Your 4-Step Microscopic Colitis Treatment Plan

A Guide To Demystifying Microscopic Colitis & the Healing Strategies That Work

• What Is Microscopic Colitis?|
• What Triggers MC?|
• Conventional Treatment Options|
• Why the Key to the Plan Is Restoring Gut Health|
• Step 1: Choose an Elimination Diet Treatment for Microscopic Colitis|
• Step 2: Trial Probiotics for MC|
• Step 3: Integrate Stress Management Strategies for Microscopic Colitis|
• Step 4: Employ These More Advanced Troubleshooting Techniques for MC|
• Keeping Microscopic Colitis 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 the 4-step treatment plan to improve microscopic colitis symptoms, let’s first understand what microscopic colitis is, what triggers it, and why, with conventional treatments available, the 4-step treatment plan is more promising.

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, in which the inflammation is easy to see.

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 abdominal pain, fatigue, and weight loss [1].

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 dysbiosis, gut leakiness, and inflammatory changes that lead the immune system to attack healthy cells in the gut can be a bit of a puzzle.

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

• The genes you inherit [1] 
• Being female, and 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, 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 experience fecal incontinence.

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 your 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 and ulcerative colitis [9], as well as multiple sclerosis and lupus [10, 11]

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

Step 1: Choose an Elimination Diet Treatment 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

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

On the Paleo diet, you eat mainly whole foods that are similar to those our ancestors would have eaten. This means avoiding ultra-processed foods and choosing whole foods like berries, fresh vegetables, grass-fed meats, eggs (if you tolerate them), 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 your exposure to foods that can cause your 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. 

You may also find that certain foods allowed on the Paleo diet don’t go down well or cause you symptoms like hives, sniffles, fatigue, or gut distress, so it’s important to experiment with any diet you try for reducing inflammation. 

By controlling inflammation with your diet, you calm your symptoms and create a healthier environment for your gut bacteria, which thus improves your gut microbiome [17, 18]. In cyclic fashion, a healthier microbiome reduces inflammation further [19, 20]. 

The Low-FODMAP Diet

If you’re already following a whole-foods, unprocessed meal plan, or if the Paleo diet doesn’t reduce your chronic diarrhea after a few weeks, then you 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 your 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, you can reintroduce foods and fine-tune your eating according to your tolerances (more on this in the Reintroducing Foods section, below).

Take Care With Fiber, Fat, and Caffeine

Generally speaking, when you’re in the middle of an MC flare, you may do better with a diet that isn’t high in fiber or fat. 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 suit your needs when you are having 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 your fat intake may be wise during a flare. Though you want to keep your 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. You can 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, when you have active MC, you may want to experiment with going with and without that morning espresso.

Reintroducing Foods 

The Paleo and low-FODMAP diets are both variations on elimination diets. While finding and eliminating the foods that you are sensitive to can be very helpful for microscopic colitis, narrowing your diet very much isn’t healthy in the long term. Diversity in the diet appears to be important for both nutritional adequacy and microbiome health [30].

It’s important to start reintroducing foods and testing your tolerance to them when your MC symptoms have been stable (in remission) for a month or two. This can be a worrisome time, as you may find that your gut is not ready to tolerate some foods, and you start feeling symptoms again. However, you may be surprised by how well you can tolerate other foods that were once problematic. Being patient with food reintroduction is key: you can always try again at a later date. 

Remember, it’s not all or nothing with food sensitivities. You may be able to have a little of a certain food, while bigger quantities start to stimulate symptoms. Over time, you will find your way and your gut will respond better.

Is It Important To Remove Gluten and Dairy for MC?

We don’t have a solid answer to this. Although MC patients are more likely than healthy people to have celiac disease [31, 32], a study from 2019 found no link between gluten intake during adulthood and the risk of women without celiac disease developing 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, though 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 you to try reintroducing one or both as you start to feel better (per the Reintroducing Foods section, above). If you tolerate them, they can be helpful for rounding out your diet nutritionally. 

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

Step 2: Trial 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: Integrate Stress Management Strategies 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 exacerbate 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: Employ These 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 I want you to have a couple other strategies in reserve for occasional flares, or for when your 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 your 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 the nutritional status in these patients. 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 your calories come from elemental shakes and the rest come from food) can reduce gut symptoms and flares in Crohn’s patients [61]. 

This means you have lots of flexibility if an all-liquid diet doesn’t sound appealing. You can eat one or two enjoyable anti-inflammatory meals per day while giving your system a break the rest of the time with an elemental shake.

Herbal Antimicrobials

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

If you’ve made all the gut-positive changes we’ve discussed but still have some symptoms, herbal antimicrobials might be the next step. They can help you 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 your gut and giving your healthy microbes a better chance at flourishing. In other words, they rebalance the ecosystem in your 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 your gut, you can get something called a die-off reaction as the dying bugs release toxins and activate your immune defenses. This is temporary, but you may have to bear with some flu-like symptoms for a few days before you feel better again.

Herbal antimicrobials are more powerful than you might think, so I don’t suggest you take 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.

Keeping 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.

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