A Functional Medicine Approach to Healing IBS

So, your doctor says you have IBS - Irritable Bowel Syndrome.

This diagnosis can either feel like a relief or a nightmare.

On the one hand, an IBS diagnosis means some of the causes of digestive issues like Crohn’s, Ulcerative Colitis, and Celiac disease have been ruled out - that’s a good thing. 

But on the other hand… IBS is essentially a name for “something’s wrong but we don't know what.”

And in the functional medicine, holistic approach I use - that’s not a good enough answer. In fact, it's not an answer at all!

An IBS diagnosis leaves people to suffer through their symptoms alone - which is bad enough - but even worse, it ignores the root cause of the issue.

And because the gut is so integral to overall health, issues in your gut inevitably lead to more health issues - hormones, mental health, weight concerns, thyroid issues, and more.

So why do we accept this? Why do doctors tell you that you “just” have IBS and send you out the door?

Because treating IBS isn’t easy! There’s no one pill that can fix it, because no two people have the same causes. It requires a multi-step, hands-on treatment approach that usually needs to be tweaked in real time. That’s not the kind of care most standard MDs are able to provide.

Don’t worry - I got you! Today I’m going to share my approach to treating IBS.

But buckle up, because this isn’t a quick 3-step process (sorry!). Today, we’re diving deep into the nitty gritty of treating one of the trickiest conditions out there. 

 

You’re Entitled To More Than One Problem

In Chinese medicine school, I often heard the saying “You’re entitled to more than one problem at the same time.” This was the tongue-in-cheek way of saying it’s the norm, not the exception, for a patient to have multiple contributing factors to any health challenge they faced. 

And this is especially true in the case of IBS because the gut is so intricately connected to every part of the body, but also because one gut issue - like inadequate digestive secretions (due to stress, medications, etc.) - can create the environment for another problem to arise. 

That’s why the treatment plan I use for IBS has a lot of steps. Because you may have low stomach acid, or bacterial overgrowth, or a parasite… but that’s more than likely not going to be the only issue you’re dealing with. Instead of obsessing over discovering the one root cause of your IBS, my approach works systematically through the most common issues, creating a powerful foundation for lasting health.

So let’s peel back the layers, step-by-step, and tackle this together. 

 

Start From The Top and Work Down

Most people don’t think of it this way, but the mouth is actually the start of the gut. The mouth has its own microbiome that directly influences the composition of the large intestine microbiome. In fact, research has shown that simply brushing your teeth 3x daily can measurably lower levels of candida in the stool. 

94% of Americans have some degree of gingivitis and the mouth and sinus are home to fungal strains including Candida species (present in 75% of participants), followed by Cladosporium (65%), Saccharomycetales (50% for both), Aspergillus (35%), Fusarium (30%), and Cryptococcus (20%). In addition, gram negative bacteria such as Enterococcus faecium, E faecalis, Escherichia coli,  Klebsiella pneumoniae, and Proteus mirabilis are also common in the mouth. These are the same bacteria most commonly overgrown in cases of Small Intestine Bacterial Overgrowth (SIBO). 

The best defense is controlling bacteria levels in the mouth with your oral hygiene routine. I recommend Dentalcidin toothpaste and Biocidin Dental Rinse as an important first step for anyone with dysbiosis or candida, SIBO, IBD, IBS, gas that clears the room, or a history of poor dental health. 

 

Optimize Your Gut Terrain

Once you’ve got your new oral hygiene routine in place, the next step is to optimize your gut terrain and environment.

Before we ever run a stool panel, clear a pathogen or take those precious leaky gut supplements, and especially before we start going down side rabbit holes like mold, we need to replace any missing digestive secretions and work on meal hygiene and transit time. This literally sets the stage for a healthy gut.

Digestive secretions include stomach acid (HCL), bile, and pancreatic enzymes. HCL is secreted by parietal cells in the stomach in response to the smell and taste of food, as well as distension in the stomach and small intestine (distention occurs when food enters the stomach). 

HCL is particularly important for the breakdown of protein. Most importantly, however, HCL acts as the first domino for all the other digestive secretions. Without adequate HCL, all other secretions will suffer!

The #1 reason for inadequate HCL? Stress. HCL release is triggered via the vagus nerve which connects the brain and the gut. Vagus nerve activation requires a parasympathetic state of the nervous system. You might know this as the “rest and digest” mode. Eating while stressed, busy, or otherwise unfocused is therefore a major cause of low HCL. Other causes include the use of PPIs and other acid-blocking meds, as well as the presence of certain bacteria in the gut like H. pylori, which can denature HCL. 

Adequate HCL then triggers the release of bile from the gallbladder. Bile is necessary for the digestion of fats, but bile also acts as an antimicrobial in the small intestine, helping to prevent bacterial overgrowth. Bile also collects toxins for the liver to secrete. Bile levels can be impacted by inadequate HCL, dehydration, gallbladder issues or removal, and exposure to high levels of toxins. If bile is inadequate it can lead to dysbiosis of the microbiome and deficiencies in fat soluble vitamins like A, D, E, and K and nutrients. 

Pancreatic enzymes are secreted by the pancreas and play key roles in breaking down carbs like sugar and starches as well as fats. Pancreatic enzymes allow starches to be broken down in the small intestine, rather than fermented, preventing bacterial and fungal overgrowth. Pancreatic enzymes act as a bactericidal against Escherichia coli, Shigella species, Salmonella species, and Klebsiella pneumoniae, and have fungistatic activity against Candida albicans. The release of pancreatic enzymes is dependent on adequate HCL. 

HCL, bile, and enzymes can all be supplemented if needed, but there are other things you can do as well. First up, make sure you’re hydrated. Proper hydration is necessary for the production of digestive secretions - think of water as the key ingredient. Secondly, slow down and really chew your food. Thorough chewing allows time for the brain to signal the gut that food is coming, and the gut to secret HCL and bile in response. 

With my one-on-one clients I utilize gut testing to check enzyme levels, and often supplement HCL, bile, and enzymes as needed.

 

What About Probiotics?

I tell my clients to introduce fermented foods as tolerated - even if that’s only a single strand of sauerkraut to start. 

Beyond that, certain probiotics can be really helpful. Some strains support secretory IgA, which protects the mucosal barrier of the gut. Those include spore based probiotics, S. boulardii, L. plantarum, L. Reuteri, and B. lactis.

Generally well-tolerated probiotics include OrthoSporeIG, or MegasporeBiotic. For those who are highly sensitive, you may want to start with HU58 instead, which is a single spore organism.

Probiotics can also support specific symptoms of IBS. For diarrhea, S. boulardii works well. I like Floramyces. For constipation, Optibac  (1-4 doses per day) or HN019 strain of Bifidobacterium lactis (Xymogen’s Probiomax) are my favorites. BioGaia Protectis drops, which contain Lactobacillus reuteri DSM17938, are my favorite for bloating. And in general, many IBS patients benefit from Ideal Bowel Support which contains L.plantarum 299V. 

 

Address Motility & Transit Time

Addressing motility and transit time goes hand-in-hand with optimizing the terrain of the gut. Bacteria in the gut bloom like a coral reef after meals. If food and bacteria are moving through the gut and into the large intestine, that’s a great thing. But if food isn’t moving as it should, bacteria can bloom in the small intestine, and that’s a problem.

Bacterial overgrowth in the small intestine (SIBO) is a factor in as many as 80% of all IBS cases. (That being said, it’s not the only cause of IBS. I see it more often as a contributing cause - more the “branch” than the “root” of IBS!)

Motility is controlled by the migrating motor complex (MMC), an electrical wave that originates in the brain via the vagus nerve. The MMC acts like a broom, sweeping food and bacteria through the small intestine and into the large. Many factors can contribute to a deficient MMC, including bacterial overgrowth itself, which can secrete toxins that disrupt the vagus nerve. 

To improve motility, I use prokinetics (not to be confused with laxatives), which help trigger normal MMC function, as well as other approaches to keep bowels moving regularly. But if motility issues are chronic, it’s a sign of an impaired gut-brain axis. Modalities that can heal the gut-brain axis include:

• Neuroplasticity
• Biofeedback
• Frequency Specific Microcurrent 
• Vagal nerve stimulation
• Acupuncture
• Therapy like EMDR, or somatics for trauma

 

Nutrition Based On Symptoms

Once the gut terrain and motility have been addressed, it’s time to look at your diet. For all my clients dealing with IBS or other gut issues, I have some basic diet recommendations:

• Paleo or Autoimmune Paleo as a foundation
• Focus on nutrient dense foods, including gut-healing foods like bone broth, 24-hour yogurt, and sauerkraut (just start small)
• Gluten, dairy, and added sugar-free
• Avoid eating the same foods day after day - variety is key
• Stay well hydrated
• Practice good meal hygiene (sitting down to eat, avoiding screens while eating, slowing down, chewing thoroughly)
• Incorporate fermented foods as tolerated (start really small)
• Incorporate fiber-containing plants as much as tolerated

While many people want to skip these simple diet changes, they matter. It’s a foundation, not an aside. You will not get better if you’re only eating gluten free toasted waffles, even if you tolerate them well! By the same token, if you’ve found you can stay symptom-free by eating a very limited diet, we eventually need to expand your phytonutrients and nutrients in general if you want to actually get better (and enjoy eating again!). 

For those patients with more specific concerns, I do often trial special therapeutic diets like the Specific Carbohydrate diet (SCD), low-FODMAP, or low histamine. Having diarrhea 15 times per day? Try the SCD Diet. (Just make sure you don’t skip the essential Intro phase!) Tons of bloating, belching, and some loose stool or constipation? I’d suggest a low-FODMAP trial. And for those with lots of rashes, headaches/migraines, hives, itching, anxiety, insomnia, brain fog, sudden episodic diarrhea after meals, and allergies with foods, I will try a low histamine diet. (And some may need to take it a step further and follow low nickel - especially if rashes or eczema are present - or have salicylate or oxalate intolerances as well.)

 

And Now We Test

You might be surprised to see that only now am I considering testing  - stool testing, breath tests, or even hormone panels. The truth is that there is so much to work on long before any labs need to be ordered. And for some people, simply improving the health of the oral microbiome, optimizing the gut environment, and making some nutrition changes are all that is needed to completely resolve symptoms! I too often see people on fancy gut protocols, who aren’t getting results, simply because they have addressed the foundation first! Bottom line: don’t skip ahead!

But once we’ve covered the basics, testing can provide invaluable information that leads us forward in the right direction and saves you a ton of wasted time, energy, and money. 

My two essential tests are multiple stool panels and hormone testing. In addition, I often find breath testing for SIBO, organic acids tests, and food sensitivity testing to be valuable tools, as well. 

 

Why You Need Hormone Testing for A Gut Problem

It might seem odd if your symptoms are all in your gut, but hormone testing is a must-have tool for treating IBS. Why? Because your struggle with inflammation in the gut, and your ability to resolve it, is to some extent limited or empowered by how harmonious and optimized your hypothalamic–pituitary–adrenal (HPA) axis is. Cortisol, the primary “stress hormone” whose production and release is controlled by the HPA axis, is like your own endogenous prednisone. If cortisol levels are sky high, or have tanked and are too low, the body can’t repair tissues (like leaky gut) or resolve inflammation. Trophic hormones like DHEA are also essential for tissue repair. Stress and cortisol also inhibit secretory IgA, the most important immunoglobulin for repairing the mucosal barrier of the gut. I think of secretory IgA like the immune system of the gut. 

Most of my clients have some level of hormone dysfunction - but once we know what it is, we can take active steps to mitigate it. I recommended actively addressing stress and trauma with tools like therapy, EMDR, vagal nerve stimulation, and tools like the Gupta Program or the Inaura platform. 

 

Order These 2 Stool Tests

I always use two stool tests to detect pathogens like H. pylori, fungal overgrowth, and parasitic infections. Right now my favorites are GI Map and Parawellness. To get started, I prefer to use tests that focus on identifying pathogens vs. microbiome tests like BiomeFx or the Genova Panel. While general microbiome wellbeing is incredibly important, if pathogens aren’t first tested and cleared, they will usually impede any improvements to the health of the microbiome. (That said, I do love the BiomeFX for really targeted rebuilding of the beneficial microbiome after we’ve “weeded” the garden!) 

That being said, the microbiome is essential in understanding why pathogens are a problem for some people but not others. It’s not just about what pathogens are present, but how your body responds to the pathogen. This is akin to the concept in Chinese medicine of Wei Qi. Wei Qi has its roots in the Kidney Qi (your core energy, or how strong you were when you came in, based on genetics, and how well you’ve nurtured that with nutrition, lifestyle, and exposure). 

Wei Qi is the concept that the hand of cards you were dealt (genetics), under the influence of the exposures you’ve had or lifestyle you’ve chosen or been able to afford = your resilience. You might have also heard of this concept as “epigenetics.” Chinese medicine practitioners have been talking about it for 5,000 years! 

Pathogens can shift or suppress the immune system, increasing susceptibility to SIBO and other opportunistic dysbiosis. Parasites and gut infections degrade the protective lining of the gut, called the mucin lining, to decrease secretory IgA levels. They do this to stay alive: they need to degrade the immune system in the gut to prevent being destroyed.

In addition, many parasites can mimic or directly trigger IBS or Inflammatory bowel disorders including Giardia lamblia, Entamoeba histolytica, Cyclospora, and Cryptosporidium. In one study, blastocystis infection was found in 67% of IBS patients, and other research found that the prevalence of blastocystis, cryptosporidium and giardia is higher in IBS patients than in controls, and likely play a role in the development of IBS. 

If you’re thinking, “There’s no way I have a parasite,” think again! Risk factors include simple things like travel outside the U.S. and swimming in lakes/oceans/rivers. Lots of food intolerances - or food intolerances that change frequently - are also a warning sign for parasites, as parasites are able to “switch” the immune system from innate immune response (the TH1 immune system) to the “food allergy” response (TH2 immune system). Many people report no obvious symptoms. That’s why I test everyone, across the board.

 

Creating Your Custom Treatment Plan

One we have test results in hand, it’s time to create your customized healing strategy. While no two cases of IBS are the same, there are some general rules I follow:

 

#1 Start With H. Pylori (If Present)

Because H. pylori breaks down stomach acid, as well as “partners” with and encourages other pathogens, if it is present, it’s where I start. (H. pylori also promotes histamine synthesis and can contribute to histamine induced symptoms).

 

#2 Clear Other Pathogens

Once H. pylori has been addressed I move down the list of parasites such as Endolimax nana, Giardia, Entamoeba coli, Entamoeba histolytica, etc.

 

#3 Candida & SIBO

Next, I like to tackle candida overgrowth and SIBO. I often clear candida first, especially in the case of methane-dominant SIBO, because there is a strong association between candida and methane SIBO, and the SIBO often won’t respond to treatment unless the candida is cleared first. 

 

#4 Find & Treat Other Factors (If Needed)

If candida is not clearing after appropriate clinical steps, or, if SIBO won’t resolve after appropriate treatment, I look “further down the rabbit hole” for other things that could serve as impediment to those resolving like:

• Heavy metals burden
• Mycotoxins (Mold exposure)
• Other biotoxin issues like Lyme and tick-borne diseases, chronic viral infections

(And if a patient has a known history with these  - like a mouthful of mercury amalgam fillings, or once lived in a moldy apartment, or known tick bites - I skip ahead and test for these issues earlier.)

 

Let’s Talk About SIBO

Like I mentioned earlier, SIBO is an underlying cause of IBS in as much as 80% of cases. But that doesn’t mean SIBO is the only cause of your IBS. SIBO is often just one aspect of a bigger set of issues. In fact, I often see patients who have had four or more rounds of SIBO treatment and still have symptoms. Why?

Often it’s because they have other parasites or pathogens that haven't been treated. Another common reason is that they actually have SIFO - small intestine fungal overgrowth. A 2015 study showed 25% of patients with unexplained GI issues actually had SIFO. SIFO symptoms are the same as SIBO symptoms, but common SIBO treatments like rifaximin and neomycin are just fuel on the SIFO fire. SIFO can be treated, too - it just requires a different treatment. 

 

Exceptions to the Rule

Now you know my basic treatment approach for IBS - but there are some exceptions. If someone is too overburdened, run down, or “weakened”, by what they’ve endured in body burden, often combined with a lifetime or period of high stress, sleep deficit, limited nutrition (because of what they can’t tolerate, or what is available), and poor assimilation, and are running on a deficit - they may need a different approach.

In these cases, a person may be too vulnerable to tolerate pathogen removal, either because it would leave them more vulnerable to another pathogen, or damage the microbiome itself. (Even natural agents can cause damage - looking at you, Oregano oil!)

A few weeks of support for healing gastritis, esophagitis, or leaky gut prior to digging in to increasing enzymes or HCL levels or endeavoring to clear a pathogen can make all the difference. They may also need several weeks of gentle detox support. I might use Chinese herbs, immunoglobulins and/or probiotics for  secretory iGA support, or treatments aimed at supporting HPA Axis normalization.  I think of this as strengthening Spleen (digestive) Qi and Wei Qi. 

 

Retest, Rebuild, Revitalize

We’ve already covered a lot, but we’re not done yet. In fact, these three final steps might be the most important. Please don’t skip them!

#1 Retest

Once we’ve completed our first round of treatment, it’s time to retest. Failure to retest is the most common reason people relapse after treatment. Yes, it really is worth the time and money! Retesting gives us insight into how you responded to treatment, if further treatment is needed, or if problems have been resolved. The only exception to this is SIBO testing: if your SIBO symptoms are 90% or more resolved, we often don’t need to retest, because SIBO doesn’t always look perfect on paper.

#2 Repair & Rebuild

We have already started the process of improving the gut terrain and environment. Now is the time to kick it into high gear and increase both probiotic and prebiotic foods. These help “bulletproof” the microbiome, preventing future infections and problems. Now is also the time to add supplements for anti-inflammation and leaky gut repair (butyrates, glutamines, curcumins, immunoglobulins, prebiotics, probiotics, nutrients like vitamins A, D etc). 

This is also the right time to utilize advanced microbiome testing like BiomeFX. We can use that information to focus on further diversifying the microbiome, because diversity is strength.

#3 Revitalize

Finally, I focus on detox support, nutrient replacement, and optimization of other systems that may have been impacted as innocent bystanders of the gut issues. Using an organic acids panel like ION, I take a look at liver detox, antioxidant status, amino acid status, neurotransmitter status, leaky brain, skin, and lungs, mitochondria and metabolism, and inflammation throughout the body. 

Even if you do every other step in the process, missing this one is like missing the icing on the cupcake. (I know, bad analogy for someone practicing nutritional medicine, even if it’s a gluten free, sugar free cupcake!). 

This step is WHY we bother doing the rest. You set out to clear your IBS because you don’t want to run to the bathroom 10 times per day. You don’t want to struggle to get to sleep, stay asleep, think clearly, or deal with rashes or autoimmunity.  You don’t want an overburdened detox system and excess oxidative stress to cause you to age prematurely. But clearing the gut and supporting the microbiome will only get you part way to relief (very far, but not entirely). 

For long term resilience and vitality, here’s what else I’m looking at:

• Replacing missing nutrients
• Supporting detox pathways
• Glutathione status
• Ability to optimally metabolize (aka use for energy) carbs, fats, and proteins, 
• Omega fatty acid balance
• Mitigating inflammation
• Supporting mitochondrial function
• Lowering oxidative stress
• Optimizing brain function

Healing IBS Is A Journey

In case you haven’t picked up on it yet… healing IBS isn’t a “quick and easy” process. But most things that are really worth it in life take time and effort. You likely are not going to see impressive results by just taking a few supplements or cutting gluten from your diet.

But that’s not a reason to get discouraged. Trained practitioners like myself have years of experience, working with thousands of clients.There’s nothing more gratifying than helping a patient  - especially if that patient feels they have tried “everything” - peel back the layers of their IBS one by one and finally find relief!

If you need support healing IBS, I want to invite you to book a complimentary, no-obligation chat with my team. We’ll hear your story and let you know how we think we can help. 

>>> Schedule your free consultation here

Living with IBS is hard. You don’t just have to accept this as your normal. We would love to help. 

---

by Kyle Leahy