Marie-Noelle Marquis (00:07):
Welcome to the AIP Summit Podcast, your go- to resource for taking control of your autoimmune health presented by AIP Certified Coaches. Hi, I'm Marie-Noelle Marquis.
Jaime Hartman (00:16):
And I'm Jaime Hartman, and we're here to equip you with the tools, knowledge, and support you need to effectively use the autoimmune protocol.
Marie-Noelle Marquis (00:24):
And today we are talking all about the gut and how to decode your flares.
Jaime Hartman (00:37):
Today, we are bringing you the audio from a session that was presented at the seventh annual AIP Summit, which was held live in January 2026. The speaker is functional nutritionist and AIP Certified Coach, Jennifer Franchak. And her session was on the Gut-Immune Connection in Autoimmune Disease. You will hear her explain how flare-ups are not random, but that they are messages from an overprotective immune system. She'll also talk about how gut health and microbiome imbalances can lead to immune system confusion and inflammation. And the presentation will include practical steps for improving gut health and managing autoimmune flares.
Marie-Noelle Marquis (01:22):
As Jaime mentioned, this is the audio from a session that was presented at the seventh annual AIP Summit. So if you want the full experience of her presentation, including the slides and the Q&A that followed it, you can find it in our archives, which all supporting members of the AIP Summit Community have unlimited access to. There'll be a link in the show notes for you to learn more about how to become a member.
Jaime Hartman (01:45):
That's right. And this episode is coming out on Monday, March 16th. So if you are listening to it that week, you should know that this month we are having a free encore rebroadcast of the whole seventh annual AIP Summit that will be starting on March 19th. That's this Thursday. I'll be sure to put a really prominent link in the show notes for that as well. And if you're listening to this later in the year, just visit our website to find out when our next encore will be or become a supporting member of the AIP Summit Community.
Marie-Noelle Marquis (02:18):
Awesome. All right. So now let's listen to Jennifer's presentation and then we'll be back afterwards to add some of our thoughts and wrap up the episode.
Jennifer Franchak (02:33):
Okay. So like I said, I'm so excited to be here today because we are going to be diving into something that can feel incredibly frustrating when you're living with autoimmune disease. And that's when you have flare-ups that seem to come out of nowhere. And before we dive in, I just want to briefly share a little bit about why this work matters so much to me. I'm a functional nutritionist and an AIP Certified Coach, and over the years, I've developed a framework that I call the autoimmune harmony method. And this is the process that I use to help women understand their flare patterns, calm their immune system, and take back control of their health in a way that's sustainable and not overwhelming. And this is also personal for me because for years I dealt with exhaustion and inflammation and brain fog, and I was repeatedly told that nothing was wrong.
(03:20):
And that might sound familiar to you. And when I began focusing on my gut health and identifying my own triggers, everything started to change. My energy improved, my thinking cleared, and my digestion finally calmed down. And now I started to see the same patterns in my own clients. And I noticed that when gut communication breaks down, flare-ups start to feel unpredictable. And that's exactly what we're going to be talking about today. We're going to discuss why your flares aren't random, why they're actually messages, how the gut shapes immune safety, and what you can start doing to calm your immune system. Now, when I talk with women who are living with autoimmune disease, one thing that I hear over and over again is my flares feel totally random, and it feels like symptoms come out of nowhere. You have no control over when they hit. And one day everything could be fine, and the next day you're suddenly exhausted and you're inflamed, you might be bloated or in pain, and you have no idea what set it off.
(04:23):
And if that's been your experience, I just want to let you know something right from the start. Your flares are not random. They're actually messages from an immune system that has become a little overprotective, almost like it's forgotten what's safe. And let me just explain what I mean by that. So your immune system is like a really smart security guard, and it's always scanning your body and asking you, "Is this safe or is this something that I need to respond to? " But when your gut becomes inflamed or out of balanced, and we'll talk more about why and how that happens in just a moment, that security guard starts sending mixed signals. So instead of responding to only true threats, the immune system can start reacting to everyday things like foods you used to tolerate, normal stress in your day, and in the case of autoimmunity to your own tissues.
(05:16):
But what I want you to understand is that this is not a failure of your body and it's not your immune system malfunctioning. It's also not attacking you for no reason. What's actually happening is that the internal communication between your gut and immune system has become unclear. And when signals that are coming from your gut become disrupted or unclear, the immune system has a harder time interpreting what's safe, which makes your immune responses more unpredictable. And here's what we know from the research about why this happens. You know how I just compared your immune system to a really smart security guard? Well, what's actually happening is that your immune system is constantly performing something called immune surveillance. So it's scanning your gut lining and your bloodstream and your tissues to decide what's safe and what's not. When your gut is healthy, then your immune signaling is calm and accurate.
(06:14):
But when your gut is stressed or inflamed or imbalanced, your immune cells are then receiving mixed messages about what's safe, which makes them more reactive and less tolerant. So you can experience things like flareups that come out of nowhere, but the truth is they're not coming out of nowhere. They're happening because your immune system doesn't feel safe. So I'd like to invite you to reframe the way that you think about your symptoms because this shift can make such a big difference in how you approach your health moving forward. So first of all, your flares, they're messages from your body. They're not signs that your body is failing. And I want you to remember that when you have a flare up, your body is trying to get your attention and your immune system is saying that something felt unsafe and it reacted because it's trying to protect you.
(07:06):
So when you shift from my body is attacking me to my body is communicating with me, you start to become curious instead of fearful and you start to recognize patterns instead of panicking. And this reframe is so important and it's the foundation for everything that we're going to talk about today. So earlier I mentioned that a lot of this immune confusion begins in the gut, but now I just want to take you a little bit deeper into why that happens. What disrupts the accuracy of immune signaling in the first place? So the gut is where most of your immune system lives, and it's constantly communicating, sampling, and sending signals that help the immune system to tell the difference between what's safe and what's not. When the gut environment shifts though, because of inflammation and stress and changes in the microbiome or impaired barrier function, those signals that guide your immune system become unclear.
(08:04):
So let's just take a closer look at how the gut and the immune system are supposed to communicate when things are working well and what breaks down when flare-ups start happening. So like I said, your gut is the first place where your immune system gathers information and about 70 to 80% of your immune cells live in and around the gut, and especially in a network called the GALT, which is your gut-associated lymphoid tissue. And I promise you there will not be a quiz at the end of this. I just want you to kind of soak in this information and try to understand how beneficial understanding this will benefit your health. Your gut is constantly being exposed to the outside world through food and microbes and chemicals and nutrients, and your immune system stays close by to monitor what's coming in, and then it decides how to respond.
(09:00):
And when everything is working the way that it should, your gut and your immune system communicates smoothly. They recognize what's safe and what needs attention, and then they can respond in a calm and coordinated way. Now, there are three main components that help your gut immune conversation stay clear.
(09:21):
The first one is the gut microbiome. Your intestines, as I'm sure you've heard, are home to trillions of microbes, and research shows us that beneficial bacteria play a major role in immune regulation and tolerance, and they produce short-chain fatty acids like butyrate, which help immune cells to distinguish between harmful and harmless exposures. Now, when these beneficial microbes are present and balanced, good things happen. The immune system receives steady, predictable signals, inflammation stays low, and your body maintains tolerance to foods and normal daily exposures. So this is the ideal state. This is what we want because this is where the immune system stays calm, but alert. Now, the second component that helps to maintain healthy communication between the gut and the immune system is the mucosal barrier, and this is a thin protective layer that lines your gut, and its job is to allow nutrients to pass into the bloodstream, keep irritants, toxins, and partially digested proteins out of the bloodstream, and maintain a controlled barrier between the outside world and your internal immune system.
(10:30):
So mucosal health is extremely important here, and when you have a healthy mucosal barrier, it means that the immune system only sees what it's meant to see, and this prevents it from overreacting. And the third component that supports your gut's ability to regulate immune responses appropriately is immune signaling. And this is essentially the communication channel between the gut and the immune system. So every second, your immune cells in your gut are releasing chemical messengers. And these are things like cytokines, metabolites, and other signaling molecules that report what's happening in the digestive environment. It's really, really cool when you learn about this. And these signals help the immune system to figure out if everything is calm and functioning normally, or if there's irritation, imbalance, or potential threats that the immune system needs to react to. And this is what happens when the immune system is the gut and the immune system are communicating properly.
(11:32):
The gut filters what comes in, the beneficial bacteria educate the immune system, and the immune system responds calmly and appropriately. There's a rhythm to it, a sense of order. But when that communication starts to break down, the immune system loses important context. So it no longer has the information that it needs to accurately tell the difference between something that's harmless and something that's potentially harmful. And here's the part that many people have never been told or don't really understand is that your gut microbes play a huge role in this. And like I mentioned earlier, many of them directly influence immune signaling, meaning that they help to decide which immune pathways get activated and which ones stay quiet. So when beneficial or good bacteria decline, the gut lining becomes irritated or permeable, which is what you probably know as leaky gut. And when stress or inflammation disrupts the normal signaling between the gut and the immune cells that surround it, that's when this communication breaks down and the immune system becomes more reactive, more sensitive, more likely to respond to everyday foods and stressors, or even your own tissues as if they were threats.
(12:50):
And this is also when flare-ups start to feel unpredictable, not because your body is broken, but because that communication loop between your gut and your immune system isn't functioning the way that it should. So now that you hopefully understand how the gut and the immune system should communicate and what it looks like when that communication goes off track, I just want to show you what I use to identify what's driving that breakdown beneath the surface. In my practice, I use a tool that gives me the clearest picture of what's happening, and that's the GI MAP test. So if you're not familiar with it, the GI MAP is a functional stool test that looks at DNA fragments from bacteria, yeast, viruses, and parasites. And it also measures several markers that tell us about how your digestion is functioning, gut inflammation, and how the immune system is functioning inside of the intestines.
(13:46):
And I really love using this test because it gives us objective data about what's happening beneath the surface. And these are things that we can't just tell from symptoms alone. Symptoms are important where they're important to observe and they give us clues, but the GI map helps us to understand the why behind those symptoms. And this test helps us to evaluate how well the gut and the immune system are communicating and whether the immune system is getting clear, accurate signals, or whether something in the gut is creating the kind of mixed messages that can lead to flareups.
(14:21):
And it's also incredibly validating for my clients to finally understand the reason behind their symptoms that have felt so confusing often for many years. So I'm talking about symptoms like bloating and food reactions and flare cycles, because instead of just guessing, we're looking at concrete data that shows us exactly where that communication is breaking down between the gut and the immune system. And that information is really helpful because it helps us. It allows us to be more precise when we go in and support the body with food and lifestyle and supplementation. So once we have that full picture of what's happening inside of the gut, I start looking for patterns. And I've noticed that there are some patterns that tend to show up over and over again, and I just want to highlight some of those for you. So when I look at someone's GIMAP test, one of the first places I look is at the beneficial bacteria section, and we call these keystone and commensal bacteria.
(15:19):
Now, commensal bacteria are like the everyday helpful microbes that support your digestion and support nutrient absorption and immune balance, and they help to keep things stable. Keystone bacteria are like the anchor species of the gut microbiome. They're very important. And even at low levels, they influence the entire ecosystem, they affect gut barrier strength, inflammation, and immune tolerance. So when these species are low on a GI map, it tells me that the gut is missing the exact microbes that it needs to help regulate immune signaling. Now, here's why this matters. These beneficial microbes directly influence something called immune tolerance, and immune tolerance is your body's ability to tell the difference between what's dangerous and what's not. Now, a healthy immune system knows how to ignore harmless things like food, your own tissues, or friendly gut microbes. So it's only reacting to when there's a real threat like a virus or pathogen.
(16:19):
And each of these microbes plays a slightly different role in keeping that communication clear. So when these beneficial species are low, the gut is then sending fewer of those calming signals the immune system depends on. And that's when immune tolerance naturally decreases. Your immune system is constantly gathering information based on which microbes are present, what foods are coming in, and whether the gut lining is inflamed or stable, and whether your body is running on stress hormones or staying in a calm and regulated state. All of these things that I just mentioned, these are all inputs that help to shape how your immune cells communicate. And when your microbiome is balanced, those signals are clear. But when your beneficial bacteria drop and inflammation rises, those signals become harder to interpret, which is what I mean when I say that the immune system becomes confused. Now, these are some signs of lower immune tolerance, which again means that the immune system is reacting to things that shouldn't normally be a problem.
(17:25):
So when beneficial bacteria are low, it usually means that the gut isn't sending those stabilizing signals that the immune system relies on. And without those signals, like I said before, the immune system becomes much more reactive. Now, another marker that I pay really close attention to on the GI MAP test is something called calprotectin, and this is one of the most well-studied indicators of inflammation inside the gut. And calprotectin is made by something called neutrophils, which are a type of white blood cell, and they show up in the gut lining when there's irritation or inflammation. So when this number is elevated, when calprotectin is elevated, it's not diagnosing a condition, it's just telling us that your gut lining is inflamed and your immune system is actively responding to something. And this matters because the gut lining isn't just for digestion. It's actually a major interface between your immune system and the outside world.
(18:21):
So when that lining becomes irritated or inflamed, immune cells in the area release more inflammatory signaling molecules, which then have downstream effects throughout the whole body. Calprotectin also doesn't tell us why the gut is irritated. That's why we look at the rest of the GIMAP test. But again, it does give us very strong clues that the immune system is already activated and on high alert. And when the immune system is already activated in the gut, it becomes much easier for everyday foods, stress, or microbial imbalances to trigger a flare up.
(18:58):
Now, there's one more pattern that I usually see a lot on the GI MAP test that adds even more stress to the immune system, and this one usually surprises people. It's actually the presence of hidden infections or microbial overgrowths. And when I talk about infections, I'm not talking about something dramatic. I'm talking about infections that are more like background disturbances that the immune system has to keep responding to. And when the immune system is busy managing these low grade issues behind the scenes, it becomes more and more reactive to everything else. The GI MAP test, like I said earlier, measures microbial DNA. So it picks up on organisms that normally live in the gut or ones that you've been exposed to in the past. So if something shows up on a test, it doesn't automatically mean that you have an active infection. It may just mean that that organism is present or slightly overgrown.
(19:52):
In many cases, a lot of these microbes have always, always been present. It only becomes an issue though when there's overgrowth, so too much of it, or imbalance, so not enough of the other beneficial microbes, or when it's showing up in a place it doesn't belong. So location of these bacteria are very important too, and those changes can alter how the immune system interprets what it's seeing. So I just want to share with you a few examples of organisms that usually show up on a GI map and that can contribute to an immune response. And the first one you've probably heard of, it's H. Pylori or Helicobacter pylori. And this is a great example of a microbe that can act as both a troublemaker and a normal resident of the gut. And around half the world's population actually carries H. Pylori, and in most people or many people, it can stay completely dormant and harmless for years.
(20:48):
And interestingly, some research even suggests that it may play a beneficial role in regulating stomach acid and helping to shape immune responses. But the problem is what happens with H. Pylori is when other gut imbalances show up. And I'm talking about low beneficial bacteria, irritation in the gut lining and high stress. That's when H. Pylori can shift from being a background resident to something that adds to immune reactivity. And when it becomes active or overgrown, then it increases inflammation, it irritates the stomach lining, and it can sense signals that put your immune system on high alert. So it's not automatically good or bad. Again, it's all about balance and whether or not it's quietly coexisting or if it's actively creating stress that your immune system has to constantly respond to. Now, the next thing I want to highlight is opportunistic bacteria. And these are microbes that naturally live in the gut and in small amounts, they usually don't cause any problems.
(21:50):
So the issue, again, isn't that they're bad, it's that they're opportunistic, and that means that they tend to take advantage of situations where the gut environment is stressed or out of balance. When beneficial microbes are low, when the gut lining is irritated, or when the immune system is overwhelmed, that's when these opportunistic species can start to overgrow or shift into areas where they don't belong. And that shift really matters because research shows us that when opportunistic bacteria become dominant, they can increase lipopolysaccharide production or LPS. And LPS is a toxin-like molecule that can be found on the outer surface of certain gut bacteria. And when the gut bacteria, or excuse me, when the gut barrier is stressed or leaky, that's when LPS can enter circulation into the bloodstream and act as a powerful immune trigger. And this activates the immune system and drives inflammation throughout our body.
(22:48):
So again, that goes back to why repairing and maintaining that gut barrier is so important. Opportunistic bacteria also irritate the gut lining, which makes the gut barrier more permeable or leaky. And opportunistic bacteria also stimulate immune activation, which keeps the body in a more reactive or on alert state. So again, it's not about the presence of these bacteria. Most people have them. It's the level, the location, and the balance that really determine whether or not they support health or contribute to inflammation. And yeast behaves in exactly the same way. So let's just take a moment and talk about yeast, specifically Candida. A small amount of yeast in the gut is completely normal. It's supposed to be there and in a healthy microbiome, your beneficial bacteria help to keep it in check. So again, the issue isn't presence, it's overgrowth. And when yeast become too abundant, they can produce byproducts that irritate the mucosal lining of the gut.
(23:51):
So we don't want them to overgrow because again, it can irritate the gut lining. And once that gut lining is irritated, it becomes much easier for the immune system to misinterpret harmless inputs like food or stress as potential threats. Also, yeast overgrowth competes with the beneficial bacteria for space and nutrients, and this means that there will be fewer of those calming regulatory signals that help to support immune tolerance. So again, yeast is not inherently dangerous, but when it's overgrown, it changes the gut environment in a way that keeps the immune system on high alert. Now, the last marker that I want to highlight on the GIMAP test is one that gives us a lot of insight, and it's called secretory IgA or SIG-A. And this is a crucial part of your immune system because really it's the primary antibody that lines your gut and it protects you from unwanted microbes, food particles, and environmental irritants.
(24:47):
So basically, it's your gut's first line of defense, and it's what helps your immune system to stay calm when it encounters something harmless and get appropriately activated when something actually needs attention. So let me just explain what I'm talking about. Your gut is exposed to thousands of different substances every day. Some of these things are totally safe, like proteins from your foods. Others might be more challenging and a little more tricky like bacteria, yeast, or environmental exposures. So when Sig A is at a healthy level, your immune system can sort through these different exposures or antigens smoothly, but when Sig A is low, that sorting system gets kind of overwhelmed. So your gut doesn't have the same level of protection or clarity, so then your immune system ends up working much harder and reacting more. And something really important to understand is that chronic stress is one of the biggest factors that lowers secretory IgA.
(25:47):
That's why this is such an important clue because it tells us how well your gut and your immune system are working together. And it also tells us how well it's able to handle everyday exposures without tipping into a flare. And this is one of the biggest reasons, again, why I love using the GI MAP test, not as a medical diagnostic tool, I'm not a doctor, and definitely not as a replacement for your doctor, but as a window into actually what's happening in the gut. Now, I worked with a woman named Kate who had ankylosing spondylitis, and her main struggles were chronic constipation, bloating, deep fatigue, and a lot of joint and back pain. And what made this so frustrating for her was that she had already cleaned up her diet. She was eating mostly whole foods, very little processed food, basically no sugar. She felt like she was doing everything right, but she still felt bloated and inflamed and stuck dealing with random autoimmune flares.
(26:46):
So when we ran her GI map, her symptoms started to become much more clear because we saw that she had low levels of keystone bacteria, which meant that her immune tolerance was low. And we saw that she had bacterial overgrowths, which meant that her immune system was constantly responding. And she also had something called elevated zonulin, which we didn't talk about, but that showed us that her gut lining was more permeable than it should be. So she essentially, she had leaky gut going on, and that gave her immune system even more to react to. So when we went through her results together and I explained what everything meant, she told me that it was the first time that she actually understood what was going on inside of her body. And seeing it laid out on paper was a relief for her because it started to connect the dots behind her symptoms.
(27:35):
And the best part for me was being able to show her that these were things we could actively work on rebalancing so that she could start to reduce her symptoms. So we started by removing gluten and dairy, which she had been a little hesitant to do, but within a couple of days, she noticed that she was feeling less bloated and less puffy. And at around two weeks, her bowel movements became regular. And this was something that she had struggled with for years, honestly, since she was a small child. So this was a huge breakthrough for her. Now, once we had the basics in place, I used the GI MEP results to build her a three-month rebalancing supplement protocol, which included nutrients to repair her gut lining. And over the next couple of months, her symptoms started improving, her energy began to stabilize, her pain started to go away, and her flares became less frequent.
(28:27):
And we were really excited to see her updated blood work, which showed that her inflammation levels were back in normal range, and that was without medications. So why am I telling you this? I wanted to share this story so that you could see a real life example of why the gut immune connection matters. Because when you actually see what's happening inside of the gut, instead of guessing or assuming, the whole picture suddenly starts to make a lot more sense. You're able to understand why symptoms are happening, which parts of the internal terrain need your support and what steps make the biggest impact. And once you know what's really happening, it's so much easier than to build a plan that's focused, effective, and truly works for your body. And this is exactly where a framework that I use in my autoimmune harmony method comes in. It's called the 5-R framework, and it's a well-established approach in the functional medicine world.
(29:22):
And once we use the GI map to understand why the gut immune connection is struggling, this framework helps us to take clear supportive steps towards healing. So when someone is dealing with autoimmune flares like my client, Kate, the first step that I guide them through is removing the things that are overstimulating the immune system or irritating the gut lining. And that includes foods that trigger inflammation, but also microbial stressors like the overgrowths that we talked about. We focus on creating a healthier gut environment where the overgrown microbes naturally lose their advantage and the beneficial bacteria can thrive again. And And the way that we remove foods that trigger inflammation is by following the AIP elimination phase. Now, at the same time that we're eliminating certain foods, we also bring in many, many anti-inflammatory nutrient dense foods, as many as possible really, to support the gut and the immune system.
(30:19):
Now, before we move on, I just want to show you a few ways that you can start to implement this remove step at home. You can remove gluten or dairy for two weeks and observe how your body responds. You can reduce or remove packaged or highly processed foods. You can reduce or remove added and artificial sugars. And of course, if you feel ready, you can work through the AIP elimination and reintroduction diet, which is really the gold standard. I highly recommend that. Now, the second step in our framework is to replace. And one of the most overlooked pieces is making sure that the digestive system actually has what it needs to function properly. So if you have low stomach acid or if your digestive enzymes aren't working well, or if your nutrient levels have been depleted over time, then even the best food choices can't fully support you in healing because your body isn't breaking down or absorbing those nutrients effectively.
(31:17):
So this is a step that I tailor heavily for each client. I look at their health history. I look at their GI map results and their lab work because all of those things give me clues about where their digestion may be struggling and which nutrients might be missing. When digestion is supported, two really important things start to happen in the body. First, you absorb nutrients more effectively, and these are things like glutamine and zinc and omega-3 fats, which are basically the raw materials that your gut lining needs to repair and stay strong. So absorbing those nutrients is very, very important. Next, better digestion means fewer partially digested food particles and fewer irritating byproducts that are reaching the immune system. And that gives your immune cells clear, calmer information to work with instead of constant mixed signals. But I want to just encourage you that even if you haven't run a GI map test, you can actually start, you can absolutely start supporting this step.
(32:19):
Now, a really easy first step to do this would be to pay attention to how you eat. And what I mean by this is slowing down and really thoroughly chewing your food well. It may not feel like much. You might be thinking, "Oh my gosh, that's so simplistic. How could that help me? " But it honestly can make such a big difference in how you break down your food and how you absorb your food. Another really easy option is adding a cap full of apple cider vinegar into a glass of water before meals, because this can gently boost your stomach acid and help your body to break down food more effectively. Now, one little caveat with that, if you're on medications, if you have a history of any type of ulcers in your stomach or anything like that, always run this by your doctor first, but that can be a very helpful step.
(33:09):
Also, adding polyphenol-rich anti-inflammatory foods to each meal will help to calm your inflammation and support a healthier gut environment. Now, once you've taken out the major irritants and the gut environment starts to settle, the next question becomes, who's actually living in the gut? Because even if things are calmer, if you have an imbalanced microbiome, it can still send mixed signals to your immune system. And that's why the next step in this process is reinoculation. Now, when I talk about reinoculating, I'm not just talking about taking a probiotic. I'm talking about restoring the balance of beneficial microbes that directly shape inflammation, immune tolerance, digestion, and even your mood. And this phase is all about rebuilding the beneficial bacteria that help to calm your immune system. Research shows us that specific microbes play a major role in supporting short-chain fatty acids like butyrate, which works to strengthen the gut lining and helps to regulate inflammation.
(34:11):
When these beneficial microbes are depleted, like we talked about earlier, the immune system ends up doing more work than it should, and it's constantly responding to signals that normally wouldn't cause a reaction, right? And this explains why low beneficial microbes can contribute to more reactivity, more food sensitivities, and more inflammation. So once we understand which microbes are depleted or struggling, then we can be much more intentional about how to support them. And instead of trying to throw random probiotics at the problem, we can focus on supporting the actual species that are missing or depleted with diet and lifestyle so that the gut can rebuild a resilient microbial community and one that can support immune balance for the long term. So here are some ways that we could do this, and I want you to think about trying this too. First of all, a more diverse diet will lead to a more diverse gut microbiome.
(35:10):
And that doesn't mean that you need to add everything at once, especially if you're struggling with digestive issues, but it does mean trying to slowly expand the variety within your diet. So trying different vegetables and not falling into the trap of eating the same foods over and over again, and eating probiotic rich foods, which is a great way to reinoculate the gut with beneficial microbes that support digestion, immune balance, and overall inflammation control. These foods naturally give us living bacteria that can help to crowd out harmful microbes and strengthen the gut lining. Now, I'm sure you're thinking, "Well, what about probiotic supplements?" And there is a time and a place for them, and I do use probiotics with my clients, but the types and brands that I use really vary based on their symptoms and their health history and their GI map data. And something really important to understand is that not everyone benefits from the same strains and more is not always better.
(36:11):
So if you're not sure which probiotic is right for you, you can still absolutely support your gut microbiome by using the food-based strategies that we just talked about, because all of these help your beneficial microbes to grow naturally. And when we support the gut microbiome with everything that I've just outlined, those healthy microbes produce anti-inflammatory compounds that, like I said earlier, strengthen your gut barrier and help to regulate your immune signaling, which means that your immune system gets clear information and you have fewer surprise flares. Now, once you've removed major irritants and started adding in nutrient-dense anti-inflammatory foods and your digestion has a bit more support, the next step is to repair the gut lining itself. And this is so important because this is where so much of the immune confusion begins. Your gut lining is only one cell thick, just one, which is hard to believe, right?
(37:08):
And those cells are opening and closing all day long to absorb nutrients, but when they're under chronic stress from inflammation and dysbiosis, which is an imbalance in the good and bad bacteria, certain infections or even long-term nutrient deficiencies, those cells can start to separate more than they should. And that's what I mean when I talk about intestinal permeability or leaky gut. And when that gut lining becomes more leaky or more permeable, that's when small food particles, bacterial fragments, and other particles can slip through the gut barrier into the bloodstream and activate the immune system. And over time, that constant exposure makes the immune system more reactive because it's being asked to respond to too many signals.
(37:55):
So repairing the gut barrier becomes extremely important for reducing flareups. And this is where we focus on giving the gut lining the nutrients that it needs and the conditions that it needs to calm down and rebuild. We also look at patterns on the GI map, like we talked about earlier, like elevated calprotectin, low secretory IgA or microbial imbalances, because those tell us why the gut lining is stressed in the first place, and that helps us to support the gut lining in a targeted way. But even if you don't have testing in front of you, there are some simple steps that you can start doing right away to strengthen your gut lining. So when your gut lining is irritated, one of the easiest ways to support repair is to choose foods that calm rather than stress your digestive system. Also, specific nutrients help to nourish and rebuild the mucosal layer.
(38:48):
And I have some of those foods and nutrients outlined on the slide so you can start to incorporate those into your daily routine. Now, the last step of our 5R framework that really ties everything together, and honestly, it's the piece that I see many women overlook and not really prioritize the most, but it's very important. And that's your nervous system. Because here's the thing, you can be eating perfectly. You could be taking the right supplements and following all the steps that I just gave you, but if your stress physiology is constantly activated, then the gut has a hard time staying calm and the immune system is going to stay on high alert. And this is where I like to remind my clients that healing isn't just about what you eat, it's about the environment inside of your body, and we want to focus on creating a healing environment.
(39:39):
So chronic stress is important to focus on because it affects the gut and immune function in three major ways. It weakens the gut barrier. So elevated stress hormones, specifically cortisol and catecholamines can loosen tight junction proteins in the gut lining. And these junctions are the structures that help to keep the gut barrier intact. So when they open up, more particles cross into the bloodstream and that exposes the immune system to things that it shouldn't be reacting to, and that exposure alone can be enough to trigger flares. Second, chronic stress depresses your gut's immune defense. So we talked about this earlier, but secretory IgA is your gut's first line of immune protection. It sits along the mucosal surface and helps to regulate how your immune system responds to microbes in food. And when stress is high, secretory IgA levels drop and that leaves your gut more vulnerable and the immune system is more reactive.
(40:38):
And finally, it alters the gut microbiome. So chronic stress has been shown to reduce the diversity of beneficial microbes, specifically bifidobacterium and lactobacillus species. And these microbes are really important because they play a key role in immune tolerance and inflammation control. So when they decline, the gut environment becomes more inflammatory. So if you've gone through periods of significant stress in your life and you've noticed that around that time you've had more flareups, I promise you it's not all in your head. It's physiology. There's a real reason behind why that's happening and stress doesn't just affect your mood, it literally changes your gut environment. And once we understand how deeply the nervous system influences the gut and immune function, the real question becomes, what can we do to support this part of healing in a way that's realistic? And here's some things that I focus on with my clients, and you can try these two.
(41:36):
You can incorporate daily micro moments into your day for stress management. So you don't need a 60 minute meditation session, you just need small, repeatable cues that tell your body it's safe so that your nervous system can calm down. And these little routines help to shift the body into parasympathetic mode, which is the state where digestion and repair and immune regulation actually happen. So I've included some examples of what I'm talking about on the slide so that you can start to try those and bring those into your daily life. Something else that you can focus on supporting is your circadian rhythm. Gut microbes and immune cells both follow a daily rhythm. So when your bedtime is inconsistent or you're eating late, maybe you're scrolling on your phone later than you should be when you should be sleeping, those rhythms get disrupted. So establishing a daily routine can help to reset those rhythms, which supports steadier digestion, better immune regulation, and fewer flare-like responses.
(42:38):
And again, not everything that stresses the nervous system feels stressful. We already talked about how what's going on in the gut can be a hidden stressor to the immune system, but we also want to pay attention to hidden lifestyle stressors. When we work on these underlying stressors, then your body finally has room to heal. So this is why the rebalance step is not optional. It's really essential because it helps the gut to stay calm, the immune system to stay grounded, and it helps your body to feel safe again. So we covered a lot today. I tried to pack a lot into this session. I just want to take a moment to briefly pull all of these pieces together. We talked about why your autoimmune flares don't come out of nowhere. They're messages from an immune system that's become overprotective and a little confused about what's safe.
(43:26):
We looked at how that confusion begins in the gut where about 70 to 80% of your immune system is constantly listening, responding, and trying to keep you safe. You learn how gut microbes and inflammation and stress and nutrient depletion all shift the way that your immune system reacts and how tools like the GIMAP test can help us to finally see what's happening beneath the surface. And then we walk through the 5R framework and learn how each step helps to heal the gut and calm the immune system. So my hope today with all of this is that you not only leave with some more knowledge, but with a greater sense of clarity and maybe some relief knowing why your body has been reacting the way that it has, but also knowing that there are concrete steps that you can take to start shifting things in the right direction.
(44:15):
So before we move on to questions, I just want to share two quick free resources that you can use to pull some of these strategies into ... Or put some of these strategies into action right away. The first one is the Autoimmune Harmony Roadmap, and it's a guide that I created, a downloadable guide. And inside, I walk you through my three-step autoimmune harmony method that I mentioned earlier, and it contains some really great tools and information that will help you to decode your personal flare-ups and start healing leaky gut. So if you want a clearer sense of your personal patterns and your triggers, this is a really great place to start. You can just scan the QR code and go ahead and download that. Now, second, if you want some more ongoing support, I'd love to invite you to subscribe to my YouTube channel. I post weekly videos specifically for midlife professional women with autoimmune disease, and each video is designed to help you understand your flare triggers, heal your gut, and take practical doable steps so that you can take control of your autoimmune flares.
(45:18):
So thank you again for joining me today, and now I would love to answer any questions that you have for me.
Jaime Hartman (45:31):
This was a really great presentation, and I really appreciated the way she emphasized that healing is not just about adhering to a diet, but is about creating a supportive internal environment, which can require a lot of changes or adjustments to your lifestyle. I'm grateful for Jennifer's wisdom and her generosity in sharing it. Now, you heard her near the end referencing a QR code that linked to a free resource, which obviously you can't use a QR code in an audio only podcast. So I will put a link for that in the show notes along with a link to where you can learn more about working with Jennifer. Marie-Noelle, what did you take away from this presentation?
Marie-Noelle Marquis (46:14):
I would say first of all, I love that she starts off by really emphasizing the importance to reframe how we look at flares, particularly that, as you mentioned, the start of the episode, it's not our body attacking us or a failure or a malfunction, but that it's our body communicating and sending us a message. I think that taking a minute to pause from all the noise around us, from the typical negative phrases out there, and actually take that moment to connect with what is happening, reframing it for a positive thinking, I think that's tremendously healing on its own. I think she also does a really, really great job at clearly illustrating how the gut and the immune system connect and then the importance of the immune system feeling safe so that it can communicate the right information. So thinking in terms of safety and the immune system wanting to protect us and alert us that something's wrong, I feel like there's such important words and images to bring to our healing because we all know what safe feels like and we know what unsafe feels like.
(47:24):
So suddenly I feel like we start having more compassion for our immune cells and for ourselves when we do actually understand where that behavior's coming from. And then side note, I really like that she points out and talks about probiotics and how not everybody needs it, not all strains are initially good for everybody. I just think it's like, obviously it's not the core of her presentation, but that's a good thing, a good reminder that I see with clients or friends and families that just will pick the brand of antibiotics that just contains the most gazillion microbes and it just might not actually be the right fit for you. So I think it's just a great reminder and I really appreciate her taking the time to mention that. Honestly, this was one of my favorite presentation this year, and I really recommend you guys checking out the full presentation, downloading her guide as well.
(48:22):
Yeah, I think that was really great. What about you, Jaime? What are your takeaways from this?
Jaime Hartman (48:28):
You know I was really struck by the framing of the immune system as being a really smart security guard that's always asking if whatever it's seeing is safe or something I need to respond to. I know that when I first learned what an autoimmune disease was when I was first diagnosed with one, I was told that in autoimmune disease is what happens when your immune system attacks you, which just made me feel like my body was malfunctioning or that my body was my enemy. But if you instead think about the immune system as a surveillance system and that autoimmune disease is just what happens when that surveillance system gets mixed messages about what is safe, I feel a lot more empowered and even can have a sense of self-compassion.
Marie-Noelle Marquis (49:11):
Yeah. Well, listeners, we really hope that Jennifer's presentation has, again, made it clear that AIP is not just a diet, but it is a protocol with multiple branches and that there are multiple ways to approach it. Through this podcast, AIP Certified Coaches bring you the resources so that you can feel confident about doing AIP on your own, but with the knowledge that you are not doing it alone.
Jaime Hartman (49:35):
And if you liked what you heard today, we hope you'll check out the Spring Encore Rebroadcast of the entire seventh Annual AIP Summit starting on March 19th, or consider becoming a supporting member of the AIP Summit Community where you can access our entire archives. We'll be back with another podcast episode in two weeks, so make sure you subscribe to the AIP Summit Podcast in your favorite podcast player if you haven't already.
Marie-Noelle Marquis (49:58):
And if you'd like to leave us a rating and a review, it will help others find this podcast where we are committed to helping you use the power of the autoimmune protocol to elevate your wellness journey to new heights.
Jaime Hartman (50:14):
The AIP Summit Podcast is a Gutsy By Nature production. Content presented is for informational purposes only and is not intended to be a substitute for medical advice, diagnosis, or treatment. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a medical condition.
