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Your 4-Step Microscopic Colitis Treatment Plan

Written by Dr. Michael Ruscio, DC on November 15, 2024

Written by Dr. Michael Ruscio, DC on November 15, 2024 — Reviewed by Hilary Watts

• What Is Microscopic Colitis?|
• What Triggers MC?|
• Conventional Treatment|
• Restoring Gut Health|
• Step 1: Elimination Diet|
• Step 2: Trial Probiotics|
• Step 3: Stress Management|
• Step 4: Advanced Troubleshooting|
• Keep Treatment Simple|

On the face of it, “microscopic colitis” sounds like it might not be as big a deal as “ulcerative colitis.” However, like other inflammatory gut conditions, microscopic colitis can significantly decrease your quality of life with unpleasant symptoms that include watery, non-bloody diarrhea and stomach cramps. 

In this article, I’ll share with you the approaches we take in the clinic to help patients with a microscopic colitis diagnosis. Fair warning: Microscopic colitis treatment often takes the path of two steps forward, one step back. However, the overall trajectory will be toward improvement when you focus on the fundamentals of improving your underlying gut health. 

Before we cover my 4-step treatment plan to improve microscopic colitis symptoms, let’s first understand what microscopic colitis is and what triggers it. Then we’ll look at why the 4-step treatment plan is more promising than conventional treatments.

What Is Microscopic Colitis?

Microscopic colitis (MC) gets its name because the changes in the gut that cause it aren’t obvious to your doctor (usually during a colonoscopy procedure). For a positive diagnosis, you’ll therefore need a tissue sample (biopsy) to be examined under the microscope. MC differs from Crohn’s or ulcerative colitis, the other types of inflammatory bowel disease, which have obvious inflammation to the naked eye.

However, like Crohn’s disease and ulcerative colitis, microscopic colitis is caused by abnormal reactions of the immune system.

There are two subtypes of microscopic colitis: lymphocytic colitis and collagenous colitis. 

• In lymphocytic colitis, the colon lining contains more white blood cells than normal. 
• In collagenous colitis, the colon lining may or may not contain more white blood cells than normal, but the collagen band under the colon lining is thicker than normal. 

Though these subtypes are slightly different, they cause exactly the same symptoms.

The most common symptom of microscopic colitis is frequent, watery diarrhea 1. This occurs because the affected part of the colon is the inner lining, which stops taking up water correctly when it is inflamed. That leaves a lot of water inside the colon to come out as watery diarrhea.

As well as very frequent bowel movements, other symptoms include 1:

• Abdominal pain
• Fatigue
• Weight loss

As with all chronic conditions, microscopic colitis may flare up in reaction to certain triggers, like diet or stress, and then subside again for a while.

What Triggers MC?

Figuring out what triggers the microbial imbalances, leaky gut, and inflammatory changes that lead the immune system to attack healthy cells in the gut can be a puzzle.

However, with microscopic colitis, we know that some of the contributory factors may include: 

• The genes you inherit 1 
• Being female 2
• Being older 2
• Smoking 1
• Drinking too much alcohol 3
• Using certain medications that damage the gut, such as 1 4 5:
  • Non-steroidal anti-inflammatory drugs (NSAIDs, like ibuprofen)
  • PPIs (proton-pump inhibitors used for acid reflux)
  • Statins for reducing cholesterol 
  • Hormone replacement therapy and oral contraceptives
  • Beta blockers
  • Selective serotonin reuptake inhibitors (SSRI antidepressants)
  • Pembrolizumab (an immunotherapy drug)

Although you can’t do anything about your genes or the sex chromosomes you’re born with, making sure you don’t smoke and cutting down on alcohol could make a lot of difference to your microscopic colitis symptoms.

Conventional Treatment Options

Two of the most common conventional treatments to keep microscopic colitis under control are budesonide, a steroid medication to calm inflammation,  and loperamide, a common anti-diarrhea medicine. Bile acid sequestrants (binders), such as cholestyramine, can also help to improve symptoms of MC diarrhea by binding to the bile acids in your gut 6. 

While these conventional medicines can be effective, they only treat the symptoms of microscopic colitis without addressing the cause, and they can have unpleasant side effects. I prefer to focus more on the underlying causes of microscopic colitis and how you can treat them for longer-term results.

To add some context here, microscopic colitis can be very upsetting and disruptive. During a flare, you might have to visit the bathroom up to (or more than) 10 times a day and during the night 1 7. You may also have trouble controlling your bowel movements.

These severe symptoms can lead to patients feeling that they will need complex or expensive tests, procedures, or supplements. It also makes them vulnerable to exploitation by uninformed or unethical purveyors of these tests and treatments.

In reality, the solution can be a lot simpler when you introduce diet and lifestyle steps that can rebalance your gut microbiome and immune system.

Why the Key to the Plan Is Restoring Gut Health

As with the other inflammatory bowel diseases, MC appears to be caused by the body’s immune system attacking healthy cells in the lining of the colon (large intestine). Thus, microscopic colitis may be considered an autoimmune disease 8. 

This is where improving gut health is so important. We don’t have specific MC research, but dysbiosis (an imbalanced gut microbiome) is a hallmark of several other autoimmune inflammatory diseases, such as Crohn’s disease, ulcerative colitis, multiple sclerosis, and lupus 9 10 11

Moreover, improving gut microbiome health with measures like probiotics and fecal microbiota transplants has been linked to improvements in, or a reduced risk of, some autoimmune conditions 9 12 13 14 15.

Step 1: Elimination Diet for Microscopic Colitis

Though there is no single diet that works well for everyone with MC, it makes sense to choose a way of eating that can tamp down inflammation and an overzealous immune system. 

At the clinic, we’ve found a couple of anti-inflammatory dietary patterns that seem to work particularly well for MC. These are the Paleo diet and the low-FODMAP diet.

The Paleo Diet

For my clients who aren’t severely flared, I suggest they start with the Paleo diet because it’s a less restrictive elimination diet. However, if they already eat a whole-foods, unprocessed diet but still have MC symptoms, I recommend they move straight to the low-FODMAP diet (see below).

The Paleo diet includes mainly whole foods that are similar to those our ancestors would have eaten. It excludes ultra-processed foods but features whole foods like berries, fresh vegetables, grass-fed meats, eggs (if tolerated), healthy fats (like olive oil and avocados), oily fish, nuts and seeds, and fresh fruits in moderation.

The Paleo diet is an anti-inflammatory diet that helps to calm inflammation by minimizing exposure to foods that can cause the immune system to overreact 16 17. Common immune-provoking foods include sugars, unhealthy fats (like trans fats or too much lard), chemical sweeteners, and common allergens. 

For some people, certain foods allowed on the Paleo diet don’t go down well or cause symptoms like hives, sniffles, fatigue, or gut distress. Part of personalizing the diet is to experiment with any diet you try for reducing inflammation.

Controlling inflammation with diet can calm symptoms and create a healthier environment for gut bacteria, which thus improves the gut microbiome 17 18. In cyclic fashion, a healthier microbiome reduces inflammation further 19 20. 

The Low-FODMAP Diet

If the Paleo diet or similar whole-foods, unprocessed meal plan doesn’t reduce a client’s chronic diarrhea after a few weeks, I assume they could be reacting to certain carbohydrates called FODMAPs. 

FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) are often found in healthy foods. However, because they can cause certain bacteria in the gut to proliferate, they can contribute to immune activation and inflammation in the colon. 

Most of the research on the low-FODMAP diet shows that it benefits people with irritable bowel syndrome (IBS) 21. However, there are also good studies that show a benefit for those with inflammatory bowel disease 22 23 24. 

Given that the first, most restrictive, elimination phase of the low-FODMAP plan is only short-term and can yield helpful insights about food sensitivities, the diet is usually worth trying. Later on, it’s safe to reintroduce foods and fine-tune the diet according to personal tolerances (more on this in the Reintroducing Foods section, below).

Take Care With Fiber, Fat, and Caffeine

Generally speaking, when stuck in the middle of an MC flare, a diet that is lower in fiber or fat may help. Put simply, too much fiber or fat can irritate an already sensitive digestive tract.

There’s still no scientific consensus on whether IBD patients should limit fiber in general, but it’s a good idea during a relapse or flare 25. Although the Paleo diet can have a decent amount of fiber from veggies, nuts, and fruit, the low-FODMAP diet is fairly low in fiber and may be more helpful for MC diarrhea.

Diets high in fat (especially animal fat) have been correlated with changes in gut microbes that are associated with intestinal inflammation 26. Thus, watching fat intake may be wise during a flare. Though it’s important to keep total fat intake from going too high, some types of fat are less concerning. 

Omega-3 fats and unsaturated fats from plants seem to have anti-inflammatory benefits for the gut 26. The Paleo diet emphasizes lean grass-fed meats and fish—which contain significant amounts of omega-3 fats—and the unsaturated fats in olive oil and many plants. It’s easy to design a low-FODMAP diet to do the same.

There’s some debate on whether coffee and other sources of caffeine, like energy drinks and chocolate, can exacerbate diarrhea 27 28. However, anecdotal evidence suggests that caffeine might stimulate the gut in unhelpful ways for those with MC 29. Though coffee may have health benefits, I suggest that my MC clients experiment with foregoing that morning espresso.

Reintroducing Foods 

The Paleo and low-FODMAP diets are both variations on elimination diets. While finding and eliminating the foods that seem to cause reactions can be very helpful for microscopic colitis, narrowing the diet too much isn’t healthy in the long term. Diversity in the diet is important for getting enough nutrients and keeping the gut microbiome healthy 30.

Once my clients’ MC symptoms have been stable (in remission) for a month or two, it’s time to start reintroducing foods and testing their tolerance to them. This can be a worrisome time, as they may find that their gut is not ready to tolerate some foods, and they start feeling symptoms again. However, my clients are often surprised by how well they can tolerate foods that were once problematic. Being patient with food reintroduction is key: It’s always an option to try again later. 

The good news is that it’s not all or nothing with food sensitivities. Sometimes a little of a certain food is no problem, while bigger amounts start to stimulate symptoms. Time and experimentation will guide the way to better food tolerance.

Is It Important To Remove Gluten and Dairy for MC?

We don’t have a solid answer to this. MC patients are more likely than healthy people to have celiac disease 31 32, but one study found that healthy women who ate gluten as adults  were not more likely to develop microscopic colitis 33. 

Unfortunately, that study didn’t look for gluten’s effects on active MC, and no good research seems to exist on using a gluten-free diet to treat it or any inflammatory bowel disease 33 34. 

In terms of dairy, evidence doesn’t support IBD patients removing it, but they have often chosen to avoid it 35. 

Some people with MC do find that they benefit from cutting down on dairy and gluten. This could be one reason (along with the anti-inflammatory benefits) that the Paleo and low-FODMAP diets can work so well for inflammatory bowel conditions. 

A good rule of thumb is to play it safe and remove dairy and gluten at first. But I encourage my clients to try reintroducing one or both as they start to feel better (per the Reintroducing Foods section, above). If well tolerated, gluten and dairy can help round out the diet nutritionally. 

Of course, anyone with a confirmed diagnosis of celiac disease or lactose intolerance will need to stay off gluten and dairy, which is no big deal if you take care to balance your diet with other nutritious foods. Gluten-free grains, like oats, quinoa, brown rice, corn, millet, and buckwheat, can replace wheat, barley, and rye. And non-dairy calcium-rich foods, like tofu, nuts, seeds, sardines, and green leafy veggies, can replace the calcium found in dairy.

Step 2: Probiotics for MC

Probiotics are supplements that contain various types of good gut bacteria. They are well documented to help with IBS symptoms, like bloating and abdominal pain 36 37 38 39. As far as an IBD treatment, there is also some good evidence that probiotics can improve the symptoms of ulcerative colitis 12 13 40.

But when it comes to taking probiotics for MC specifically, there’s hardly any research. Only one small randomized controlled trial seems to have compared probiotics to a placebo for MC, collagenous colitis in particular. In that study, the probiotics were slightly but not significantly better than placebo at improving diarrhea 41. Another small trial that compared probiotics to an IBD drug called mesalamine found the probiotics group of MC patients had no change in stool frequency 42.

That evidence may seem damning, but both of these studies were tiny, and the strongest one (with a placebo control) had procedural flaws that compromised the quality of its evidence 43 44. What this means is that we need a lot more well-designed research to provide an evidence base for treating MC with probiotics. 

Until then, we’ll rely on what we do know about probiotics: they are generally safe and effective for reducing inflammation in IBD 45 and for treating diarrhea in various other conditions 46. 

In the clinic, we’ve had positive results when giving MC patients probiotics. In particular, we’ve found that we get the best results when we use the three main categories of probiotics together. These are a Lactobacillus/Bifidobacterium blend, Saccharomyces boulardii, and soil-based probiotics.

If taking all three feels daunting (and you don’t like taking a pile of different supplements everyday), we’ve formulated an easy all-in-one product. Three-in-one triple therapy sticks are particularly convenient for traveling, as they are shelf-stable and don’t require refrigeration.

In any case, when incorporating probiotics for your microscopic colitis, it’s a good idea to work with a trusted healthcare practitioner who can help you troubleshoot any issues that come up.

Step 3: Stress Management for Microscopic Colitis

Though we don’t have research on how stress plays into microscopic colitis specifically, we do know that psychological stress contributes to inflammatory bowel disease in general 46 47. As a result of the gut-brain connection, chronic mental stress can worsen IBD symptoms and contribute to flares. In turn, heightened gut inflammation during a flare may contribute to worse mental health 48.

In reality, when you have microscopic colitis, you don’t need science to tell you that stress impacts your symptoms and that the disease itself can be stressful, especially on days when you need to plan your life around bathroom visits. 

Fortunately, stress-busting techniques can add up and start to break through the stress-flare cycle. Here are some science-backed ways to relieve stress and feel better. 

Slow Breathing. A 2023 meta-analysis found that breathwork, including slow breathing, was effective for reducing stress 49. To feel more centered and less overwhelmed, practice breathing in slowly through your nose. Let your breath flow as deep down into your belly as is comfortable, then breathe out gently and fully through your mouth (counting to 5 or 6 on the inhale and exhale can help). Try doing this for 5 minutes anytime you feel stress creeping up on you.

Yoga. This popular mind-body practice is perfect for helping you deal with stress. It has also been shown to help improve IBD (though not specifically microscopic colitis) 50 51. 

Moderate Exercise. The type of exercise that is likely best for most people with a high stress load and inflamed intestines is zone 2 exercise, which raises the heart rate but isn’t very intense. Brisk walking or slow jogging is zone 2 for most people, and if you can enjoy nature while you exercise, so much the better.

Meditation. Although the mechanisms are still unclear, meditation appears to change brain structure, modulate brain function, and reconstruct brain networks, stabilizing the autonomic (involuntary) nervous system 52. There are many good apps, such as Insight Timer or Headspace, with free or subscription-only guided meditations to get you started.

Cognitive Behavioral Therapy (CBT). CBT can relieve stress and also reduce inflammation, especially when you’re really stressed out 53. In CBT, a licensed mental health professional helps you break down overwhelming situations into smaller parts while also helping you adopt healthier thinking and behavior patterns. 

Probiotics. High-quality research has found that probiotics may be able to help reduce mental distress 54 and perceived stress 55 56 57, while reducing inflammation 56. 

This is by no means an all-inclusive list of de-stressing solutions, but you’ll likely find one or two strategies here that work for you. Minimizing gastrointestinal symptoms is your goal, so try to work in practices that have the best calming effect on your gut.

Step 4: More Advanced Troubleshooting Techniques for MC

Most of the time, eating healthier, reducing food triggers, taking probiotics, and dealing with stress can lead to noticeable improvements in microscopic colitis symptoms. But it’s good to have a couple other strategies in reserve for occasional flares, or for when MC symptoms are proving harder to resolve.

Elemental Diet

The first of these is an elemental diet, which is a liquid diet in which the nutrients are partially broken down, so the digestive system has less work to do. 

An elemental diet formula is hypoallergenic and anti-inflammatory. Semi-elemental diet formulas are similar, except they contain larger intact proteins, unlike the broken-down amino acids in elemental formulas. Both come as a powder that you simply mix, blend, or shake up with water. 

Drinking shakes instead of eating actual food might seem a little unappealing, but elemental diets have been shown to work quickly to improve inflammatory gut conditions. 

Again, we don’t have data for MC specifically, but in Crohn’s disease an elemental diet can significantly reduce disease activity 58 59. 

And in one small study, an elemental diet was at least as good as corticosteroids at inducing remission in Crohn’s patients. However, the elemental diet appeared to be more effective than the meds at improving their nutritional status. This was probably thanks to the elemental diet restoring their gut linings to a healthier (less leaky) state 60.

A day or two on an elemental diet is usually enough to achieve results. But even a “half” elemental diet (where up to 50% of calories come from elemental shakes and the rest come from food) can reduce gut symptoms and flares in Crohn’s patients 61. 

This means there is lots of flexibility if an all-liquid diet doesn’t sound appealing. I have clients who eat one or two enjoyable anti-inflammatory meals per day while giving their system a break the rest of the time with an elemental shake.

Herbal Antimicrobials

The other potential addition to a microscopic colitis treatment armory is a natural antimicrobial that contains herbs like oregano oil and berberine.

For my MC clients who have made all the gut-positive changes we’ve discussed but still have some symptoms, herbal antimicrobials might be the next step. They can help shake off any lingering gut infections that could be stimulating inflammation and contributing to MC flares.

Herbal antimicrobials work by removing the pathogens that shouldn’t be in the gut and giving the healthy microbes a better chance at flourishing. In other words, they rebalance the ecosystem in the gut for the better, and their effects can be game-changing for some.

Research suggests that herbal antimicrobials may help effectively treat Crohn’s and ulcerative colitis 62 63. This means there’s reason to suspect they may help other inflammatory gut diseases, including MC. 

One word of warning, however: Herbal antimicrobials can sometimes make you feel worse before you feel better. When antimicrobials kill the “bad-guy” microbes in the gut, something called a die-off reaction can occur as the dying bugs release toxins and activate immune defenses. This is temporary, but may cause some flu-like symptoms for a few days.

Herbal antimicrobials are more powerful than you might think, so I don’t suggest that anyone takes them lightly. Please work with a knowledgeable clinician who can help you adjust your dosage and protocol if needed. For more on how to use them, take a look at a brief description of my Great-in-8 Action Plan or the detailed version in Healthy Gut, Healthy You. The products we use in the clinic are meant to be used over a two-month schedule.

Keep Microscopic Colitis Treatment Simple

After a diagnosis of microscopic colitis, you might feel a bit alone because this inflammatory bowel disease doesn’t have as much recognition as Crohn’s and ulcerative colitis. 

However, you can rest assured that the treatment program for MC doesn’t need to be unique or especially complicated. A step-by-step approach to tackling underlying gut inflammation with diet and lifestyle changes can be simple and effective for MC, much like it can be for the other inflammatory bowel diseases.

That said, the waxing and waning nature of MC symptoms can be hard to deal with. If yours is a more stubborn case and you’d like support, we’d be happy to give you more personalized guidance. Just contact us at the Ruscio Institute for Functional Health.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.