When most people start the Autoimmune Protocol, they naturally focus on the food: what to remove, what to eat instead, and how to navigate all of the planning that comes with a major dietary change.
But one of the most important things happening during AIP is often something you can’t actually see—changes happening inside the gut itself.
Because AIP isn’t just designed to remove potential food triggers. It’s also designed to support systems commonly affected in autoimmune disease, including the gut lining, the microbiome, nutrient status, and immune regulation.
And those changes don’t always happen quickly or in a straight line.
For many people, healing happens gradually over time. Digestion may become more stable. Energy may improve. Foods that caused symptoms early on may become tolerable much later in the process.
In this episode of the AIP Deep Dive series, Mickey explains what’s actually happening in the gut during AIP and why healing often continues long after the elimination phase ends.
She explores intestinal permeability, the microbiome, nutrient density, lifestyle factors, and why healing is often more about rebuilding resilience than achieving perfection.
00:00 – Introduction and Mickey’s personal gut healing story
04:35 – Why the gut matters in autoimmune disease
09:10 – Intestinal permeability (“leaky gut”) explained
14:10 – How the microbiome shifts during AIP
17:55 – Why nutrient density supports repair
21:30 – The role of lifestyle, stress, and sleep
25:31 – Why healing isn’t linear
31:22 – Wrap-up and key takeaways
When most people start the Autoimmune Protocol, they understandably
Mickey:focus on the food, what foods you're removing, which foods to include, and
Mickey:how to do all of the meal planning.
Mickey:But one of the most important things happening during AIP is often something
Mickey:that you can't actually see: changes in your gut environment itself.
Mickey:Because AIP isn't just designed to remove potential food triggers, it's
Mickey:also designed to support some of the systems that are commonly affected
Mickey:in autoimmune disease, including the gut lining, the microbiome, nutrient
Mickey:status, and immune regulation.
Mickey:And changes in these areas don't always happen quickly or
Mickey:in a perfectly straight line.
Mickey:For a lot of people, healing happens gradually and over time.
Mickey:Maybe digestion becomes more stable, maybe energy improves, or maybe certain
Mickey:foods that cause symptoms early on become tolerable much later in the process,
Mickey:which is always a delightful surprise.
Mickey:This was definitely true for me.
Mickey:When I first started AIP, my gut health was clearly struggling.
Mickey:I had celiac disease, years of nutritional deficiencies from both autoimmunity and a
Mickey:very depleted vegan diet, and my digestion itself was just not functioning well.
Mickey:My bowel habits weren't regular, I dealt with bloating frequently, and even though
Mickey:I experienced progress in the elimination phase, my early reintroductions
Mickey:honestly did not go very well.
Mickey:And I remember feeling at the time just so disappointed.
Mickey:But looking back now, I can see that my body simply needed more
Mickey:time, more nourishment, and more support before it was ready for
Mickey:some of those foods once again.
Mickey:And over the years, as I consistently focused on nutrient density, lifestyle,
Mickey:and supporting my gut health, my tolerance changed dramatically.
Mickey:Foods that once felt completely off the table for me, like certain
Mickey:nightshades, and eventually even dairy, became tolerable much,
Mickey:much later in my healing journey.
Mickey:And even now, I can usually tell when my gut health is starting
Mickey:to trend in the wrong direction.
Mickey:For me, that often looks like bloating after meals or changes
Mickey:in digestion or bowel regularity.
Mickey:Those are signs that I need to just go back and refocus on the basics, the
Mickey:things that we have honestly talked about over and over on this podcast.
Mickey:More fermented foods, more fiber, more nutrient-dense meals, and
Mickey:better overall recovery habits.
Mickey:So today we're going to talk about what is actually happening in the gut during
Mickey:AIP, including things like intestinal permeability, the microbiome, nutrient
Mickey:density, and why healing often continues well beyond the elimination phase itself.
Mickey:Because understanding gut healing on AIP can help you approach
Mickey:healing with just a little more clarity, patience, and confidence.
Mickey:Welcome back to the Autoimmune Wellness Podcast.
Mickey:I'm your host, Mickey Trescott, and this is another installment
Mickey:in our AIP Deep Dive series.
Mickey:So far in this series, we've covered the full framework of the Autoimmune
Mickey:Protocol from transition to elimination to reintroduction, along with the
Mickey:foundational role of nutrient density and lifestyle practices that support
Mickey:healing throughout the entire process.
Mickey:If you're new here, make sure you start with episodes 51 and listen through
Mickey:55 for a complete overview of every single phase of the Autoimmune Protocol.
Mickey:Today, we're diving into one of the biggest questions underneath all of it.
Mickey:What is actually happening in the gut while somebody is doing AIP?
Mickey:Because while most people focus on those food lists, the real story is what those
Mickey:dietary and lifestyle changes might be supporting behind the scenes , or
Mickey:more specifically, inside your gut.
Mickey:We are going to talk about the gut lining, the microbiome, immune
Mickey:regulation, nutrient status, and why so many people notice that their
Mickey:tolerance to food changes over time.
Mickey:So if you are somebody who has some experience with elimination,
Mickey:maybe you are feeling frustrated that your reintroductions haven't
Mickey:gone well, this episode is for you.
Mickey:And before we get started, just a reminder that this podcast
Mickey:is intended for educational and informational purposes only.
Mickey:It's definitely not medical advice, and always work with your qualified healthcare
Mickey:provider when making changes to your diet, supplements, or treatment plan.
Mickey:Okay, let's jump into it.
Mickey:So before we talk about gut healing itself, we first need to understand
Mickey:why the gut matters so much in autoimmune disease in the first place.
Mickey:Because the gut is not just responsible for digesting food, it's also deeply
Mickey:connected to the immune system.
Mickey:In fact, a large portion of the body's immune activity is associated with the
Mickey:gut and the tissues surrounding it.
Mickey:The digestive tract is constantly interacting with the outside world
Mickey:through everything that we eat, drink, and are exposed to, so the immune
Mickey:system has to stay in very close communication with it at all times.
Mickey:And one of the gut's biggest jobs is deciding what is safe, what is harmful,
Mickey:and what should be actually absorbed into our body, and what should we keep out.
Mickey:So the gut is functioning both as a barrier and a communication center.
Mickey:On one hand, it needs to allow nutrients from food to pass through so that your
Mickey:body can use them for energy, repair, hormone production, immune regulation,
Mickey:and all of the other things that keep you alive and functioning well.
Mickey:But at the same time, it also has to prevent unwanted things from crossing
Mickey:into the bloodstream unnecessarily, things like pathogens, toxins, and
Mickey:partially digested food particles.
Mickey:And that balance is so important because when the gut environment becomes
Mickey:disrupted, whether that is from chronic inflammation, infections, medications,
Mickey:stress, poor diet, lack of sleep, or a combination of all of the above,
Mickey:the immune system can become more activated and more reactive over time.
Mickey:Think about how that affects people with autoimmune disease, right?
Mickey:And this is where we start hearing terms like intestinal permeability,
Mickey:immune dysregulation, systemic inflammation, and microbiome imbalance.
Mickey:Now, I want to be really careful here because there is a lot of
Mickey:misinformation online about gut health.
Mickey:The gut is not the only driver of autoimmune disease, and we don't
Mickey:want to oversimplify something that is actually very complex.
Mickey:Autoimmune disease involves genetics, environment, immune function,
Mickey:infections, stress, hormones, and many other overlapping factors.
Mickey:But what we do know is that the gut plays an important role in immune
Mickey:regulation, and intestinal permeability is associated with autoimmune
Mickey:disease in the scientific literature.
Mickey:In fact, every autoimmune disease that has been studied has been
Mickey:associated with this condition.
Mickey:We also know that many people with autoimmune disease experience
Mickey:digestive symptoms or signs of impaired gut function, whether that is
Mickey:bloating, reflux, constipation, food reactivity, or irregular bowel habits.
Mickey:And even beyond digestion itself, the gut can influence things like your energy
Mickey:levels, your mood, your skin health, inflammation, nutrient absorption.
Mickey:That last part is especially important because if your digestion and absorption
Mickey:are compromised, it becomes much harder for the body to get the nutrients that it
Mickey:needs for repair and immune regulation.
Mickey:And honestly, this is again a really big piece of my own story.
Mickey:I already mentioned that before AIP I had been dealing with undiagnosed
Mickey:celiac disease, along with being super depleted from a vegan diet that left
Mickey:me with multiple nutrient deficiencies.
Mickey:I was low in nutrients that are incredibly important for immune health
Mickey:and tissue repair, things like B12 and iron, my digestion itself was
Mickey:clearly not functioning optimally.
Mickey:And at the time, I didn't fully understand how connected all of these things
Mickey:were, but looking back, it makes a lot of sense that my body needed time and
Mickey:consistent nourishment before it could tolerate a wider variety of foods again.
Mickey:This is one of the reasons why AIP is structured the way it is.
Mickey:People often just think that it's a long list of foods to remove,
Mickey:but the protocol is really trying to do a couple things at once.
Mickey:Reduce that inflammatory burden, support nutrient density, create a more stable and
Mickey:nourishing gut environment, and give the immune system an opportunity to calm down.
Mickey:All of these things don't happen perfectly or instantly, but gradually over time, and
Mickey:it doesn't just happen during elimination.
Mickey:This is a key theme of this episode, and what I want everybody to take away today.
Mickey:For many people, gut healing and improved tolerance continue long
Mickey:after reintroductions begin, and sometimes even for years afterwards.
Mickey:So with that foundation and idea in mind, let's talk more specifically about one of
Mickey:the concepts people hear about most often when discussing gut health and autoimmune
Mickey:disease, intestinal permeability, sometimes called "leaky gut".
Mickey:Now, this phrase can sound dramatic, and honestly, it sometimes gets used
Mickey:in ways that are oversimplified or exaggerated, but the underlying concept
Mickey:itself is very real and well-established in the scientific literature.
Mickey:Your intestinal lining is designed to function as a selective barrier.
Mickey:You can think of it as almost like a finely woven filter.
Mickey:Its job is to allow helpful things through, like nutrients, water,
Mickey:vitamins, minerals, amino acids, fatty acids, while keeping larger particles,
Mickey:pathogens, and unwanted substances from crossing too easily into the bloodstream.
Mickey:And one of the ways it does this is through structures called tight junctions.
Mickey:These are tiny protein connections between the cells lining the
Mickey:intestinal wall that help regulate what passes through and what stays out.
Mickey:And under healthy conditions, those tight junctions open and
Mickey:close in a very controlled way.
Mickey:They're dynamic, they're responsive, and they are a part of your normal physiology.
Mickey:But when the gut environment is under stress for a long period of time, those
Mickey:barriers can become less regulated, and when that happens, larger particles might
Mickey:pass through more easily than they should.
Mickey:The immune system definitely notices that, and because the immune system is
Mickey:constantly monitoring what crosses this barrier, it might respond with increased
Mickey:immune activity and inflammation.
Mickey:That's essentially what we mean when we talk about increased
Mickey:intestinal permeability.
Mickey:Now importantly, this isn't something unique to autoimmune disease alone.
Mickey:Intestinal permeability can be influenced by many different factors, including
Mickey:chronic inflammation, infections, certain medications, disruptions to your
Mickey:sleep, stress, dietary factors, alcohol, and other changes in the microbiome.
Mickey:And stress is a really big one here.
Mickey:People often think of stress as purely emotional, but the body
Mickey:experiences stress physically, too.
Mickey:Lack of sleep, over-training, illness, under-eating, blood sugar instability
Mickey:all cause chronic physiological stress, and they all influence gut
Mickey:function and barrier integrity.
Mickey:This is one of the reasons I always emphasize that healing on AIP isn't
Mickey:just about food, because you can theoretically eat this perfect elimination
Mickey:diet, but if your nervous system is constantly overwhelmed and your body
Mickey:never gets a chance to shift into repair mode, healing becomes so much harder.
Mickey:And this is also where I think people sometimes misunderstand
Mickey:what AIP is actually doing.
Mickey:The elimination phase is not magically healing the gut overnight.
Mickey:What it's really doing is helping reduce some of the ongoing inputs that
Mickey:might be contributing to inflammation or barrier stress for each person
Mickey:while simultaneously increasing nutrient density and creating
Mickey:conditions that better support repair.
Mickey:That distinction is important.
Mickey:Removing triggers alone isn't enough.
Mickey:The body also needs adequate nutrients, enough calories, protein, micronutrients,
Mickey:sleep, stress regulation, and time.
Mickey:And for many people, quite a bit of time.
Mickey:I think my own experience really reflects this.
Mickey:When I first started AIP, again, my digestion was really struggling.
Mickey:I was super bloated every time I ate.
Mickey:I had really irregular bowel habits.
Mickey:I had all these nutrient deficiencies, and I just had very little resilience
Mickey:when it came to reintroducing foods, even though I had been in
Mickey:the elimination phase long enough to experience some solid improvements.
Mickey:And early on, I interpreted those failed reintroductions as proof that my gut
Mickey:was perhaps permanently dysfunctional, and that I would likely need to eat
Mickey:this super restricted diet long term.
Mickey:And I know many of you might be in this exact same situation.
Mickey:Now I see those reactions differently.
Mickey:For me, they were signs that my gut environment and immune system still needed
Mickey:more support and more time for healing.
Mickey:And over the years, that turned out to be the case.
Mickey:As my nutrient status improved, my digestion became more stable, and my
Mickey:overall health became more resilient, my tolerance to foods gradually expanded,
Mickey:too, slowly and steadily over time.
Mickey:And I think that's an incredibly important message for everybody to hear because
Mickey:early reactions during reintroductions do not necessarily mean never again.
Mickey:Sometimes they just mean not yet, and that can be really hard to trust when
Mickey:you're in the middle of the process.
Mickey:Healing is often less about flipping a switch and more about gradually
Mickey:rebuilding capacity over time.
Mickey:So now that we've talked about the gut lining itself, let's move into
Mickey:another major piece of the gut-healing conversation, the microbiome, and
Mickey:what tends to shift there during AIP.
Mickey:The microbiome refers to the community of bacteria and other microorganisms
Mickey:living primarily in the digestive tract.
Mickey:And while there's still a lot we're learning about it, we know that
Mickey:the microbiome plays important roles in digestion, immune
Mickey:regulation, inflammation, and even things like metabolism and mood.
Mickey:And importantly, your microbiome is not static.
Mickey:It changes in response to diet, stress, sleep, medications, illness,
Mickey:environment, and lifestyle factors.
Mickey:It is so responsive.
Mickey:This is one of the reasons why AIP can create such significant shifts for
Mickey:some people, especially if their diet beforehand was low in nutrient density or
Mickey:heavily reliant on ultra-processed foods.
Mickey:When somebody starts AIP, they're often reducing many of the things
Mickey:associated with microbiome disruption, including those processed foods, those
Mickey:additives, excess sugar, and foods that may be increasing inflammation or
Mickey:digestive symptoms for that individual.
Mickey:And then at the same time, they're usually increasing foods that help support
Mickey:microbial diversity and gut health.
Mickey:Fiber-rich vegetables, colorful plant foods, fermented foods, seafood,
Mickey:healthy fats, and a much wider range of micronutrients and phytonutrients.
Mickey:And those shifts can influence the gut environment pretty
Mickey:significantly over time.
Mickey:One of the things researchers are especially interested in is the production
Mickey:of compounds called short-chain fatty acids, including one called butyrate.
Mickey:These compounds are produced when the gut bacteria ferment certain
Mickey:types of fiber, and they help support the cells lining the colon and play
Mickey:a role in maintaining gut barrier health and regulating inflammation.
Mickey:Now, I don't think you need to memorize terms like short-chain fatty acids,
Mickey:unless you're a nerd like me, but I do think it's helpful to understand
Mickey:that the foods we eat are constantly influencing the environment inside
Mickey:the gut and the organisms that are living there and that keep us healthy.
Mickey:And sometimes when that environment starts changing, people actually feel a
Mickey:little bit worse before they feel better.
Mickey:This is something I like to normalize because it can be unsettling
Mickey:if you're not expecting it.
Mickey:So as you are increasing your fiber, your vegetables, your fermented foods,
Mickey:or maybe you're just starting with shifting away from highly processed
Mickey:foods, you might temporarily notice some more bloating, some gas, some changes in
Mickey:your digestion, or just your gut feeling a little bit different than usual.
Mickey:And while ongoing severe symptoms should absolutely be addressed right
Mickey:away, some temporary adjustment during major dietary changes can
Mickey:be a normal part of adaptation.
Mickey:The microbiome is responding to a completely different food environment
Mickey:than it might have been used to before, and sometimes the gut just needs a
Mickey:little bit of time to adapt to new routines, more fiber, different foods,
Mickey:and a changing microbial environment.
Mickey:And interestingly, some of the AIP research has suggested that changes
Mickey:in symptoms and quality of life might be related to, at least in part, the
Mickey:effects on the gut environment and microbiome-mediated immune regulation.
Mickey:Again, this is still a very much evolving area of research.
Mickey:I don't want to oversimplify it, but it does support the broader idea that
Mickey:foods and lifestyle patterns we repeat consistently can influence the gut
Mickey:ecosystem in meaningful ways over time.
Mickey:And that brings us to a really important part of the conversation, the role of
Mickey:nutrient density in repair and rebuilding.
Mickey:You've heard me say this before.
Mickey:One of the biggest misconceptions people have about AIP is that a lot of people
Mickey:think the benefit just comes from the removals, but you guys, if you've been
Mickey:listening to any of these episodes, you know that one of the most therapeutic
Mickey:parts of AIP is often what gets added in.
Mickey:Because gut healing and immune regulation require raw materials.
Mickey:The body cannot repair tissue, produce enzymes, regulate inflammation, maintain
Mickey:that gut lining, or support the immune system without adequate nutrition.
Mickey:And this is especially important in autoimmune disease, where nutrient
Mickey:deficiencies are incredibly common.
Mickey:Years of inflammation, digestive dysfunction, restrictive diet, chronic
Mickey:stress, medication use, or malabsorption can all deplete the body over time,
Mickey:and that depletion is significant because nutrients are not optional
Mickey:extras when it comes to healing.
Mickey:This is one of the reasons why nutrient density is such a central principle of
Mickey:the Autoimmune Protocol, why I wrote the book The Nutrient Dense Kitchen.
Mickey:We are trying to increase the concentration of vitamins, minerals,
Mickey:amino acids, healthy fats, and phytonutrients that support all of
Mickey:these things that we want to happen.
Mickey:And this is where some of the hallmark AIP foods really do the heavy lifting.
Mickey:Things like bone broth, collagen-rich foods, organ meats, seafood, colorful
Mickey:vegetables, healthy fats, fermented foods, and high-quality proteins.
Mickey:These foods provide nutrients that are deeply involved in repair processes.
Mickey:For example, amino acids like glycine, glutamine, and proline are important for
Mickey:connective tissue and gut lining support.
Mickey:Zinc and vitamin A are involved in maintaining the integrity
Mickey:of the intestinal barrier and supporting immune function.
Mickey:Omega-3 fats help regulate inflammation and are just so helpful
Mickey:to maintaining a healthy microbiome.
Mickey:Iron and B vitamins are essential for energy production and oxygen transport.
Mickey:And many colorful plant foods provide fiber and phytonutrients that help support
Mickey:both the microbiome and the immune system.
Mickey:This is also one of the reasons that the updated AIP framework puts such
Mickey:a strong emphasis on inclusion and abundance, not just restriction.
Mickey:The question isn't only what are we removing, it is also are
Mickey:we consistently nourishing the body enough to support healing?
Mickey:Because those are two different things.
Mickey:And honestly, this was a major lesson for me personally.
Mickey:When I started AIP, it wasn't just about removing foods.
Mickey:It was about finally giving my body nutrients it had been
Mickey:missing for a very long time.
Mickey:And I noticed over many years, you guys, I've been doing this now for 15
Mickey:years, the more consistent I am with nutrient-dense foods, the more stable
Mickey:my digestion and resilience have become.
Mickey:And the research on AIP reflects this as well.
Mickey:Some of the researchers studying AIP have proposed that at least part of the
Mickey:positive changes that people experience may be related to improvements in
Mickey:nutrient status, effects on the gut environment, and changes involving
Mickey:the microbiome and immune regulation.
Mickey:And in studies involving autoimmune disease and inflammatory bowel disease,
Mickey:participants often showed improvements not just in symptoms and quality of
Mickey:life, but also in their digestive symptoms, energy, and well-being.
Mickey:Now, of course, nutrition isn't just the entire picture, which brings
Mickey:us to the next equally important piece of gut healing, lifestyle.
Mickey:Because even the most nutrient-dense diet can't fully compensate for chronic stress,
Mickey:poor sleep, and nervous system overload.
Mickey:Here is something that I think people really need permission to hear.
Mickey:Healing doesn't happen in isolation from the rest of your life.
Mickey:Your body is constantly taking in information from your environment.
Mickey:How much stress you're under, whether you feel safe, whether you're resting,
Mickey:whether you're sleeping, whether you're overextended, whether your nervous
Mickey:system ever gets a chance to settle.
Mickey:All of that influences digestion and immune function, and we actually
Mickey:know from research that stress itself can directly affect the gut.
Mickey:Stress can influence intestinal permeability, digestive function,
Mickey:inflammation, motility, and even that composition of the microbiome.
Mickey:Which means you can be eating an incredibly nutrient-dense food, but
Mickey:if your body is constantly stuck in a high-alert state, healing just
Mickey:becomes that much more difficult.
Mickey:And sleep can be a huge part of this.
Mickey:Sleep is when the body carries out so much of its repair work.
Mickey:Immune regulation, tissue repair, nervous system recovery.
Mickey:All of those processes are deeply connected to sleep quality.
Mickey:I think people often underestimate how much poor sleep can affect their
Mickey:digestion and their inflammation.
Mickey:And then there's stress management.
Mickey:Now, I want to be really clear here because this conversation
Mickey:can easily become frustrating for people living with chronic illness.
Mickey:Stress management doesn't just mean relax or meditate, and it
Mickey:doesn't mean that your illness is your fault because you're stressed.
Mickey:Honestly, we are under much more stress than a normal, healthy person.
Mickey:But what it means is recognizing that chronic stress changes physiology, and
Mickey:if we can support the nervous system more consistently, we often create
Mickey:a better environment for healing.
Mickey:That might look like better boundaries, more rest, therapy, breathing practices,
Mickey:spending more time outside, reducing overcommitment, asking for help,
Mickey:or simply creating more consistency and predictability in daily life.
Mickey:And importantly, it does not have to look perfect to matter.
Mickey:Movement is another important piece here, too.
Mickey:Not extreme exercise or punishing workouts, but gentle, supportive movement
Mickey:can improve circulation, support motility and digestion, regulate stress hormones,
Mickey:and positively influence the microbiome.
Mickey:Things like walking, mobility work, some strength training, yoga, stretching.
Mickey:Literally whatever is appropriate and accessible for you to move your body
Mickey:in a way that brings you joy and helps grease everything up a little bit.
Mickey:These things are going to help the body and the gut function better overall.
Mickey:And I think one of the biggest mindset shifts people experience over time
Mickey:with AIP is realizing that healing is much broader than just food.
Mickey:In the beginning, a lot of us focus just on elimination.
Mickey:I was definitely here myself.
Mickey:And that makes sense because the food piece feels really
Mickey:tangible and measurable.
Mickey:But over time, you might realize that these other factors matter a lot too.
Mickey:I know for me personally, when my gut health starts trending
Mickey:in the wrong direction, it's usually not just about food.
Mickey:Yes, I probably need some more fermented foods or some more fiber or
Mickey:some more nutrient-dense meals, right?
Mickey:But when I step back and look honestly, I also often realize I've been
Mickey:stressed, I've been sleeping less, I've been doing too much, or I have been
Mickey:disconnected from the routines that help me feel grounded and regulated.
Mickey:And that's important because it reminds us that gut health is dynamic.
Mickey:It's not something that you fix once and you never think about again,
Mickey:but it's something that responds to the overall conditions of your life.
Mickey:So now that we've talked about food, nutrients, the microbiome, and lifestyle,
Mickey:let's move into another incredibly important part of this conversation,
Mickey:and that's why healing so often feels nonlinear and why ups and downs during
Mickey:the process are completely normal.
Mickey:So when you look at long-term healing, symptoms can shift, tolerance can
Mickey:change, and the body can become more resilient in some ways
Mickey:while still struggling in others.
Mickey:And honestly, this is a completely normal phenomenon when you're talking about
Mickey:rebuilding systems that might have been under stress for years or even decades.
Mickey:I've said this before, healing is not like flipping a switch.
Mickey:It's rebuilding capacity and resilience, and that rebuilding takes time.
Mickey:This is especially important when it comes to gut health and reintroducing foods.
Mickey:I think sometimes people assume that the goal of reintroductions is just
Mickey:to pass or get these "yes" foods back into their diet immediately.
Mickey:But reintroductions are really giving you information about where your body is
Mickey:right now, and sometimes that information is, "This food is okay," sometimes,
Mickey:"This food is firmly in the gray area," and sometimes it's, "This food might be
Mickey:increasing inflammation or disrupting my digestion enough that I just need
Mickey:to take it off the table for now."
Mickey:That process of deciding kind of which category each food is in can be really
Mickey:discouraging in the moment, especially when your symptoms temporarily flare.
Mickey:During this reintroduction process you might notice more bloating or changes in
Mickey:your bowel habits, or maybe some of your primary autoimmune symptoms come back,
Mickey:and you're just kind of bummed about that.
Mickey:And understandably, it makes you feel a little bit like you've gone
Mickey:backwards, but often what you're actually doing is learning which inputs
Mickey:are still placing stress on your gut and immune system at the stage of
Mickey:healing that you're at right now.
Mickey:And that information can become incredibly useful moving forward.
Mickey:Because when you identify foods that are consistently disrupting digestion
Mickey:or increasing your inflammation and then removing those foods, again, while
Mickey:continuing to focus on nutrient density and all of the lifestyle things that
Mickey:we've talked about, that gut environment might continue to improve over time.
Mickey:This is something that I really wish more people understood.
Mickey:Gut healing does not stop when reintroductions begin.
Mickey:In many ways, reintroductions are a part of the healing process itself.
Mickey:They are helping you identify which foods support your resilience, which foods might
Mickey:still be too inflammatory, and which foods your body might not tolerate now, but
Mickey:that you might be able to revisit later.
Mickey:And that was absolutely my experience.
Mickey:When I didn't tolerate many early reintroductions, I found that incredibly
Mickey:discouraging because I thought healing was supposed to happen faster or that
Mickey:I would get at least a few foods, but really, I reacted to everything.
Mickey:But looking back now, it makes perfect sense.
Mickey:I was coming from years of celiac disease, all of the nutrient
Mickey:deficiencies, just really messed up digestive dysfunction, inflammation.
Mickey:I was just completely depleted, and my body needed much more rebuilding
Mickey:than I understood at the time.
Mickey:And I ended up being delighted to see over the years, my
Mickey:tolerance continued to evolve.
Mickey:Some foods that caused obvious symptoms early on became tolerable much later.
Mickey:Certain nightshades improved over time.
Mickey:Even dairy, which I had a borderline anaphylactic reaction to back in the day,
Mickey:has eventually become something that I can tolerate in certain forms after many,
Mickey:many years of focusing on my personalized protocol and overall gut health, which
Mickey:is something that I never expected.
Mickey:And I think that this is such an important perspective because it reminds you that
Mickey:food tolerance is not fixed forever.
Mickey:The body is dynamic.
Mickey:And while not every food works for every person, many people do find that
Mickey:resilience and flexibility improve over time as their overall health improves.
Mickey:And this is where tracking can be so helpful because when you're living
Mickey:inside the process day to day, it's easy to focus only on what's still hard.
Mickey:You forget that maybe your digestion is more stable than it was six months ago,
Mickey:your energy crashes are less severe, your skin has improved, your recovery
Mickey:from stress is better, or that baseline inflammation is lower than it used to be.
Mickey:Those forms of progress are absolutely important.
Mickey:And I really want to normalize that healing often happens in layers.
Mickey:Sometimes digestion improves before energy does.
Mickey:Sometimes sleep improves before your pain levels change.
Mickey:Sometimes food tolerance expands while stress resilience is lagging behind.
Mickey:And honestly, I think one of the most powerful shifts during AIP
Mickey:happens when you stop measuring healing only by perfection.
Mickey:So the goal is not becoming a person who doesn't have any symptoms,
Mickey:never reacts to anything, and never has difficult stretches again.
Mickey:Honestly, that is a very unattainable goal, right?
Mickey:The goal is to become more resilient, more stable, more supported, more capable of
Mickey:recovering and connected to your body, and able to use the information to live
Mickey:your life in the way that you intend.
Mickey:This is a much more realistic and sustainable definition of healing.
Mickey:And when you understand that healing is a long-term rebuild rather than a quick
Mickey:fix, it becomes easier to stay grounded during the inevitable ups and downs.
Mickey:So to wrap up today, I hope this episode helps clarify what's really
Mickey:happening during gut healing on AIP.
Mickey:While elimination is often the most visible part of the protocol, a lot
Mickey:of the deeper work is happening behind the scenes, supporting that gut lining,
Mickey:influencing the microbiome, improving nutrient status, calming that immune
Mickey:activation, and creating conditions that allow the body to repair over time.
Mickey:And importantly, those changes don't always happen quickly or all at once.
Mickey:Gut healing is often gradual.
Mickey:It can continue long after the elimination phase is over, and even throughout
Mickey:reintroductions as you learn which foods support your body best right now.
Mickey:That's why early reactions don't necessarily mean failure or forever.
Mickey:Sometimes they're simply information that the gut and immune system still
Mickey:need a little bit more support, more stability, or more time.
Mickey:Like I said many times in this episode, that has definitely been true in my
Mickey:own experience, and over time, as I focused on all of these areas that we
Mickey:talked about today, my tolerance to foods changed dramatically in ways I
Mickey:never would have expected early on.
Mickey:So if you're somewhere in the middle of this process, I hope this episode
Mickey:gives you a better understanding of what your body might actually be
Mickey:working on underneath the surface.
Mickey:Thank you so much for joining me for this episode of the Autoimmune Wellness
Mickey:Podcast, and I will see you next time.