Gut Health Explained: The 5R Functional Medicine Plan to Heal Your Microbiome

Dr. Julia Ward
Gut health affects far more than digestion.
In this educational class, Dr. Julia Ward explains how the microbiome influences inflammation, immunity, hormones, mood, and brain function — and how we restore balance using the Functional Medicine 5R framework.
When the gut becomes inflamed or imbalanced, symptoms often appear throughout the body — including fatigue, brain fog, joint pain, skin conditions, anxiety, and autoimmune concerns.
In this webinar, you’ll learn:
• Why gut health is a central control system in the body
• The connection between inflammation and the microbiome
• Why stress directly impacts digestion and immune balance
• The 5R Functional Medicine Framework:
– Remove
– Replace
– Repair
– Reinoculate
– Rebalance
• Practical daily steps to begin supporting gut healing
This class offers a clear, science-informed roadmap to long-term healing and resilience.
📥 Download the Gut Health Handout (PDF):
http://drjuliaward.com/wp-content/uploads/2026/02/Gut-Health-Handout.pdf
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Balanced Body Functional Medicine is a patient-centered practice focused on identifying and addressing root causes of chronic health concerns through advanced testing, personalized care, and nervous system support.
⚠️ This video is for educational purposes only and does not constitute medical advice.
Chapters:
00:00 Why Gut Health Matters
03:40 Signs Your Gut May Be Struggling
09:10 How Inflammation Spreads Beyond the Gut
14:25 The Functional Medicine 5R Framework
16:10 Remove
18:45 Replace
22:00 Repair
25:40 Reinoculate
28:30 Rebalance & Nervous System Regulation
33:00 What You Can Start Doing Now
38:20 Tracking Patterns & Biofeedback
41:30 Personalizing Care & Testing
45:00 Long-Term Healing & Resilience
Full Transcript
Why Gut Health Matters 0:00
All right, we're doing gut health first because it is just so foundational to overall health, why your gut matters. So basically, the gut is a living ecosystem. There's over 100 trillion microorganisms in your body. in your gut, which is more cells than the rest of your body, so they kind of outnumber us. And so these microbes do a number of things. So they're digesting fibers that we can't break down ourselves. They're making a lot of nutrients that need like B12, folate, vitamin K. they are producing short chain fatty acids which are controlling inflammation.
and they training our immune system to kind determine what's safe and what dangerous. And keep in mind that 70% of our immune system is actually in the gut. So this is influencing our mood, energy, and inflammation. When the microbiome gets disrupted, we can develop irritable bowel, reflux, bloating, brain fog, anxiety, depression, autoimmune disease, chronic fatigue, skin issues, hormonal imbalance. The gut is not reacting, it's really driving the whole system. And again, 70% of the immune system is living in the gut.
Most of this is embedded in the gut wall, and it's deciding which food is safe, which microbes belong, what should be attacked. When the lining is damaged or the microbiome is unbalanced, this can lead to autoimmune conditions and chronic infections that become really hard to clear. So this is really important, especially for chronic infections, things like Lyme, mold, long COVID, anything with chronic inflammation.
Microbiome, Immunity, and Inflammation 1:58
So stress, basically, this talking to the gut-brain connection, and the vagus nerve. The vagous nerve is the longest nerve in our body. It starts in our head and basically goes and innervates many of the organs in the body, including the digestive organs. But when we're chronically stressed, this can cause like a reduced stomach acid, it can slow digestion, and it changes the makeup of gut microbiome and leads to leaky gut. And leaky gut, just to remind people, is not anything that you can see on a colonoscopy.
It's a microscopic. So if you were to flatten out the entire digestive system, there's just one cell layer that separates the inside of our stomach and intestine from the Inside of Our Body. And those cells that line this are held together like tight junctions. But when we, you know, there's a variety of different things that can cause it to become leaky or kind of come apart like that. So medications, stress, toxins in the environment, all these things cause that lekey gut situation. And when you have that leaky gut, that's really the source of a lot of inflammation.
And, when we realize how large our intestines really are, if you were to flatten out the entire digestive system, you could actually cover a small, or cover the size of the tennis court. So when our gut is inflamed, it causes a load of inflammatory load on the body. So basically, there are certain steps that we're going to do to heal the gut, and the first one is to remove the irritants. So this is looking at your diet, limiting alcohol and inflammatory seed oils, what's particular for you and causing your irritants.
So for many people, it's gluten, not necessarily a true gluten allergy, which is celiac, but more of a sensitivity. Dairy is the same way. You can be eating some very healthy foods, But if it is causing an inflammatory reaction in you, then that's not a good thing.
Stress, Vagus Nerve, and Leaky Gut 4:45
The next one is to replace what's missing. A lot of people don't have enough digestive enzymes and stomach acid. Our stomach actually decreases as we age, so we need to replace it. And many people are on a proton pump inhibitor to decrease the acidic production in their stomach. And while this does, in the immediate term, will decrease those reflux kind of symptoms, you know, that burning sensation that you get in your throat from acid going up the wrong way into your esophagus, it stems from not having enough acid.
And you can see that on this slide, on the picture, there's a valve between the esphophagus and the stomach, and when there is not enough It loosens that that valve so that whatever's in the stomach can go back up into the esophagus and even though it's not as acidic as it should be, it still going to burn the Esophagus and still give you that sensation of reflux. So other things you can do are, you know, chewing thoroughly and slowing down to meals. I know I'm definitely guilty of this when I am busy and I just try to eat fast on the go and that's definitely not healthy.
Drinking plenty of water but not during the meal. You don't want to dilute your meal with too much water. And the main thing is weaning off of these proton pump inhibitors because they were not meant to be taken long term. All the package inserts will say six weeks is the most, but we all know if you haven't personally been on them, a lot of doctors are prescribing these for years and years. And the downstream effect of this is that you're not breaking down your food, you are not absorbing the nutrients that your need because you don't have enough acid to digest your foods.
So that's the biggest argument for getting off of these proton pump inhibitors. Then we want to re-inoculate with some good microbes, and we could do this through diet, you know, eating different plant foods. And again, I'm totally guilty of this, of just eating the same thing day in, day out, because that's what I am used to. It's a regimen, but adding variety to your diet is very helpful for your gut microbiome. Including fermented foods like yogurt, sauerkraut, kimchi, and then making sure you're getting enough fiber from fruits, vegetables, whole grains maybe or maybe not, depending on how sensitive you are to gluten.
And then probiotics. And people ask me about prebiotics all the time. I like prebiotics. They feed the cells of the colon. However, I wouldn't start them right away. If you have potentially pathogenic bacteria, you don't want to feed those as well. So you want make sure that nothing harmful is there. Okay, and then repairing the gut lining. This is done with, again, colorful vegetables, healthy fats, bone broth, some other anti-inflammatory foods, possibly some targeted nutrients. We use a lot of something called an immunoglobulin.
Immunoglobulins are present in colostrum or pre-milk, and they actually are meant to seal up a baby's gut. This is, you know, all babies are born with a leaky gut, but the coloster really helps just kind of seal it.
Healing the Gut: Remove, Replace, Re-inoculate 8:27
And not only that, it sort of tells the immune system, hey, don't need to react to this food as well. So we have a serum-derived colastrum, meaning that there's no dairy at all in it, But again that just helps seal up that leaky gut and there's a nice little diagram of what leakey gut looks like. Rebalancing the nervous system, this was one that traditional medicine has not really ever addressed, and I think functional medicine is just now coming around to this. But we have to really take stock of where you are with your nervous systems if you're chronically stressed.
And some people have been stressed for so long that they don't think that their stressed anymore. I know I was in this constant You know, kind of state of fight or flight when the kids were younger and I was working full time. I'm raising five kids. And running from here to there. Um, and you just, you're just used to being so stressed all the time that you forget that your stressed. But that really does a number on your, um, on. So making sure that you're getting enough sleep in, doing some sort of mindfulness, some breathing, whatever works for you.
There's no one size fits all. Thank goodness there's a variety of different things that can do. You just have to find what works best for. If you need extra help, there is a program called Primal Trust. Which takes you through some daily exercises on how to regulate your brain and nervous system, how do like calm things down. And they actually have just come out with a new newer program that started this week. It's called a daily regulate and it's five minutes a day for 40 days. So for people who feel like they're too busy for, um, a lot of different things, this is just a nice, quick and easy program.
That teaches you some kind of basic exercises that you can do during the day to calm down the nervous system. All right. And then building a healthy plate. You know, we want half of the plate as vegetables, a quarter with protein and a corner with healthy fats. Now, this is going to vary. Some people are Some people do well on like a carnivore diet. Other people are more keto and the ketogenic diet has a little more fat in it. It just sort of depends on what your goals are. But in general, this is a good way to start.
So things that you can do right away is to try and add one new plant food to your diet. Drink plenty of water. That's really especially important because we're all slightly dehydrated and that makes a huge difference. I'll tell you a personal story of how I realized that hydration was so important. We were on a cruise ship one time and we were up all night dancing and I was completely dehydrated. And we're on the side of the boat looking up into the stars. And my husband was trying to point out all these different things in the sky to me.
I'm like, it's all blurry. What are you talking about? I started drinking water. The more water I drank, the more crystal clear the night sky became. It was like my eyes could suddenly focus. And I think that's kind of amazing. But the eyes are very sensitive to not only hydration but nutrients as well. That was sort of a fun little experiment. And then keeping a journal of what's going on, especially if you do have gut issues, tracking your meals, digestion, energy, noting your stress level, and then bringing it to your next appointment so we can kind of go over what it was that was setting you off or what seemed to work.
So functional medicine, you know, we're targeting, trying to target the root cause, not just treating the symptoms. So further testing that we can do include like a stool test, and that's a complete like DNA analysis of what's going on with your stool. It looks at inflammatory markers. And at some point we could go over what a school test looks like and what kind of information we get from that.
Repairing the Gut Lining and Nervous System 13:11
I've also been using a new test that's a blood test. It's from a lab called Cyrix Labs, and they will look at markers in your blood that kind of show how your immune system is reacting to your gut microbiome. So it can tell if you've got a bacterial or a fungal overgrowth in the gut And it does what they call a T cell map, so how your immune system is reacting in general, like are you more inflamed versus not. It also looks at very specific species of candida that might be present that actually produce some acid that breaks down that barrier in the gut.
So that's really interesting too. Okay, and that was about it. I'm sorry if I was rushing through this, but my talking points got sort of thrown off. But it does leave us time for questions. Does anyone have any questions? If no questions, that's fine. I'm going to probably do a podcast interview with someone on gut health in the next few weeks or so, so I'll let you guys know about that. I probably could Google it. I'm sensitive to gluten. When I get it, I don't digest as well. Is homemade bread, would that have the same effect?
Is it the gluten in it? Or is it that the preservatives and other things in store bought bread that cause the problem? No, it is the gluten. The gluten is protein in wheat. And because in this country especially we've had the genetically modified crops to get more gluten and more production of wheat, the GMO wheat that we get in the country is virtually undigestible and it will cause leaky gut. I have patients that are very sensitive to gluten, but if they go to Europe, they can eat some bread there.
I lived in France for many years and I never had this problem there because they don't allow genetically modified crops over there, so that's the difference. But there are some supplements you can take if you know you're going to have a meal with gluten in it that will break down the gluten for you. It's just not something you want to rely on every day. Yeah, no, I just like making bread. So yeah. Yeah. And I think you could you can maybe order some flour from From Europe or you know from sources that don't have the genetically modified.
Okay, you give that a try. Thanks. Let's see any any other questions or No, it was a good review. I mean, you and I talked about this five years ago when I first came to see you. Yeah. Good. Okay. That's why we start with gut health so often because it really does affect the whole body and, you know, there's a very strong gut-brain connection because it is producing the, that's where a lot of our neurotransmitters are produced, is in the gut. And so again, when the got is off because of one reason or another, it affects our mood.
It really does a number. Then there is a gut skin connection too. When people come to see me and they have psoriasis or hives or whatever other skin condition going on, the first thing I ask is like,
Healthy Plate, Hydration, and Tracking Symptoms 17:28
what's going with your gut? Because usually that is an issue that we need to address. And then I did just recently, it hasn't been published yet, but I just did a podcast interviewing a doctor who is an eye specialist. And she was talking about how the gut really affects our eye health as well. So that will be out pretty soon. What did you say about our health? kind of in a general way. In a sense like, again, if your gut health is not on track, it's going to affect your eyesight and the eye health in general.
Wow. Yeah. What is your opinion about that, or have you seen the new research on the thiamine for irritable bowel? Have you see that research? I have not, but I will certainly look into that for thiumine. Yes. Thiamin is B1, and that is an essential nutrient that when we're deficient in that that can cause all kinds of problems. Another test that I use is something called Nutrival. It's from Genova. And it will look at a variety of different micronutrients like your B vitamins on the inside of the cell instead of just in the blood or plasma.
So it tends to be a little more accurate for like what you're looking at. But it also looks at some amino acids and it looks other markers that have to do with oxidative stress and mitochondrial function. So that's a nice test to do if you're curious, am I low on certain vitamins or amino acids. I have a question. And then go ahead. I'm sorry about that. Sorry to interrupt. No. Okay. Um, I wanted to ask about, um, with the, Um. Like rebalancing or the stress or sleep or something. What, what exactly should we be looking for?
Cause I feel like in a way that I am not paying, like you were saying, you know, your, never you, were you saying about stress that you've been so stressed for so long that she don't identify that your in a stressful situation and so I was like, so i was wondering like what kinds of things, can you look for to know if you're having a certain situation because, for example, I'm sorry my dog is okay.
Testing for Gut Issues and Nutrient Status 20:18
the, I've seen in pictures before I started coming to you that if you looked at me, you'd be like, oh, she looks like bloated or, um, whatever, but I didn't feel like I was bloat. Or if asked me what does bloating feel, like? I would never tell you. I'd like to have no earthly clue what being bloaty feels like. If I look like have inflammation or something. Um, so what are some of the things like that we should look for or like look for the way that we feel or something like that to know that that is indeed a problem.
Yeah so one of the things is like a heart rate variability and a lot of people are wearing an apple watch or an aura ring or a whoop strap or. Something like and you can kind of track your heartrate And the more variable it does, the healthier you are. When it narrows in range, that indicates stress. So that's definitely one. As far as your abdominal symptoms go, a lot of people tell me, every time I eat, I'm getting bloating. And they can literally feel their stomach expanding kind of a thing. OK.
I think if you're having that degree of bloathing, you generally know. And then, keep in mind too, like if you're having a lot of bloating, especially every time you eat, you may have a condition called SIBO, which is small intestinal bacterial overgrowth, and it's just sort of a migration of the bacteria from the large intestine into the small intestine where it should not be. And it just, it causes a lot of gas and bloating. And there is a very specific test we have. It's a breath test that we can do that tells us, do you have SIBO or not?
And if so, what type? Because there's, a few different varieties that you can have, but yeah, that's something to keep in mind. Yeah. Okay. Thank you. Oh, I was also going to mention we have a really good food allergy and sensitivity test and especially if people are having digestive issues or they can't lose weight or if they're having any kind of allergy issues. That's a really good one to do because it looks, it's, a blood test that looks at your immune reaction to a variety of different foods.
There's like a list of, I want to say like 88 different food.
Q&A: Gluten, Bloating, SIBO, and Food Sensitivities 22:48
And it is looking for true allergy, which is an IgE reaction. And IgG, which is a sensitivity, and these IgGs sensitivity reactions are sort of the delayed reaction. So you can eat the food today, but you wouldn't get symptoms until two to three days later. And that's what makes it hard to pinpoint. Like if you're just trying to do an elimination diet on your own, you can do this it's just really difficult because you've got to eliminate all foods that you think might be potentially causing some sort of reaction and then very slowly like once every three days add in a new food and you have to keep a really close journal about what's going on.
The other thing that this blood test tests for is complement. Complement is part of the innate immune system and when it is present it just makes inflammation worse. So this test is looking at actually four different variables for a list of 88 different foods. And from that we can really pinpoint like what do you need to avoid and what's okay for you to eat. It's usually surprising. It's not forever, it's just at this moment in time. And it could be perfectly healthy foods. Just as an example, we recently did the food allergy test on myself and my husband and found out that we're both reacting to egg whites.
Well, come from the bodybuilding world where we live on egg white. So that was a bit of a shock. But we managed to cut them out and actually feel better now because of it.
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