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If you are struggling with constipation and look 6 months pregnant with belly bloat by the end of the day, you could have intestinal methanogen overgrowth (IMO). You can relieve the bloating and rebalance your gut with changes to your diet and by killing the excess methanogens which will eventually restore regularity.

Here’s all the info you need to treat IMO.

What is IMO?

IMO was previously known as methane dominant SIBO (small intestine bacterial overgrowth), but the more we learn about SIBO, the more we understood the name, methane dominant SIBO, was not really accurate. The B in SIBO stands for bacteria, and methanogens are typically not bacteria; they’re actually archaea. We also now know that methanogens can be present throughout the intestinal tract, both small and large intestine, and not just isolated to the small intestine like SIBO.

Often when people have SIBO or IMO, their first diagnosis will be Irritable Bowel Syndrome (IBS), which is really a fancy way of saying ‘we don’t know what’s wrong with your gut.’ Up to 80 percent of IBS cases are actually SIBO. (source)

If you’ve been diagnosed with IBS, please get tested for SIBO. You can order your own breath test (a kit that comes to your house and that you can do at home) via this link. It’s the Small Intestinal Bacterial Overgrowth 3-Hr Lactulose test. You’ll need a qualified practitioner to interpret the results for you, but it can be such a relief to find out what’s causing your uncomfortable symptoms after years of hearing doctors say they don’t know why you have IBS. (speaking from experience via the clients with whom I work).

Note that you cannot accurately diagnose SIBO via a stool test, though there are markers on a stool test that can indicate SIBO. A breath test is the only way to accurately diagnose SIBO. Many GI doctors are not very familiar with SIBO, IMO, or breath testing, so make sure you find either a doctor of nutritionist who doesn’t dismiss your symptoms or deny you the testing you request.

What Are Methanogens?

Methanogens produce methane gas and can overgrow in the small bowel (intestine) or the colon (large intestine). So, the name Intestinal Methanogen Overgrowth is really more fitting. While methane is associated with constipation, hydrogen gas produced in excess with SIBO is associated with diarrhea. Methane gas slows transit time while hydrogen speeds it up. So when you have too many methane producers, you get constipation.

Methanogens are present in and are an essential component of the intestinal ecosystem. Typically they’re kept in check by the other bacteria in your gut. That’s why it’s important to have diverse and good numbers of bacteria in your large intestine.

Having methanogens in our digestive tracts provided an evolutionary advantage because they slow digestive motility and allow more calories to be extracted from food (see this post for more about how too many of the wrong microbes in your gut can make you fat), but their ability to survive also makes an overgrowth more difficult to treat. (source)

In excess, methanogens cause the severe depletion of short chain fatty acids (SCFAs), such as butyrate, which supports intestinal cell energy production and repair. People with SIBO and IMO are very often SCFA deficient, and these fatty acids are crucial for gut health because they feed your colon cells.

Intestinal Methanogen Overgrowth Symptoms

The biggest symptom associated with IMO is constipation, because the methane gas produced by methanogens slows transit time way down. Other symptoms include the following:

  • belching
  • bloating, especially bloating that worsens over the course of the day
  • nausea
  • IBS
  • IBD
  • being overweight or obese, weight loss resistance
  • blood sugar dysregulation
  • malabsorption of nutrients, especially iron
  • heartburn
  • anxiety
  • fatigue

You are at increased risk of IMO if you

  • are elderly
  • take antibiotics and medications that suppress stomach acid production: proton pump inhibitors  (PPIs) and H2 blockers
  • have gastroparesis or Celiac
  • have diabetes (type 2) or low stomach acid
  • have adhesions in the gut due to surgeries or injury

How Intestinal Methanogen Overgrowth Wrecks Your Gut

The high levels of methanogen archaea in the intestines (large and/or small) cause malabsorption, preventing the body from properly absorbing and using nutrients. I often see iron deficiency (mostly in women) and B vitamin deficiencies in those with IMO and SIBO.

Archaea, like bacteria, like to eat/ferment the carbohydrates that you eat. When you eat carbs (like vegetables, fruit, bread, dairy, for example), the methanogens get excited because they’re getting fed too. They then ferment the carbs you eat and release methane gas as a byproduct of fermentation, and that causes you bloating and slows transit time, which means you will be constipated.

A main problem with constipation (and there are many) is that when stool moves too slowly through your colon or sits in your colon and doesn’t move, the toxins and hormones bound up in the stool awaiting excretion get reabsorbed into your system. That’s not good for you and can cause estrogen dominance, even more bloating, acne, and can increase your toxic load. You don’t want to hang onto the trash that’s supposed to be taken out!

Also, the fermentation process causes damage to your intestinal tract cells which will cause leaky gut. This is a main cause of malabsorption, meaning you are not absorbing all the nutrients from your food, setting you up for deficiencies. And leaky gut causes a whole host of other problems (read all about it here) including joint pain, increase in food intolerance, mood issues, and an increased risk for autoimmune disease.

How to Treat Intestinal Methanogen Overgrowth

First you want to confirm that you have IMO. You can do this via breath and stool testing. If you have any of the symptoms I describe, especially the chronic constipation and bloating, I would recommend both tests. The GI MAP stool test I use will detect methanogen overgrowth in the large intestine, and the breath test will detect IMO in the small intestine. You can order both here. If you have IMO in the small intestine, your breath test will show elevated levels of methane gas that are produced by the methanogens. In the large intestine, high levels of methanobacterium will show up on the GI MAP like this 👇

Once confirmed, there are a couple different routes to take. If you have IMO in the small intestine you can take 2 antibiotics, rifaximin and neomycin, followed by an anti-microbial herbal protocol. (source) I think this is the most effective treatment. Rifaximin and neomycin are minimally absorbed antibiotics so they don’t cause as much damage to the overall microbiome as typical antibiotics.

The herbs that work best to treat IMO in the small and large intestine are berberines, GI MicrobX, garlic, oil of oregano, and neem. You can also take Atrantil for the bloating. Read more about SIBO and methane treatment in this post. Note that SIBO and IMO are treated differently, and IMO takes longer to treat.

Vitally important is that you need to make sure your elimination pathways and lymphatic system are operating well, or you’re going to feel much worse on this protocol due to potential die-off. That means you need to be pooping better, hopefully at least once per day, before you start on this protocol to ensure that the dead bacteria and methanogens have a place to exit your body as you’re killing them off.

Magnesium oxide or Colon Rx, a magnesium-triphala combo, can help combat constipation until you successfully knock back the methanogens that are causing the constipation. You could also consider enema if nothing else is helping. Also try dry skin brushing, sauna, hot water with lemon first thing in the morning, and drink plenty of water! Dehydration is a main cause of constipation (along with too many methanogens).

The most important part of the whole shebang is the leaky gut healing phase which comes after you’ve successfully killed off the IMO. How long you’ll need to do the protocols depends on how severe the overgrowth, but you must follow up treatment with leaky gut repair to heal and seal the gut. Here’s my post on how to heal leaky gut. Expect the process to take about six months in all on average (and this is a conservative estimate).

A low FODMAP diet may help relieve your bloating, but studies have shown it doesn’t effectively decrease the methanogen levels.


IMO can occur in the small or large intestine (or both) and is caused by poor diet, poor gut motility, antibiotic use, PPIs, general dysbiosis, or even food poisoning. You can use a lower FODMAP diet to relieve bloating while you use anti-microbial herbs to kill the excess methanogens. IMO is frustrating to treat and can take a while. so I recommend seeking the help of an experienced practitioner to help you navigate the process to ensure success.

Have you successfully overcome IMO? Leave me a comment below!

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I work with many IMO and SIBO cases. Sadly, many of these cases are people who’ve been to several different doctors and are still struggling. Apply to work with me here if you’d like help once and for all.  

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