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What is Microscopic Colitis and How to Treat It Naturally

Written by Dr. Michael Ruscio, DC on November 18, 2024

Written by Dr. Michael Ruscio, DC on November 18, 2024 — Reviewed by Hilary Watts

If you’re struggling with frequent watery diarrhea that occurs on and off, microscopic colitis (MC) may be to blame. 

What is microscopic colitis? It’s a type of inflammatory bowel disease (IBD) that isn’t as well known as Crohn’s disease or ulcerative colitis. Research suggests it may be on the rise, especially in older people. 

Microscopic colitis is a new kid on the research block, so we don’t know a lot about the best ways of treating it. Traditional management of microscopic colitis involves removing potential triggers, taking various pharmaceuticals , and in rare cases, having surgery. 

These treatment options may be somewhat helpful, but they don’t necessarily target the root causes of the condition. 

Without targeting the underlying causes of any disease, including MC, we’re more likely to cycle through feeling better and then feeling worse again. That can make anyone feel like a forever patient, but it doesn’t have to be that way. 

The first step to getting off the MC rollercoaster is to understand what it is and what’s causing it.

What is Microscopic Colitis?

Microscopic colitis (MC) is a little-known inflammatory bowel disease that impacts the colon (large intestine). You’ve probably heard of ulcerative colitis and Crohn’s disease. They’re more common forms of IBD and easier for doctors to see during a colonoscopy, a test that allows a gastroenterology surgeon to look at the intestines. 

In contrast, microscopic colitis usually looks like normal colon tissue because you need a  microscope to see it. Looking like normal tissue means doctors can easily overlook MC as a cause of symptoms and diagnose it as something else, like irritable bowel syndrome (IBS) 1. 

An accurate MC diagnosis requires a colon biopsy (tissue sample) and a histology exam of the cells lining the inside of the large intestine. These epithelial cells form the surface of the intestinal mucosa and release protective mucus along the digestive tract. In microscopic colitis, these cells are damaged.

Under a microscope, the epithelium can help a doctor figure out which of the two best-known types of microscopic colitis is present. The subtypes are 2:

• Lymphocytic colitis (LC): Has more lymphocytes (white blood cells, a type of immune system cell) in the colon lining.
• Collagenous colitis (CC): Has 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, non-bloody diarrhea (up to 15 times a day)
• Urgent need to have a bowel movement, often at night
• Fecal incontinence (lack of control of bowel movements)
• Abdominal pain or bloating
• Joint pain
• Weight loss
• Fatigue

As you can see, MC can heavily impact your quality of life. And if it isn’t well-controlled, it can also cause nutritional shortages and dehydration 2. 

We don’t know exactly why people develop MC, but there are several possible causes and risk factors.

Causes and Risk Factors of Microscopic Colitis

Like other chronic inflammatory conditions, MC probably results from both genes and the environment. 

Factors that may raise the risk of 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. But for those who keep having symptoms, there are no FDA-approved medications for MC. Most doctors prescribe drugs designed to treat Crohn’s disease or ulcerative colitis, but they often don’t work for MC 4.

When removing triggers like medications and smoking puts MC into remission for only a short time, addressing gut health with natural therapies can offer more complete healing. In our experience in the clinic, clients with persistent MC have relieved their symptoms with our 4-step treatment guide.

4-Step Treatment Guide for Microscopic Colitis

MC involves chronic inflammation of the gut lining—which often implies a leaky gut and dysbiosis—followed by malabsorption. Our treatment needs to target these factors. 

In addition to what a gastroenterologist will likely recommend—to stop smoking and replace offending medications with safer ones—a combination of diet, lifestyle, probiotics, and antimicrobials can pave a path to fuller healing.  

The approach we take in the clinic is to add in a spectrum of natural solutions designed to:

• Heal the underlying causes of gut inflammation
• Restore balance in the immune system
• Improve the gut microbial environment 

Not only can this approach lead to quick symptom relief, but it can also allow for more food freedom, spending less on unnecessary supplements and tests, and a quicker return to normal life. 

I prefer food-first treatments, so I generally start with dietary changes. As I discuss in Healthy Gut, Healthy You, resetting the gut with an elemental diet before making dietary changes can address many gut symptoms quickly. So, that is where I’ll 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 the digestive system a chance to rest and heal. 

The elemental diet has long been prescribed for treating other kinds of IBD because it can lower inflammation, reverse the underlying causes of autoimmune disease, and prevent flare-ups 5.

I recommend my MC clients start with a 2–4 day “fast” in which they replace their normal solid foods with Elemental Heal. Even if they feel better after two days, they often continue for the full four days to achieve full improvements in energy, digestive symptoms, mood, sleep, and mental clarity. 

Occasionally, some people have a negative reaction when fasting. If they don’t feel better after the second day, then I have them stop. When it’s time to transition back to solid foods, we get to figure out which diet will give them 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: 

• Reduce the burden on the immune system
• Lower inflammation
• Reduce the foods feeding harmful bacteria or fungi 

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 move to a more restrictive diet only if a client’s symptoms don’t improve. Here’s what this might look like:

• For clients following a standard Western diet (meaning they regularly eat ultra-processed foods and sugar), a good option is a Paleo diet. It consists of whole foods that are anti-inflammatory and can give the immune system a rest and protect the body from inflammation 6.
• Those who follow a wholesome meal plan like a Paleo diet but don’t feel well after eating may be reacting to certain sugars called FODMAPs. These fermentable sugars can activate unfriendly gut bugs or help too many bacteria grow in the small intestine (where they shouldn’t be). That can activate the immune system and inflame the large intestine, so, a good next step is to try a low FODMAP diet 7.
• If their symptoms improve on a low FODMAP diet, then we stick with it for several weeks before adding limited foods back in. But if their symptoms aren’t improving enough, we’ll consider a Paleo low FODMAP diet or the Autoimmune Protocol 8. Both options are more restrictive, but they may give needed relief to start reintroducing foods.

Diet is a powerful treatment, but it’s not the be-all and end-all approach. A healthy diet won’t do much if the lifestyle isn’t supporting gut health. So, once the diet is in place, we bring in step 2 and create a supportive lifestyle.

Lifestyle Changes for Microscopic Colitis

Along with diet, lifestyle changes can help reverse MC symptoms and improve quality of life. 

One truth I’ve discovered from working with many different clients is that those who have the most balance in their lifestyle tend to have better outcomes overall. 

Does this require stressing out about designing the perfect lifestyle? Definitely not. But creating a healthy lifestyle offers a lot of low-hanging fruit that can help us heal. 

Making supportive lifestyle changes is about creating a healthy foundation. It may not sound exciting, but without a healthy foundation, other strategies won’t be as impactful. Here’s a chart with my favorite science-based lifestyle tips:

Improving the diet and lifestyle is often all our clients need to relieve their microscopic colitis symptoms. But for those who have lingering issues, we move to step 3 and incorporate probiotics.

Step 3: Probiotics for Microscopic Colitis

Once our MC clients have created a healthy foundation with diet and lifestyle, if they’re still having symptoms, we add in probiotics. Probiotics are living microbes (bacteria or fungi) that provide health benefits by:

• Fighting harmful bacteria 12, fungi 13, and parasites 14 
• Reducing leaky gut 15 
• Reducing brain fog and inflammation 16
• Improving mood and the stress response 17

When it comes to microscopic colitis, we don’t have enough data to know if probiotics can put it into remission 18. But 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 19. 

Until more research comes in, I’ll rely on my clinical observations, which suggest that probiotics are helpful for MC.

In the clinic, we use a triple therapy approach to probiotics, which means we use the three most effective categories of probiotics together. We combine a Lactobacillus/Bifidobacterium blend with Saccharomyces boulardii and soil-based probiotics and have our clients trial them for 2–3 months.

I find probiotics to be helpful for most people. But if you’ve tried them without success, you may have:

• Had a lower-quality probiotic
• Not given a high-quality one enough time
• Not set up a healthy foundation with diet and lifestyle supports
• Used just one category of probiotics when three would have been better 

When our clients feel somewhat better after steps 1–3 but haven’t experienced complete healing, it’s time to consider herbal antimicrobials.

Step 4: Herbal Antimicrobials for Microscopic Colitis

When nagging symptoms linger after steps 1–3, a gut infection could be the issue. 

But before I get into how to treat gut infections with antimicrobials, I want to stress the importance of laying the groundwork beforehand. Working through the first steps of this gut-healing process serves to stabilize the gut and set the stage for it to respond well to antimicrobials. 

Antimicrobials—whether prescription or herbal—work by removing the “bad guys” that shouldn’t be in the gut and giving the healthy organisms a chance to thrive. They help to rebalance the ecosystem in the gut and tip the balance in favor of the “good guys.”

Not everyone can or wants to use prescription antibiotics, and there’s evidence that herbal antimicrobials can be just as powerful while causing fewer side effects. Many cultures around the world have used antimicrobial herbs to help people recover from various digestive diseases. 

Research suggesting that antimicrobials may help treat Crohn’s disease and ulcerative colitis 20 21 is encouraging for people with MC. 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:

• Small intestinal bacterial overgrowth (SIBO)
• Candida overgrowth
• Helicobacter pylori (stomach bacteria)
• Blastocystis hominis (intestinal parasite)
• Giardia (intestinal parasite)
• Other protozoan parasites and intestinal worms

This chart show the first month of the antimicrobial protocol we use in the clinic:

This chart shows the second month of the protocol:

It’s important to speak with a healthcare provider before implementing new dietary supplements, including herbal antimicrobials.

In my experience, most people tolerate herbal antimicrobial therapy well, but there is a potential to feel crummy for a little while during treatment. This can be frustrating, but those symptoms usually mean that the herbs are working. 

When they kill “bad guys”, the dead organisms can trigger the immune system and cause symptoms, but these often let up after a few days of treatment. However, when clients have symptoms that last longer than 5–7 days on antimicrobials, we stop the therapy and revisit what was working well or things we might have missed. 

4 Steps for Healing Microscopic Colitis Naturally

What is microscopic colitis? It’s a lesser-known form of inflammatory bowel disease that causes chronic diarrhea. Traditional treatment options can be helpful, but they don’t always address the underlying causes of the disease. 

If you have an MC diagnosis, I encourage you to work with a gastroenterologist or other qualified healthcare provider who will help you incorporate the 4-step natural approach in this article. This science-based plan for whole-gut healing should go a long way toward relieving you of microscopic colitis. 

If you need to find someone who can help you along the 4-step path, we’d love to help. Please 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.