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Evidence based

Evidence Based

This article is based on scientific evidence, written by experts and fact checked by experts.

Our team of licensed nutritionists and dietitians strive to be objective, unbiased, honest and to present both sides of the argument.

This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers.

What is Microscopic Colitis and How to Treat It Naturally

Written by on December 12, 2023

4 Natural Steps to Healing Microscopic Colitis Symptoms Effectively

Key Takeaways:
  • Microscopic colitis is an inflammatory bowel disease that causes chronic, watery, non-bloody diarrhea.
  • Smoking cigarettes and using certain medications (like proton pump inhibitors, selective serotonin reuptake inhibitors, and non-steroidal anti-inflammatory drugs) can increase your risk of microscopic colitis.
  • Traditional treatments for microscopic colitis include pharmaceuticals and surgery, which often don’t address the underlying causes like inflammation, leaky gut, and dysbiosis.
  • Natural treatments like elemental dieting, a low FODMAP diet, lifestyle interventions, probiotics, and antimicrobials can be extremely effective for reversing microscopic colitis symptoms and the underlying disease process.

If you’re struggling with frequent watery diarrhea that occurs on and off and wondering why, microscopic colitis (MC) may be to blame. While this type of inflammatory bowel disease (IBD) isn’t as well known as other forms, research suggests its prevalence may be on the rise, especially in older people. But because it’s a new kid on the research block, we don’t know a lot yet about the best ways of treating it.

Traditional management of microscopic colitis involves removing potential triggers, taking various pharmaceuticals (like budesonide, loperamide, cholestyramine, and lansoprazole), and in rare cases, having surgery. While these treatment options may be somewhat helpful, they don’t necessarily target the root causes of the condition. Without targeting the underlying causes, you can cycle through feeling better and then feeling worse again, which can lead you to view yourself as a chronic, complicated patient. 

The approach we take in the clinic is to add in a spectrum of natural solutions (i.e., diet and lifestyle, probiotics, and antimicrobials) that heal the underlying causes of gut inflammation, restore balance in the immune system, and improve the gut microbial environment. Not only can this approach lead to quick symptom relief, but it can also allow for more food freedom, less money spent on unnecessary supplements and tests, and a quicker return to normal life. 

With that, let’s get started by answering the question, what is microscopic colitis? 

What is Microscopic Colitis?

Microscopic colitis (MC) is a little-known inflammatory bowel disease (IBD) that impacts the colon. You’ve probably heard of ulcerative colitis and Crohn’s disease (also forms of IBD) because they are more common and easier for doctors to identify during a colonoscopy (a test that allows a gastroenterology surgeon to look at the small intestine and colon). 

In contrast, microscopic colitis usually looks like normal colon tissue upon examination, hence the term microscopic. Looking like normal tissue means doctors can easily overlook it as a cause of symptoms and misdiagnose it as something else, like irritable bowel syndrome (IBS) [1]. An accurate MC diagnosis requires a colon biopsy (tissue sample) and a microscope to evaluate the epithelial cells lining the inside of the colon (histology). 

Once identified, a doctor can figure out which of the two best-known subtypes of MC is present [2]:

  • Lymphocytic colitis (LC): Characterized by more lymphocytes (white blood cells, a type of immune system cell) in the lining of your colon.
  • Collagenous colitis (CC): Characterized by a thick layer of collagen (a type of protein) in the colon lining.

The most common symptoms of microscopic colitis can come and go, and often include [2, 3]:

  • Chronic, watery, non-bloody diarrhea (up to 15 times a day)
  • Urgency to have a bowel movement, often at night
  • Fecal incontinence (lack of control of bowel movements)
  • Abdominal pain
  • Joint pain
  • Weight loss
  • Fatigue

As you can see, MC can significantly impact your quality of life. Additionally, if it isn’t well-controlled, you can develop nutritional deficiencies and dehydration [2]. 

We don’t know exactly why people develop MC, but we’re aware of several potential causes and risk factors.

Causes and Risk Factors of Microscopic Colitis

Like other chronic inflammatory conditions, MC probably results from both genetic and environmental triggers. 

Factors that may contribute to an increased risk of developing microscopic colitis include [1]:

  • Having an autoimmune condition, especially celiac disease, but also conditions like type 1 diabetes, rheumatoid arthritis, or Hashimoto’s thyroiditis
  • Bile acid malabsorption, a digestive disease in which bile acids build up and cause diarrhea
  • Smoking
  • Using certain medications like proton pump inhibitors (PPIs like Prilosec), selective serotonin reuptake inhibitors (SSRIs like Lexapro), and non-steroidal anti-inflammatory drugs (NSAIDs like ibuprofen)
  • Having a previous gastrointestinal infection

In many cases of MC, simply removing a drug that was causing it will stop the disease process. For those who continue to have symptoms, there are no FDA-approved medications specific to MC. Most doctors prescribe drugs designed to treat Crohn’s disease or ulcerative colitis, which often don’t work for MC [4].

While removing triggers like medications and smoking may help put MC into remission temporarily, we aim to foster more complete healing by addressing gut health with natural therapies. In our experience in the clinic, patients with MC have improved their symptoms even more with natural approaches, so I’d like to walk you through our 4-step treatment guide.

4-Step Treatment Guide for Microscopic Colitis

MC is characterized by chronic inflammation of the gut lining—which often involves leaky gut and dysbiosis—followed by malabsorption, so our treatment needs to target these factors. In addition to what your gastroenterologist recommends—ideally to stop smoking and replace offending medications with safer ones—a combination of diet, lifestyle, probiotics, and antimicrobials can get you on the path to fuller healing.  

I’m a proponent of food-first interventions, so I generally start with dietary modifications. As I discuss in Healthy Gut, Healthy You, resetting the gut with an elemental diet can be an effective way to address many gut symptoms, so this is where I will begin. 

Step 1: Elemental Diet Reset for Microscopic Colitis

The elemental diet is a hypoallergenic, anti-bacterial, anti-inflammatory meal replacement shake. The nutrients (carbohydrates, proteins, and fats) in it are already partially or completely broken down into easily absorbed units, which gives your digestive system the opportunity to rest and heal. The elemental diet has long been prescribed for treating other kinds of IBD because it lowers inflammation, reverses the underlying causes of autoimmune diseases, and prevents flare-ups [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15].

I recommend starting with a 2–4 day “fast” in which you replace your normal solid foods with Elemental Heal. Start with the goal of 2 days on this elemental diet since that’s when you’ll likely begin to experience significant improvements. If you’re feeling great, then you may want to continue for the full 4 days to achieve maximum benefit with regard to energy, digestive symptoms, mood, sleep, and mental clarity. Occasionally, some people have a negative reaction when fasting. So, if you’re not feeling great after the second day, then stop at day two. Once you’re ready to transition back to solid foods, it’s time to determine which diet will give you the most symptom relief.

Step 2: Diet and Lifestyle for Microscopic Colitis

You’re probably wondering if there’s a specific diet for MC. As is true for many conditions, there’s no single perfect diet for this one. Instead, the diet can be one of many that satisfy these goals: reduce the burden on your immune system, lower your inflammation, and possibly reduce the foods feeding unhelpful or excessive bacteria. 

Fortunately, at the clinic, we have identified several dietary patterns that seem to work well for MC, and they are in line with the Microscopic Colitis Foundation recommendations. I tend to recommend starting with the least restrictive option, and to only move on to a more restrictive diet if your symptoms don’t improve. Here’s what this might look like in practice:

  • If you’re following the standard Western diet (meaning you’re routinely eating ultra-processed foods and sugar), you may want to start with the Paleo diet. It consists of whole foods that are anti-inflammatory for most people, which can give your immune system a rest and protect the tissues in your body from inflammation [16].
  • If you’re already following a wholesome meal plan (eating mostly whole, unprocessed foods and little added sugar), or if the Paleo diet doesn’t lead to significant symptom improvement after a few weeks, then you could be reacting to certain sugars called FODMAPs. These fermentable sugars can activate unfriendly gut bugs or help an overpopulation of bacteria in the small intestine (where they shouldn’t be) keep growing. That, in turn, can contribute to immune activation and inflame your colon. So, a good next step is to try a low-FODMAP diet [17, 18, 19].
  • If you’re seeing your symptoms improve on a low-FODMAP diet, then stick with it for several weeks before you start adding foods back in. But if your symptoms aren’t improving as much as you’d like, then you may want to try a combo of both diets: a Paleo low-FODMAP diet or the Autoimmune Protocol [20]. Both options are more restrictive, but they may give you the relief you need until you can start to reintroduce some of the foods you’ve eliminated.

Diet is a powerful treatment, but it’s not the be-all and end-all approach. If you’ve mostly been compliant with dietary changes for several weeks and you still don’t feel like you’ve gotten your health back, the answer probably isn’t more dietary restriction. The last thing I want is to help you become neurotic about food choices. I want you to try to relax about food and be assured that we have a lot of options for healing your symptoms. This brings me to my next point in step 2, which is lifestyle.

Lifestyle Changes for Microscopic Colitis

Along with diet, lifestyle changes can be extremely helpful for reversing your MC symptoms and improving your quality of life. One truth I’ve discovered from working with many different patients is that those who have the most balance in their lifestyle tend to have better outcomes overall. Does this mean you have to stress yourself out about designing the perfect lifestyle? Definitely not. But you shouldn’t dismiss lifestyle interventions, either, because they offer a lot of low-hanging fruit that can help you heal. 

The key to making effective lifestyle changes is to create a healthy foundation. I know it doesn’t sound exciting, but without a healthy foundation, your other strategies won’t be as impactful. Here’s a chart with my favorite science-based lifestyle tips to get you started:

Lifestyle Therapy Tips for Implementation
Restorative Sleep 
  1. Set a bedtime routine with a consistent bedtime and waking time. Avoid all-nighters and shift work if possible. Try to eat dinner at least two hours before bedtime [21, 22, 23].
  2. Avoid bright lights and screen use for at least two hours before bed [24].
  3. Modify your bedroom environment (keep it dark, quiet, and cool) to support good sleep [25].
  4. Address breathing problems, like mouth breathing, snoring, sleep apnea, or allergies by consulting with a medical professional [16, 26]. 
  5. Exercise regularly, but avoid vigorous exercise close to bedtime [27].
  6. Try taking melatonin to help you fall asleep quickly, and take probiotics for general sleep support [28, 29, 30]
Stress Management
  1. Avoid overexercising [31].
  2. Practice meditation, yoga, or deep breathing [32, 33, 34, 35].
  3. Spend time in nature [36, 37, 38, 39, 40, 41, 42, 43].
  4. Repair or release broken relationships.
Exercise
  1. Walk as much as possible every day.
  2. Do some cardiovascular training (fast walking, swimming, biking, rowing, running) 3 sessions per week [44, 45, 46] 
  3. Do some strength training (3 sessions per week) [47]. 
  4. Add in flexibility training (stretching or yoga) daily [48].
Time in Nature [36, 37, 38, 39, 40, 41, 42, 49, 50, 51, 52] 
  1. Read a book by a flowing stream
  2. Watch the sunrise or sunset
  3. Walk barefoot in the grass
  4. Practice yoga in the sun [53, 54]
  5. Go for a hike in the woods [43, 55]
  6. Create a greenspace indoors with houseplants

Just like with diet, we have a wide range of options when it comes to lifestyle strategies. Don’t feel the need to practice every single item listed here. However, consistently incorporating something from each category will likely lead to more complete resolution of your symptoms.

Hopefully, changing your diet and lifestyle will heal your microscopic colitis symptoms. If there are some lingering issues though, you can move on to step 3 and incorporate probiotics.

Step 3: Probiotics for Microscopic Colitis

Once you’ve created a healthy foundation with diet and lifestyle, you can give probiotics a try. If you’re unfamiliar with what they are, probiotics are living microbes that provide health benefits to humans. Probiotics provide their benefits by:

  • Increasing the bacterial diversity, or health, of your gut microbial community [56, 57, 58]
  • Fighting pathogens (harmful bugs) and their toxins [57, 58, 59, 60, 61]
  • Promoting a more rapid recovery from imbalanced gut organisms [57, 58]
  • Promoting a healthy immune response in your gut [57, 58, 62, 63, 64]
  • Reducing gut inflammation [56, 57, 58]
  • Encouraging the growth of healthier microbes in your gut [57, 58, 62]
  • Reducing leaky gut [57, 58, 65, 66, 67)

To sum this up, probiotics can help to improve the balance of organisms in your gut, calm your immune system if it’s overzealous, reduce inflammation, and help you get rid of “bad” bugs. 

When it comes to MC specifically, we don’t yet have enough data to know if probiotics can put it into remission [68]. That said, high-quality studies have found probiotics to be as helpful as medications for putting ulcerative colitis into remission, so it’s possible they can do the same for MC [69, 70]. But until more research comes in, I’ll rely on my clinical observations to suggest that probiotics are helpful for MC, even if indirectly.
In the clinic, we use a triple-therapy approach to probiotics, which means we use the three most effective categories of probiotics together. Specifically, we start with a Lactobacillus/Bifidobacterium blend and then add both Saccharomyces boulardii and soil-based probiotics.

What is Microscopic Colitis

Here’s how to incorporate probiotics into your routine:

  1. Try a quality formula probiotic from category 1 (Lacto/Bifido blend), category 2 (S. boulardii), and category 3 (soil-based probiotics) — take all three together. 
  2. Monitor your symptoms for 3–4 weeks. If you’re improving, continue with all three categories of probiotics until your improvements have plateaued.
  3. Once you’ve seen your maximum improvement for a while (you’ve plateaued), stay here for about a month to allow your system to calibrate to the improvements. 
  4. Reduce your dose slowly to find your minimal effective dose.  
  5. Stay on the minimal effective dose to maintain results.

I find probiotics helpful for most people, so if you’ve tried them in the past without success, you may not have given it enough time, or you may have only used one category of probiotic. It’s worth it to give it another shot using the triple therapy protocol. That being said, if you haven’t noticed any change in your symptoms after a couple of months, you can stop taking probiotics and feel confident that you’ve fully explored probiotic therapy. 

If, after steps 1–3, you’re feeling better but haven’t experienced complete healing, it may be time to consider adding in herbal antimicrobials.

Step 4: Herbal Antimicrobials for Microscopic Colitis

If you’ve gone through steps 1–3 but still have nagging symptoms, you could be dealing with an infection that’s evading your other efforts. 

But before we get into the antimicrobial protocol, I want to stress the importance of laying the groundwork beforehand. By working through the first 3 steps of this gut-healing process, you’re improving and setting the stage for optimal gut microbiota function. This requires some patience, but it ultimately allows you to respond much better to antimicrobial therapy. 

Herbal antimicrobials are powerful, and their effects have been fairly well documented. Many cultures around the world have used antimicrobial herbs to help people recover from various digestive diseases. Antimicrobials work by removing the “bad guys” that shouldn’t be in your gut and giving your healthy bacteria a chance to thrive. Essentially, they help to rebalance the ecosystem in your gut and tip the balance in favor of the “good guys.” 

In terms of IBD, research suggests antimicrobials may help effectively treat Crohn’s and ulcerative colitis [71, 72]. But until we have studies looking specifically at antimicrobials for MC, we’ll refer to the improvements we see in the clinic.

The antimicrobial plan we use in the clinic is two months long. We use two formulations for the first month and two different formulations for the second month. These formulas are designed to address infections, such as from small intestinal bacterial overgrowth (SIBO), fungi (e.g. Candida), Helicobacter pylori (stomach bacteria), Blastocystis hominis (intestinal parasite), Giardia (intestinal parasite), other protozoan parasites, and intestinal worms, all of which can impede healing.

This chart details the month-1 antimicrobial protocol:

ProductDoseTimes Per DayBottles Needed
Biota-Clear 1a3 pills22
Biota-Clear 2a2 pills22

This chart details the month-2 antimicrobial protocol:

ProductDoseTimes Per DayBottles Needed
Biota-Clear 2a2 pills22
Biota-Clear 2b3 pills22

As always, you should speak with your healthcare provider before implementing new dietary supplements.

In my experience, the vast majority of patients tolerate herbal antimicrobial therapy well, but there is a potential to feel crummy for a little while. This can be frustrating, but those symptoms tend to indicate that the herbs are working. When they kill “bad guys”, the dead organisms can trigger the immune system to fight and cause symptoms, but these often abate after a few days. 

However, if you try an antimicrobial protocol, and your symptoms last longer than 5–7 days, it’s best to stop the therapy and revisit what was working well for you. 

4 Steps for Healing Microscopic Colitis Naturally

What is microscopic colitis? It’s a lesser-known form of inflammatory bowel disease that causes chronic, non-bloody, watery diarrhea. Traditional treatment options include discontinuing potentially triggering medications, avoiding smoking, taking pharmaceuticals, and in rare cases, having surgery. While these can be helpful, they don’t always address the underlying causes of the disease. 

If you have an MC diagnosis, you’re probably working with a gastroenterologist. In addition to their recommendations—and especially if you only find temporary relief—I suggest trying the 4-step natural approach detailed in this article. If you follow this step-by-step guide, ideally with the support of a trusted healthcare provider, you will address the underlying causes of MC: inflammation of the gut lining—which often involves leaky gut and dysbiosis—followed by malabsorption. Cleaning up your diet, finding balance in your lifestyle, and adding in probiotics and herbal antimicrobials may provide powerful symptom relief and restore your quality of life.

If you complete this process and still have symptoms, check out my Great-in-8 Action Plan in Healthy Gut, Healthy You. If you’d like more personalized guidance, contact us at the Ruscio Institute for Functional Health.

The Ruscio Institute has developed a range of high-quality formulations to help our patients 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.

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.
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