How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (2023)

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 inSIBO 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!

How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (3)

Mary Vance, NC

Mary Vance is a Certified Nutrition Consultant and author specializing in digestive health. She combines a science-based approach with natural therapies to rebalance the body. In addition to her 1:1 coaching, she offers courses to help you heal your gut and improve your health. Mary lives in San Francisco and Lake Tahoe in Northern California. Read more about her coaching practice here and her background here.

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  1. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (6)

    Jeff K on 9 August, 2021 at 7:48 am

    I was diagnosed in July 19 with Hydrogen SIBO, and treated myself for that over the next 2 years with three months of antimicrobials and then 14 days of Rifaximin, followed by months of Low Fodmap and then Low Fodmap/SCD diets but never cured.
    I changed to a holistic doctor in June 2021 and took a new breath test which showed me positive for methane IMO!
    I contacted the gastroenterologist who diagnosed me with Hydrogen SIBO in 2019 and asked for a copy of the results, when they arrived it showed that I had methane(IMO) not Hydrogen back in 2019 and she had read the report incorrectly!!
    Six weeks ago I did a 21 day Elemental Diet, and all my symptoms stopped.
    I then proceeded on my own and started an antimicrobial plan.
    I chose to do 8 days of Allicin, Atrantil, rested for 4 days and then started Oregano, Berberine, Neem and Interfase Plus.
    I intend to continue to rotate all the antimicrobials that I had researched and purchased until they are all used up over the next few weeks.
    I did the GAPS introduction of bone broths for the first 8 days after the ED, and since then I have slowly reintroduced the low Fodmap/SCD diet.
    I understand it is very early days, but so far I have had no adverse reactions or previous symptoms.
    I am pinning a lot of hope and faith on the 85% success rate of the ED, but I am amazed that of all the top SIBO blogs/websites, so many of the authors promote ED but almost none have done it personally, including Allison Siebecker?

  2. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (7)

    Mary Vance, NC on 9 August, 2021 at 5:03 pm

    Hi Jeff, I’m not sure what your question is, but the Elemental Diet is not a first line therapy for SIBO, so most experienced SIBO practitioners don’t mention it as part of classic SIBO treatment. It is most often used for chronic cases with high gas levels as it does reduce gas levels pretty significantly. Really most important point to note is the ED does not address the underlying cause of SIBO, and that is the key to eradicating it. The biggest mistake in SIBO treatment is skipping the gut healing part of the process which should always include a pro-kinetic and determining your root cause so you can fix that. Always work with a practitioner on this, as SIBO can be very difficult to navigate on your own. Here’s more:

  3. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (8)

    Martin on 24 August, 2022 at 11:26 am

    Hi, Is it possible to have IMO, but not with constipation, but with diarrhea? Got the diagnosis IBS-D, but a sibo test shows IMO. And what is than a possible treatment?

  4. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (9)

    Mary Vance, NC on 24 August, 2022 at 2:30 pm

    Martin, it is possible to have IMO with diarrhea, yes. You should also do a stool test to assess large intestine microbiome. I outlined the treatment for IMO in this post, but I recommend working with a practitioner to help you. There are certain adjustments for chronic diarrhea.

  5. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (10)

    Rashaan on 29 August, 2022 at 2:41 pm

    Hello, I was diagnosed with IMO in 2019. I’ve done 1 round of Neomycin and Xifaxan, 2 rounds of just Xifaxan and 14 days of ED and my IMO is still here. I’m getting really frustrated, any advice?

  6. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (11)

    Mary Vance, NC on 29 August, 2022 at 6:33 pm

    Rashaan, the followup treatment to the antibiotics (or herbs) is the most important part of the process, or the IMO/SIBO will almost certainly recur. You need a doctor or nutritionist to walk you through the proper phases of the treatment and the pro-kinetic/gut healing phase for best results. If your IMO is small intestine, you might also consider a large intestine stool test if you haven’t done that to get a better picture of how your large intestine microbiome is affecting things.

  7. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (12)

    Marie on 22 September, 2022 at 8:27 am

    Hi Mary. I was diagnosed with IMO, but am hesitant to use neomycin (as prescribed to me), due to the risks to the kidneys and hearing. My doctor said she could check my kidney function twice weekly, but I’ve heard that hearing loss usually doesn’t come until after the regimen is stopped, and is often not reversible (except partially, through hearing aids). I would hate to never hear my kids’ laughs and friends’ conversations. How often do you see damage from a two-week course of neomycin occurring?

  8. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (13)

    Mary Vance, NC on 23 September, 2022 at 4:57 pm

    Hi Marie, i’m not a prescribing practitioner, but in the many people with whom i’ve worked who have taken neomycin, no one had any bad side effects. That said, a few did elect not to take it due to that side effect. Still, hearing loss is considered a rare side effect.

  9. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (14)

    Dave Case on 8 October, 2022 at 9:12 am

    I have IMO and had two rounds of Xifaxin and Neomycin. I know everyone is different, but I had no side effects with Xifaxan and Neomycin. I took probiotics the first time but didn’t change my diet. This time (I’m three weeks in) I’m taking probiotics twice a day and am trying the Low FODMAP diet. I also started digestive enzymes yesterday. I read where the FODMAP diet should be personalized but what does that mean? I’m pretty much non-gluten, lactose and sugar. My brain fog and fatigue has lessened recently so I don’t want to make changes but I still have bloating and gas after eating. I didn’t experience that the first time so maybe that is part of the die-off process? Also, I read where the FODMAP diet is for SIBO but needs adjusted for IMO. Your thoughts?

  10. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (15)

    Mary Vance, NC on 11 October, 2022 at 11:40 am

    Hi David, the detail of your questions indicates you need support from someone well versed in working with IMO. Everyone’s diet & protocol looks slightly different based on their health history and any other issues going on. This post may help:

  11. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (16)

    Mitchell Yawn on 20 October, 2022 at 9:29 pm

    Hi there. I’ve been dealing with issues for almost three years. I’ve gotten to a point where getting in my vehicle to work is not possible because the gas and bloating is so severe that I get heart palpitations and begin to sweat. I’ve had every test that the VA has to offer and am currently on Metronidazole for SIBO. I am following Low FODMAP as well and taking a Probiotic each day with 4,000 billion. I loved the article as it is giving me something to look at. Any other suggestions would be greatly appreciated. Losing hope and don’t want to lose my job because I can’t drive due to gas build up causing the above issues.

  12. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (17)

    Joe Sikkema on 25 October, 2022 at 11:36 am

    I have methane SIBO. I own a Outpatient Physical Therapy practice and it is quite frustrating dealing with this. Is it possible to email me the protocol? I have tried everything to no avail. Rifaxamin and Neomycin x 2, diet changes etc…No benefit. With no data supporting the methanogens NOT being a bacteria does that change the protocol? I was going to try the following: 1, Rifaxamin Neomycin x 2 weeks. Elemental Diet x 2 weeks. Natural antimicrobials and a biome disruptor x 2 weeks. But, I am not confident that this will kill the methanogens. Any help-would be greatly appreciated.

  13. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (18)

    Mary Vance, NC on 27 October, 2022 at 3:47 pm

    Hi Joe, aside from what is in the post, I would recommend working with a skilled practitioner for help. Protocols differ based on the person and their unique health history, and it is very difficult to navigate IMO alone. This post contains general information.

  14. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (19)

    Oliver D on 29 October, 2022 at 9:41 pm

    Hi Mary. Thanks for this article.

    I have IBS-D and IMO. I’m taking probiotics with L Reuteri and S Boulardii daily. Will targeted probiotics cure me? How long does it take for your microbiome to cure itself? I’m estimating 2-4 years, but I have no idea.


  15. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (20)

    Oliver D on 29 October, 2022 at 10:13 pm

    Hi Mary.

    In a comment to Martin about IMO and IBS-D, you mention adjustments in the herbal protocol to combat chronic diarrhoea. What are they?

    Thank you and all the best,

  16. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (21)

    Mary Vance, NC on 31 October, 2022 at 1:20 pm

    Hi Oliver: no, probiotics will not get rid of SIBO. and it can take months to restore gut balance, but how long depends on the person.

  17. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (22)

    Lauren on 9 February, 2023 at 7:45 am

    Are there any basic guidelines for the best diet for methane sibo? I’m just really confused which one is best if it’s low fodmap or specific carbohydrate diet. Right now I’m gluten and dairy free taking lots of antimicrobials that my naturopath recommended but I’m really struggling with my diet. I read your other article about what diet is best but I am still confused about the best diet for IMO.

  18. How to Treat Intestinal Methanogen Overgrowth (IMO) - Mary Vance, NC (23)

    Mary Vance, NC on 20 February, 2023 at 9:46 pm

    Hi Lauren, the diet guidelines are somewhat different based on the person, but here is an overview:

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