Gut Healing Part 3: How a Functional Medicine Approach Changed My Trajectory

This post is Part 3 in my ongoing Gut Healing Journey series — the continuing saga of how I navigated the confusing, landmine-filled world of gut health. My mission in sharing these chapters is simple: if even one person can skip years of frustration and dead ends because of something I learned the hard way, then it’s worth telling.

The first four chapters of this blog series are meant to share the major milestones in the journey. I do this because I want you to hear the whole “basic story” in sequence. Then in later blogs, I’ll focus on specific lessons or insights from this over-arching story. This chapter picks up where I left off — right after a huge “a-ha moment” that gave me fresh hope and a new trail to follow.

Hope Rises: A New Direction for Research

After receiving an “a-ha moment” that I had a “gut health” problem (see Blog #2 This Wasn’t Just Acid Reflux — It Was a Gut Health Wake-Up Call)  I had a new direction. I remember feeling a resurgence of energy and hope. It reminded me of those adventure movies where the hero unlocks a cipher clue box. The insides begin to click and whirr and shift, and it opens!.. to reveal the next cipher box.

Armed with the phrase “gut health,” I began to Google “best podcasts about Gut Health.” I wanted to learn everything I could about it.  I found “The Gutology Podcast” (which I binged in 2 days), and “Dr. Ruscio Radio.” I also bought the book Healthy Gut, Healthy You by Dr. Ruscio, and in the process, I was exposed to a whole new world of gut health vocabulary. 

As I consumed this content, it offered a different interpretation of my circumstances. I was fascinated by how these dots seemed to connect. Things began to make sense, and I felt something shift. I was becoming empowered.

Allow me to introduce you to some of the new terms I ran into. You might find them helpful.

Leaky Gut

In the functional medicine world, leaky gut is the main cause behind many of today’s chronic diseases. (Remember keep an open mind! I was skeptical at first, too. In fact, I still consider it possible that my diagnosis is something else! But here’s what you need to know about leaky gut)…

Leaky gut — also called “intestinal permeability” — is a condition where the lining of your small intestine becomes damaged (by things like chronic stress, certain medications (like NSAIDs), gut infections, steroids, antibiotics, imbalanced gut bacteria, excessive alcohol, or irritants in the diet such as gluten, super processed foods, and certain plant compounds like lectins). These holes in the small intestine allow tiny food particles, bacteria, and toxins to pass into the bloodstream. This “leak” can trigger immune reactions and inflammation throughout the body, leading to symptoms like fatigue, joint pain, brain fog, skin rashes, digestive issues, and even autoimmune flare-ups. It can often be improved by removing irritants, healing the gut lining, and restoring a healthy microbiome.

For years, “leaky gut” got laughed off as some woo-woo, made-up thing. Most doctors weren’t taught about it in medical school, so it never even made it onto their radar. But here’s the interesting part — research is starting to catch up. Scientists now use the term “increased intestinal permeability” and have actually measured it in people. They’ve seen how things like stress, antibiotics, infections, and even pain meds can damage the gut lining so tiny gaps form, letting food particles and toxins slip into the bloodstream. It’s been clearly linked to conditions like celiac disease and Crohn’s, and researchers are exploring its ties to everything from diabetes to Parkinson’s to depression. Even better, studies are showing that certain probiotics and diet changes can help seal up that barrier again. So while the name “leaky gut” still makes some eye-roll, the science behind it is getting harder to ignore.

Gut Microbiome

This was a term that was new to me. Did you know?….Your gut is home to a bustling community of trillions of microorganisms — bacteria, fungi, viruses, and other microbes — collectively known as the gut microbiome. These tiny residents aren’t just along for the ride; they live in a symbiotic relationship with us, meaning we rely on each other to survive. In fact, the gut microbiome is so influential that scientists call it our “second brain.” It helps digest food, make essential vitamins, regulate your immune system, control inflammation — and send chemical “orders” through a nerve superhighway that talks directly to your brain. These microbes  are alive and calling the shots. So it matters that we keep this population of good microbes alive and in balance.

The Lightbulb Went Off…

This is when I started to ask myself: “Did I unintentionally cause the problem to worsen by taking those antibiotics, acid blockers, and steroids?”

Remember how I was taking Pepcid every day to keep my stomach acid low so I could treat my LPR? And how I was also drinking alkaline water to help keep acid levels down even more?

Well… as I started reading Dr. Ruscio’s book Healthy Gut ,Healthy You, I began learning how digestion actually works, and I started to ask questions about cause and effect. Consider this:

1. Stomach acid is a microbial gatekeeper.
   It’s there to protect you — killing harmful bacteria before they reach your intestines, and triggering enzymes to break down protein. 
2. Lower acid means more unwanted guests.
   By keeping my stomach pH higher with acid blockers and alkaline water, I was making it easier for bacteria to survive the stomach and set up camp in my gut.
3. Digestive enzymes depend on acid to trigger.
   The release of certain enzymes — especially the ones that break down protein and fat — is triggered when food reaches a specific acidic pH. If your stomach never gets acidic enough, those enzymes don’t get the signal on time, and your food moves downstream partially digested — perfect fuel for bacterial overgrowth, gas, and bloating.

For months, I saw stomach acid as the enemy. My reflux was so bad that the conventional medicine approach was to just make the acid go away — so Dr. Koufman had put me on high doses (80 mg/day) of Pepcid, and I doubled down by drinking alkaline water. The goal was simple: reduce acid, reduce the burn.

But here’s the twist I didn’t see coming… what if the acid wasn’t actually the root problem? What if something deeper — like a gut microbiome imbalance — was partly causing the reflux in the first place? In that case, the “medicine” I was taking might have been making things worse, because by lowering stomach acid, I was also making it easier for bad bacteria to survive, thrive, and take over. That realization made me stop and ask: could my acid-lowering plan have been quietly feeding the very problem I was trying to fix?

Here was another possible explanation (and maybe even a root cause) for my symptoms!

Investment: I Hired My First Clinician — a Functional Medicine Doctor

I ultimately decided to “hire” one of Dr. Ruscio’s clinicians, and I met up virtually with Dr. Scott (from Puyallup, Washington!) for the first time  in August of 2024. I paid $350 for a 90 minute visit, where we went into a DEEP dive of my personal history. He was listening for anything that could give him a clue about why my symptoms were what they were. 

Dr. Scott is what is called a functional medicine doctor. A functional medicine doctor looks at health through a “root cause” lens. Instead of just treating symptoms, they dig into why those symptoms are happening in the first place—looking at things like nutrition, lifestyle, other medicines, your environment, past history, toxins in your body, and gut health. They tend to use a mix of conventional testing and more holistic tools to create a personalized plan, and they often blend “natural” approaches with modern medicine.

For the first time, I felt seen and heard by a medical professional. He didn’t think I was crazy. And he seemed very confident that he could help me solve the problem. I was told “This is what we specialize in! We’ve seen patients in worse cases than you, and so I know we can fix this.”  Together we explored alternative solutions that my other doctors would never have tried – things like anti-microbial herbal remedies, diet changes, gut healing supplements, an elemental diet, taking HCl-betaine before meals (to increase stomach acid), and even something called the IQoro device (a mouth device that claims to single-handedly cure acid reflux).

I worked with this virtual clinic for 4 months, and I saw a lot of progress with them! Here were some of the things we tried:

Remove trigger foods – the Low FODMAP diet

The first thing Dr. Scott asked me to do was switch from the Low Acid diet to a “Low FODMAP” diet. FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols – a group of fermentable carbohydrates found in foods like wheat, beans, certain fruits, and dairy that can cause gas, bloating, and digestive discomfort in “sensitive” people (like me). A Low FODMAP diet limits these foods for a short period (usually 4–8 weeks) to reduce digestive stress, calm inflammation, and allow the gut lining to begin repairing. I’ll talk more about this experience in a later blog, but you can start researching it now if you’re curious. I did notice that my burping and bloating decreased after I started eating this way.

Remove Acid Blockers

One of my big milestones was getting off the acid blockers – the Pepcid. From day one, I knew I didn’t want to be on them forever. They can be a helpful short-term tool to calm things down, but if your reflux is really being driven by a gut imbalance, the long-term goal is to heal the root cause so you don’t need them anymore. With Dr. Scott’s guidance, I weaned myself off over a two-week period—slowly lowering my dose until I was taking none. I was nervous, but what surprised me was that my progress didn’t stall. I was still improving without the acid reducer. That was the first real proof for me that my symptoms were tied to gut health, not just “too much acid.”  I share this with you because I want to show you it’s possible to get off the PPIs and the H2 blocker meds when you start taking proactive care of your gut microbiome.

Remove the Bad Bacteria

A big step in my healing journey was the “remove” phase—getting rid of the bad guys in my gut. Under Dr. Scott’s guidance, I tried antimicrobial herbs like berberine and oregano oil, and even supplements targeted to fight candida. These are designed to clear out harmful bacteria, yeast, and other overgrowths so the good microbes have a chance to thrive. I did notice my symptoms ease up during this phase—less bloating, less discomfort—but it didn’t get me all the way to the finish line. Still, I felt like I was inching closer, and I was confident that if I kept working the protocol, I’d eventually get there.

Reinoculate! I Start Probiotics

My gut microbiome was shot (with all the antibiotics and steroids I’d taken, not to mention my heavy use of antibiotics as a teenager to fight my acne). One of the first things I was encouraged to do to heal my gut was start taking a “good probiotic.” Probiotics are literally the good bacteria that live in your gut. They support digestion, strengthen the gut lining, aid in nutrient absorption, and play a vital role in regulating the immune system. 

For people like me with gut issues, probiotic supplements can help replenish good bacteria that may have been depleted by antibiotics, steroids, poor diet, or chronic stress. Take Note: Broad spectrum antibiotics wipe out bacteria indiscriminately – both harmful and beneficial ones – while steroids can suppress immune function and alter the gut environment in ways that reduce healthy bacterial populations. This is why probiotics are often a first-line tool in gut-healing protocols—they can start improving microbial balance and lowering inflammation within weeks. However, rebuilding a resilient microbiome takes time, so consistent use over several months is often recommended while the gut environment recovers.

Moving forward, I am going to think twice before EVER taking another antibiotic again — especially after all the work I’ve done to rebuild my microbiome!  If you are EVER prescribed an antibiotic or steroid, I personally think you should get yourself a good probiotic.

I’ve tried several different probiotics (including a powder version from Dr. Ruscio that was “easy” to take), but here’s what I currently use:

Bio-Complete 3 — I take one pill in the morning

Akkermansia — 1 pill per day with food, a specific strain that rebuilds the mucosal layer of your small intestine.

Repair the breach! I Start Strategic Supplementation

One of the very first things Dr. Scott had me start on was a gut-healing powder called L-Glutamine, which is food for your enterocytes — the primary cells that make up the walls of your small intestine. Well-fed enterocytes can repair and regenerate more effectively, which is essential for restoring the gut lining. Glutamine also strengthens the “tight junctions” between these cells, reducing permeability and preventing harmful particles from leaking into the bloodstream.

Here’s the thing: removing trigger foods is only half the battle. You also have to actively repair the damage that’s already there. Within just a week of taking L-Glutamine every morning, I noticed a huge difference—less bloating, calmer digestion, and just an overall “ahh” feeling in my gut. 

Supplements ended up being a really important part of my healing—something most conventional doctors never even mention. For me, the ones that made the most difference were listed below: (I’ll be updating this list to show you what I currently take)

(These are Amazon Affiliate links, and I may receive a commission if you end up using this link).

• L-Glutamine for repairing my gut lining. This is a tasteless powder you can add to your water or drink. It “feeds” the enterocytes which make up the lining of your gut. Another option that I used for a while is a gut-healing supplement from Dr Gundry called Total Restore.This one contains both L-Glutamine AND N-Acetyl-D-Glucosamine — which can help with the achy joints. This is something I only take for the “rehab” phase of my healing.
• Magnesium Citrate (350-500 mg) to keep things moving and calm my nervous system. (This totally fixed my constipation issues). You can take other forms of magnesium like glycinate or threonate — they also have the benefit of making you tired. So take it right before you go to bed!
• Vitamin D3/K (10,000 IUDs) for immune and gut health. Many people are VERY low in Vitamin D levels, and this is apparently a super important catalyst in a lot of our body’s processes. I had low levels, so I went on a high 10,000 dose for a few months. Once my D blood levels had stabilized, I backed down to 5000 IUDs per day. Make sure you are getting a blood test for Vitamin D every 3-6 months if you are on a supplement!
• Vitamin B complex – When I came down with carpal tunnel in September, 2025, I wondered if my shortage of red meat and the difficulty in digesting proteins was the culprit. My doctor was pretty sure that it was the result of a vitamin deficiency, and didn’t seem too concerned. I started taking a B-vitamin supplement. I continue to get my blood tested for this, too, to make sure I’m in range. Eventually, I discovered a different supplement from Dr. Gundry that I wanted for its polyphenol content — Dr. Gundry’s Vital Reds — and discovered that it ALSO contained all the B-vitamins. So now I drink one scoop of Vital Reds in a morning drink instead of taking the B-complex capsule. (This drink is very yummy and feels like an indulgence).
• Vitamin E – an antioxidant, and wow! Does it make my skin glow. Kurt says I have de-aged. I’m not sure if it’s the diet or this Vitamin E.
• Broc-Elite (from Mara-Labs.com) – concentrated broccoli sprouts in a pill; this contains sulforaphane, and is helpful for liver support. I take this 10 minutes before I eat my first meal.
• Creatine – I take one scoop of this a day in my morning hot beverage to support muscle repair and energy. Protein was hard for me to digest for a long time, and eventually my muscles began to weaken. Being post-menopausal, I also have to be very intentional about watching my protein intake. This supplement helps rebuild muscle and brings water back into the cell.
• Collagen Peptides – I didnt start taking these until after my healing — mostly because my protein stores were very diminished from being so sick. Plus, since I am now post-menopausal, I do whatever I can to support my joint health and collagen stores.
• Fish Oil (Omega 3) for its anti-inflammatory benefits and brain health. My blood levels showed that my Omega 3: Omega 6 ration was way off. (I had a much higher Omega 6 number. This is probably because I ate NO Omega 3 foods!)  I speculated that if I started eating Omega 3 foods every day, and drop my bad seed oils, I would be able to get this ratio to normal. FYI: fish oil capsules are typically HUGE, so I cut them open and drizzle the oil inside on my veggies. I also alternately use this algae oil, which doesn’t taste fishy, and I use it in place of my olive oil in a salad dressing base.
• Daily Probiotic – I lump this in with supplements; I use Dr. Gundry’s Bio-Complete 3 because it’s encapsulated to survive the trip through the stomach. I also take something called Akkermansia once a day, which is a particular strain that is especially healing in the gut.
• Urolithin A – for mitochondrial support. Mitochondrial health is everything when it comes to longevity. With consistent daily use, research shows improvements in cellular energy, muscle strength and cellular renewal in four months. A more recent discovery, I didn’t take these until a year into my healing. They are included here because they are a part of my long-term supplement plan now.

For a few weeks, I also tried supplementing with HCl betaine, to test increasing acid in my stomach. This is hydrochloric acid in a pill! (Crazy, right?!) Many folks with my symptoms of bloating and burping and slow digestion are actually suffering from too little stomach acid (which is why the food is sitting around fermenting!) Taking a pill before eating breaks the food down quickly, triggering the digestive enzymes. It is a common solution for many folks with acid reflux, and so it’s often tested as part of a healing regiman. For some people, it is the ticket to recovery. For others, not so much. I tried HCl 3 different times at different phases of my healing, and it would digest my food faster, but I would always feel too much heat and burning along with it – so it wasn’t for me.

You may be thinking, “Wow! That’s a lot of supplements!” Yes, for a while there I felt like I had my own pharmacy. And yes, I have done the math, and I spend about $500/month right now on these supplements. But I also gave myself permission to do so for a season. I’ll talk more about that in a later blog. But I had to make a decision to invest in my health and go “all-in.” When I started to see myself healing, it validated this investment in myself. And now that I’m mostly better, I continue to ask myself,  “Do I need these all anymore? Can I dial some of them back to test and see? What if I only do the probiotics every OTHER day?…” Do what you can. Decide your priorities.

If I had to pick my top 5, I’d point you to a probiotic, omega-3 fish oil, Broc-Elite, Vitamin D, some form of polyphenols (in Vital Reds mix), and magnesium.

Calming the Gut Down with the Elemental diet

In the early part of my healing under Dr. Scott, I asked to try the elemental diet. An elemental diet is basically a “pre-digested” meal replacement. It’s a powdered formula that contains all the proteins, carbs, fats, vitamins, and minerals your body needs—but in their simplest, broken-down forms. That means your digestive system doesn’t have to work hard at all; the nutrients are absorbed quickly, giving your gut a chance to rest and heal. My formula tasted like a vanilla shake, and it was really yummy.

When I was really inflamed, this was exactly what I needed. It calmed things down in a way nothing else had. I wouldn’t do it forever (it’s not exactly exciting to live on shakes!), but in those early flare-up stages, it was a lifesaver. That’s when I started to really believe my reflux, slow digestion, bloating, and constant burping were connected to food. On the elemental diet, my digestion sped up, my reflux dropped way down—though I still burped a lot—and it confirmed for me that my symptoms weren’t just random. I even used it for a few days after my colonoscopy and endoscopy last December, just to give my throat a break while still knowing I was getting full nutrition.

(Note: I eventually stopped using the elemental diet because I began to suspect one of its main ingredients—maltodextrin—was triggering me. Around that time, we were exploring whether I might have a candida overgrowth, so I cut almost all carbs from my diet. That’s when I noticed something interesting: my burping went down dramatically. It made me wonder if the maltodextrin (which is basically a fast-digesting carbohydrate) was feeding something in my gut that was making my symptoms worse.

Ruling Things Out, One Test at a Time

By the time I wrapped up my work with Dr. Scott, I felt like I’d come a long way. With their guidance, I had data! I had completed several tests to check for gut dysbiosis. I had ruled out an H. Pylori infection with a stool test. I took a SIBO (small intestine bacterial overgrowth) breath test and it came back negative. I checked my iron and ferritin. I checked my thyroid. I checked my hormones. My colonoscopy and endoscopy came out clean. My HIDA scan showed my gall bladder was doing okay. My abdominal scans showed no evidence of cancer. I did have fibroids in my uterus — more on that later! I was making steady progress on my antimicrobial herbs, and I had successfully weaned myself off acid blockers.

At that point, my mindset was: just keep going. Give my gut time, stay the course, and eventually it would heal. By December of 2024, my working theory was that I might have a fungal overgrowth called candida — and if I treated it for a few more months, the rest of my symptoms would finally resolve.

That’s when I discovered Dr. Gundry. And that’s when everything changed….

Some of the links in this post are affiliate links, which means I may earn a small commission if you make a purchase through them—at no extra cost to you.

Want to read more of the story?…

Read Chapter 2: This Wasn’t Just Acid Reflux — It Was a Gut Health Wake-Up Call

Read Chapter 1: How I Healed My Gut (Part 1) – Introduction

Read Chapter 4:  Breakthrough: How Dr Gundry’s Plant Paradox Changed My Healing 

This week’s Gut-Healing Recipe

Kohlrabi Fritters with Garlic-Yogurt Sauce

Preparation time: 30 minutes
Cooking time: 30 minutes
Serves: 4

Ingredients

• 4 medium kohlrabi

• 1 medium carrot, peeled

• 1 tablespoon (8 g) cassava flour, or more if needed

• 1 small pastured egg, lightly beaten

• Salt and pepper to taste

• Avocado or extra-virgin olive oil, for the pan

• 3 ounces (88 g) goat or sheep yogurt (plain goat yogurt is available at Meijer)

• 1 small clove garlic, grated

• A few fresh mint leaves, chopped

Directions

1. Grate the kohlrabi, place in the center of a cheesecloth, twist the ends of the cloth, and squeeze as much of the water out as possible.

2. Grate the carrot.

3. In a bowl, mix the kohlrabi, carrot, cassava flour, and egg. Season with salt and pepper. If you feel the mixture is too wet, add a little more flour.

4. Generously coat a large skillet with oil and heat over medium heat. When hot, add small patties of the mixture and slightly flatten them down with the back of a spatula or spoon. Fry on one side until golden brown, about 10 minutes, then flip and fry on the second side for about 10 minutes. Use a spatula to transfer the patties to a paper towel–lined plate and let drain. Repeat with the rest of the mixture, adding more oil as needed.

5. In a small bowl, add the yogurt, garlic, ½ teaspoon olive oil, and mint. Season with salt and pepper.

6. Serve the fritters with the yogurt sauce.