sometimes, “This food is firmly in the gray area,” and sometimes it’s, “This food might be increasing inflammation or disrupting my digestion enough that I just need to take it off the table for now.”That process of deciding kind of which category each food is in can be really discouraging in the moment, especially when your symptoms temporarily flare. During this reintroduction process you might notice more bloating or changes in your bowel habits, or maybe some of your primary autoimmune symptoms come back, and you’re just kind of bummed about that.And understandably, it makes you feel a little bit like you’ve gone backwards, but often what you’re actually doing is learning which inputs are still placing stress on your gut and immune system at the stage of healing that you’re at right now. And that information can become incredibly useful moving forward. Because when you identify foods that are consistently disrupting digestion or increasing your inflammation and then removing those foods, again, while continuing to focus on nutrient density and all of the lifestyle things that we’ve talked about, that gut environment might continue to improve over time.This is something that I really wish more people understood. Gut healing does not stop when reintroductions begin. In many ways, reintroductions are a part of the healing process itself. They are helping you identify which foods support your resilience, which foods might still be too inflammatory, and which foods your body might not tolerate now, but that you might be able to revisit later.And that was absolutely my experience. When I didn’t tolerate many early reintroductions, I found that incredibly discouraging because I thought healing was supposed to happen faster or that I would get at least a few foods, but really, I reacted to everything.But looking back now, it makes perfect sense. I was coming from years of celiac disease, all of the nutrient deficiencies, just really messed up digestive dysfunction, inflammation. I was just completely depleted, and my body needed much more rebuilding than I understood at the time.And I ended up being delighted to see over the years, my tolerance continued to evolve. Some foods that caused obvious symptoms early on became tolerable much later. Certain nightshades improved over time. Even dairy, which I had a borderline anaphylactic reaction to back in the day, has eventually become something that I can tolerate in certain forms after many, many years of focusing on my personalized protocol and overall gut health, which is something that I never expected.And I think that this is such an important perspective because it reminds you that food tolerance is not fixed forever. The body is dynamic. And while not every food works for every person, many people do find that resilience and flexibility improve over time as their overall health improves.And this is where tracking can be so helpful because when you’re living inside the process day to day, it’s easy to focus only on what’s still hard. You forget that maybe your digestion is more stable than it was six months ago, your energy crashes are less severe, your skin has improved, your recovery from stress is better, or that baseline inflammation is lower than it used to be. Those forms of progress are absolutely important.And I really want to normalize that healing often happens in layers. Sometimes digestion improves before energy does. Sometimes sleep improves before your pain levels change. Sometimes food tolerance expands while stress resilience is lagging behind. And honestly, I think one of the most powerful shifts during AIP happens when you stop measuring healing only by perfection.So the goal is not becoming a person who doesn’t have any symptoms, never reacts to anything, and never has difficult stretches again. Honestly, that is a very unattainable goal, right? The goal is to become more resilient, more stable, more supported, more capable of recovering and connected to your body, and able to use the information to live your life in the way that you intend.This is a much more realistic and sustainable definition of healing. And when you understand that healing is a long-term rebuild rather than a quick fix, it becomes easier to stay grounded during the inevitable ups and downs.

[00:31:22] Wrap Up and Closing

Mickey: So to wrap up today, I hope this episode helps clarify what’s really happening during gut healing on AIP. While elimination is often the most visible part of the protocol, a lot of the deeper work is happening behind the scenes, supporting that gut lining, influencing the microbiome, improving nutrient status, calming that immune activation, and creating conditions that allow the body to repair over time.And importantly, those changes don’t always happen quickly or all at once. Gut healing is often gradual. It can continue long after the elimination phase is over, and even throughout reintroductions as you learn which foods support your body best right now. That’s why early reactions don’t necessarily mean failure or forever. Sometimes they’re simply information that the gut and immune system still need a little bit more support, more stability, or more time.Like I said many times in this episode, that has definitely been true in my own experience, and over time, as I focused on all of these areas that we talked about today, my tolerance to foods changed dramatically in ways I never would have expected early on. So if you’re somewhere in the middle of this process, I hope this episode gives you a better understanding of what your body might actually be working on underneath the surface.Thank you so much for joining me for this episode of the Autoimmune Wellness Podcast, and I will see you next time.