What if your constipation was down to microbes in your gut making your digestion slow down? If you’ve struggled with constipation for a long time, you may have Intestinal Methanogen Overgrowth.

What is Intestinal Methanogen Overgrowth (IMO)?

Living in your digestive tract you have trillions of microbes. They help us digest our food, create hormones and neurotransmitters and support our immune health.

When these microbes eat sugars and fibres from your diet, they create gas as a by-product. The gasses include methane, but also other gasses like hydrogen, and hydrogen sulphide. Methanogens is the name for microbes that produce methane.

Geeky section on terminology (optional, you can skip ahead)

Methanogens are actually archaea, not bacteria. 

IMO used to be included in the condition Small Intestine Bacterial Overgrowth or SIBO. Differentiating it by the term IMO helps us be more specific about is going on in your gut. Firstly, the methanogens are not a ‘bacterial’ overgrowth, they are archaea. Also, they can overgrow in the large intestine as well as the small intestine, so Small Intestine, and Bacterial overgrowth isn’t always accurate.  

The methanogenic archaea use hydrogen to make methane. People with SIBO often have high levels of hydrogen, because hydrogen can be produced by bacteria growing in the small intestine.

If you have an overgrowth of bacteria which produce a lot of hydrogen, then you could end up with an overgrowth of methane making microbes.

In fact it takes 4 units of hydrogen to make 1 unit of methane. So when there is a lot of excess hydrogen available, microbes that use it up as a substrate could flourish. 

woman in nightdress bent double on toilet, head resting on her arm

Symptoms of Intestinal Methanogen Overgrowth

The key signs you might have an overgrowth of methanogens are

  • Constipation and slow transit time
  • Bloating
  • Nausea
  • Excessive gas
  • Possibly struggling to lose weight.

The more methanogens you have, the worse the constipation is thought to be. This is different to hydrogen SIBO, where the level of hydrogen doesn’t always match with the severity of your symptoms.

How does methane affect constipation?

There are lots of studies that show if you have methane in the gut it takes longer for food to move through your digestive tract.

The time taken to digest and then eliminate our food could even double. One study found that the total gut transit time for people who have low methane was 48 hours, but for people with high methane in the gut, it took over 84 hours!

We also know that high methane production in the small intestines can lead to a 59% increase in transit time.

The more methane someone produces the more severe their slow gut transit time will be.

How can IMO start?

There are several ways you can get an overgrowth of microbes in the small intestine including

  • damage to the Migrating Motor complex – this is an automatic nerve action that sweeps away debris, dead cells and bacteria from the intestines. When it’s slow or damaged microbes can overgrow. If you want to read more about the MMC and how it works I have written about it – 
    What is the Migrating Motor Complex & how to fix it
  • blockages and slow transit time due to adhesions – slow passage of food and lack of cleaning can lead to overgrowths
  • low stomach acid – when we don’t have enough stomach acid we are more exposed to infections
  • chronic stress – slows down digestive juices and motility of the gut

You might like to read my post if you’re interested in possible causes of SIBO – it’s called Four Risk Factors for SIBO

Testing for intestinal methanogen overgrowth

A diagnosis of IMO depends on your symptoms, as well as a test result.

There are two ways you can find out whether you have an overgrowth of methane producing archaea; a breath test or a stool test.

SIBO breath test to measure the amount of methanogens in the small intestine

To measure if you have intestinal methanogen overgrowth you can try a breath test which measures how much methane is in your breath. If you have high levels of methane in your gut, some of it will cross into your blood stream, and travel to the lungs to be exhaled. In normal conditions humans shouldn’t have high levels of methane in our breath, so the breath test shows that there are microbes in the gut producing this gas.  

In order to run the SIBO breath test you will follow a 12 hour restrictive diet with no fermentable carbs (only eating fish, meat, white bread or white rice) followed by 12 hours of fasting. At the start of the test you’ll drink a solution containing lactulose which is a sugar we can’t digest, so it travels through the gut. 

If you have methanogens in the small intestine you will see an increase in gas as the microbes start to ferment the sugars. 

  • If your lactulose breath test shows a rise of 10ppm (parts per million) of methane within the first 3 hours this would be considered positive for SIBO
  • high levels of methane at the start of your test could indicate you have an overgrowth of methanogens in the large intestine. (We can tell this because the sugar solution wouldn’t have travelled through to the small intestine straight away).

If you’re taking a PPI, such as Omeprazole or Lansoprazole, it may lower the levels of methane on a breath test.

Stool test to measure the amount of methanogens (and other microbes) in the large intestine.

Although a stool test isn’t diagnostic for SIBO, it will show the levels of methanogens in your large intestine. The main one is Methaninobrevibacter smithii.

Specific bacteria which produce a lot of methane are:

  • Bacteroides thetaiotaomicron,
  • Clostridium perfringens and Clostridium histolyticum
white woman torso with hands holding stomach for constipation

Is an overgrowth of methanogens always bad?

Some people will have high levels of methane producing microbes and have no issues with their digestion at all. 

Methane is found in the gut of around 30-50% of adults. Not all these people will have constipation, nausea or bloating. This means we can’t always blame methanogens for these symptoms.

As an aside, babies don’t normally have methanogens in the first few years, but by age 3 they will present in many children, in line with adult levels.

How to treat IMO

If you have a methane positive breath test your practitioner should give you some guidance on a personalised diet and supplements.

When I’m working with clients as part of the 3 month Gut Reset programme, some things I might consider for a client with intestinal methanogen overgrowth are:

  • reducing the methanogens and hydrogen producing bacteria with antimicrobial herbs such as oregano, garlic, berberine or others.
  • referral to a gastroenterologist to access antibiotics such as Rifaximin, Metronidazole or Neomycin.
  • Probiotics to increase the healthy friendly bacteria in the large intestine. In particular Bifidobacterium lactic HN019 is a strain of probiotic that has been shown to reduce transit time in constipation. Lactobacillus reuteri has also been shown to reduce methane production in the gut.
  • Prebiotics – where they are tolerated, I may use PHGG or GOS. To read more about prebiotics and IBS I’ve written an article here.
  • Stress management – there is a big connection between the brain and the gut. Working on our anxiety levels and emotions can help with slow transit time.
  • personalised diet recommendations to get the fibre levels right to keep the gut moving.
  • Laxatives – to keep the bowels moving. Magnesium can be helpful here, or over the counter laxatives from your pharmacist.
  • Pro-kinetics – these keep the gut motility moving. Herbs include ginger or artichoke. You can read more about prokinetics in SIBO.

Can I get rid of intestinal methanogen overgrowth naturally? 

A natural approach to reducing an overgrowth of methane producing bugs could include herbs, diet, as well as tackling your root causes.

Your first reaction to a methanogen overgrowth maybe to want to kill off the methanogens, but we can also look at how to crowd them out using probiotics and prebiotics to encourage the beneficial bacteria to grow. 

Antimicrobial herbs for IMO

Some natural antimicrobial herbs have been shown to reduce methane gasses when tested in animals, but we are lacking strong human studies with evidence. However, from clinical experience, and other practitioners working in the field we know some herbs are linked to improvement in symptoms. 

These include:

  • Garlic extract – Garlic oil has been used to reduce methanogens in vitro (i.e. in tests outside the body) using cow intestines. We use allicin, the active antibacterial extract so there is no FODMAP reaction that you might get with eating garlic. Allicin also tends not to smell on your breath like a garlic capsule might. 
  • Oregano oil – the active componant of oregano oil, carvacrol, can be used as an anti-fungal treatment, and is effective against methanogens.
  • Neem – often used in protocols to reduce hydrogen producing bacteria, neem could potentially lower methane production as well (tests in sheep showed a high dose of neem decreased methane production).

 Probiotics for high methane gas (IMO)

 If there is a lack of beneficial bacteria in the large intestine, you might find it helpful to add probiotics as a supplement to the rest of your intestinal methanogen overgrowth treatment. 



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    What causes intestinal methanogen overgrowth?

    There are many, often additive, causes of IMO. These can include chronic constipation due to undereating, or a low fibre diet. Also, issues with the Migrating Motor complex, low stomach acid or bile, obstructions in the intestines, or adhesions which slow down the passage of food.

    My blog post goes deeper on risk factors for Small Intestine bacterial overgrowth (SIBO)

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    What is the treatment for IMO?

    The first step in treating IMO is normally getting your bowel opening once a day. Allowing a comfortable passage of food through your gut helps to reduce bloating, and gas caused by blockages. This may need laxatives, fibre, physical therapy, more movement or a combination of these approaches.

    Getting rid of high methane gas production depends on the cause of your intestinal methanogen overgrowth. For example, if your slow transit time and constipation was caused by undereating, or a low fibre diet then we need to look at long term diet strategies. If your IMO was caused by an adhesion or structural blockage a diet change may not make that much difference.

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    Do natural treatments for intestinal methanogen overgrowth work?

    Yes, I’ve seen great improvement in symptoms with a holistic treatment plan for IMO. Taking a medical route can be quicker, but many people feel they want to avoid medication and prefer a combination of supplements, diet and lifestyle changes.

    However, it really does need to be an integrated approach including diet, supplements, rebuilding gut health through fibre, prebiotics and probiotics, as well as improving the gut-brain connection, including suitable exercise and stress management.

Constipation can be difficult to treat because everyone has different symptoms and triggers, but the more information we have about your condition the better. This is why testing can sometimes help. 

If you need help with your digestion please get in touch with me on email – info@goodnessme-nutrition.com or via the Contact page. 

IBS Nutritionist

Hi, I'm Anna Mapson, registered Nutritional Therapist.

I help people with IBS and SIBO get control of unpredictable gut symptoms to find long term relief from painful and embarrassing IBS without restrictive dieting.

I can help you to:

  • understand your digestion better, so you recognise your triggers
  • eat a well balanced diet, with tasty meals that are simple to prepare
  • reintroduce your trigger foods so you can get back to enjoying food again

Find more about my 3 month 1:1 Gut Reset programme. 

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