SIBO: Methane Dominant Treatment Plan

klebsiella bacterial overgrowth treatments natural treatments byron bay naturopath herbal medicine

Methane dominant SIBO, also known as methane SIBO or constipation SIBO, is a form of small intestinal bacterial overgrowth. The predominant microbe, called Methanobrevibacter smithii, is an archaeon which can convert hydrogen into methane, resulting in slowed intestinal transit. 

The most common symptoms of methane SIBO are constipation and bloating. Read on to learn what methane dominant SIBO is, what causes it, how to test for it and natural treatment options including probiotics for methane SIBO, prebiotics for methane SIBO and finally herbal medicine for methane SIBO.

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What is SIBO anyway?

SIBO is an overgrowth of bacteria in the small intestine. The cut off varies from paper to paper but it falls around 105
colony forming units (bacterial cells) per milliliter (
1). The small intestine, while not technically sterile, has far fewer bacteria than the large intestine.

So, a quick summary of SIBO

  • SIBO is a bacterial overgrowth in the small intestine
  • It can be caused by low stomach acid, poor gut motility or be a consequence of an gut infection
  • Symptoms may include abdominal pain, loose stools (diarrhea), constipation, food allergies, headaches and brain fog and the big one bloating and distention

Methane dominant SIBO – an overview

There are two primary types of SIBO and they very much depend on what types of bacteria (or Archaea) have managed to take up residence in your small intestine.

In the case of methane dominant SIBO we are starting to narrow in on the specific bugs that are fermenting and actually producing the methane that we can read in a SIBO breath test (more on that below).

Now, I can hear you thinking ‘why is this important? I know I have SIBO, why does the type of SIBO matter?’ Bear with me, it will make sense shortly.

Researchers and SIBO experts have been trying to get to the bottom of what bug is causing the methane for awhile now. Currently we have narrowed it down to a number of methanogens, primarily Methanobrevibacter smithii (1).

Methanobrevibacter smithii seems to be the main bug
responsible for the methane production

Don’t take this as me saying that your methane dominant SIBO is caused by only one bug. It is a tiny bit more complicated (as SIBO generally is). Methanogens, producing the methane contributing to your SIBO symptoms, actually need hydrogen to grow and thrive. They actually use the by product of other bacterial (hydrogen) as energy (2).

Too much information? Maybe. But the headline of this little biochemistry story is that even though you might have all the signs and symptoms of methane dominant SIBO, you probably have hydrogen dominant SIBO lurking underneath.

But don’t worry the natural SIBO plan tackles both of these subtypes of SIBO in one go.

Below is a table comparing methane positive breath tests (using lactulose or glucose) with a range of symptoms associated with IBS-C (irritable bowel syndrome constipation type).

The association between IBS and SIBO is complicated and varies depending on what breath test you use and the cut off values that are used to define SIBO. Remember me mentioning the controversies with SIBO testing? This is just a taste of it!

Ok. Now let’s talk methane dominant SIBO symptoms.

Methane dominant SIBO Symptoms

SIBO symptoms can range from loose stool (aka diarrhoea) to constipation. There is frequently symptoms of bloating and distention and possible abdominal pain. We can use your specific symptoms to make some educated guesses.

For example, methane dominant SIBO has one very specific symptom that generally (although not always) sets it apart from hydrogen dominant SIBO. That particular symptom is constipation (3).

…the production of methane causes constipation by reducing peristalsis.

Other symptoms include the following (4).

  • Fatigue
  • Bloating
  • Abdominal pain
  • Weakness
  • Malabsorption (seen as suboptimal vitamin and mineral status)

Testing For methane dominant SIBO

There is some controversy around SIBO testing. This is an article I am working on now and will be a part of the ongoing SIBO series. So moving on from the controversies you and your gut health practitioner need to make a decision. Here are the options that I have come to.

  1. Treat empirically and see if you improve. This is the cheapest option. The only downside is that we may have missed the root cause of you gut health issues. Maybe it isn’t SIBO but is actually diverticulitis. Without a baseline test it is impossible to know exactly what we are working with and whether we have successfully treated it.
  2. Pick one of the two popular sugars (glucose or lactulose) and order a SIBO breath test. Here we are working within the constraints of a single sugar breath test. Glucose is more accurate but isn’t as sensitive (meaning it has more false negatives) whereas lactulose is more sensitive but less accurate (meaning it has more false positives). All things that need to be considered. For a deeper dive on breath testing check our Complete Guide to SIBO
  3. The final option may be best reserved for people that have been unwell for a very long time. Running two seperate SIBO breath tests with different sugars side by side is helpful to make sure you don’t miss SIBO. If you really want to go all in then has a third sugar that you can run. Fructose isn’t quite as well researched  but does give you yet another baseline to work off of. It will also let you know if you are malabsorbing fructose which is a common side effect of SIBO and can really contribute to the bloating and distention commonly seen.

A SIBO breath test (image above) showing no SIBO present (on the left) and hydrogen dominant SIBO (on the right)

A SIBO breath test (image above) showing methane dominant SIBO (the methane is the top line).

Natural Treatments for Methane dominant SIBO

There are a handful of treatment aims that will help get someone struggling with methane dominant SIBO back on track and healthy.

Normalise bowel patterns (aka make you poop more)

We want to normalise your bowel patterns. Basically this means we want to improve the consistency and number of number 2’s you are doing each week. The people struggling with high methane dominant SIBO may only be have 2 or 3 bowel movements each week. This can case a whole range of unpleasant side effects as they will be reabsorbing all of the toxins that the body is trying to eliminate.

The best way to improve the number of bowel movements you are having is to provide the body with what are known as ‘bulking laxatives’. These can take the form of fiber (if you tolerate it) including

  • Ground flaxseed
  • Psyllium husks
  • Chia seeds

If these don’t increase your regularity then herbal medicines used for constipation can come to your rescue. Here we want to start low and slow using gentle herbs that help to improve movement through the bowel.

Bitter herbs like dandelion, gentian and even wormwood can improve your digestion. As a happy side effect this can improve constipation. If this still hasn’t improved the constipation picture then some stronger bowel stimulating herbs known as anthraquinone herbal laxatives can be used. These herbs are strong and there can be some issues taking them long term. Here you definitely want to be working with a trained herbalist (that’s why we make the best gut health practitioners).

Improve intestinal motility and gut transit time

One of the root causes of methane SIBO, and a reason why there is such a high relapse rate, is poor gut motility. The small intestine has a complex and elegant way to keep things moving and prevent stagnation (which leads to bacterial overgrowth aka SIBO). When you haven’t eaten for 3-5 hours a process called the migrating motor complex takes over and sweeps through your intestines. During this process you may hear gurgling noises. There are a number of things that can stop the migrating motor complex process from delayed gastric emptying (your stomach actually holds onto food too long) to infections and even liver damage (6).

I have found one of the best ways to improve gut motility, reduce constipation and just get everything flowing again is a prebiotic known as partially hydrolysed guar gum. This particular prebiotic seems to be well tolerated in most patients with SIBO. Remember start slow and gradually build up to a therapeutic dosage.

Sources for partially hydrolysed guar gum include Ariya here in Australia and Healthy Origins Sunfiber in the States.

Please be sure it is the partially hydrolysed variety. Guar gum on it’s own won’t work to improve methane SIBO symptoms.

Here in Australia a brand called Ariya makes a good partially hydrolysed guar gum.

There are a number of ways to help improve gut motility and the sweeping effects that keep bacterial overgrowth (either the hydrogen SIBO or methane SIBO) from taking up residence (overgrowing) in the small intestine.

By far the best way to improve gut motility over the long run is to limit your meal windows to every 5 hours. Basically this means you’ll need to avoid snacking. Period.

If you can’t make it 5 hours without snacking then it probably means that you didn’t eat enough during your meal window. Or, it could simply mean that you are actually thirsty. You can learn to adapt to a fasted state but if you struggle with blood sugar swings then take it slowly. Clean up your diet, eliminate foods high in sugar and refined carbs and ease yourself into the ‘no snacking mode’.

Probiotics for methane SIBO

There are a number of different probiotics that have shown good success when treating constipation SIBO. One probiotic, Bifidobacterium lactis HN019 can speed up gut transit time and reduce straining and constipation.

Another probiotic, Lactobacillus reuteri DSM 17938, has been shown to reduce methane production and increase bowel movements in people with constipation and high methane production on a breath test.

How to Reduce methane dominant overgrowth in the small intestine

This is a key point to the whole process also called the methane SIBO treatments phase. Some people have had success improving their symptoms using diet alone.

Low FODMAP diets can cut out many of the fermentable materials that the bacteria use to produce the hydrogen…that the methanogen bugs then use to produce their methane…that then causes your constipation (ahhh it’s a mess isn’t it!?). Some practitioners even turn to elemental diets to starve the bacteria out.

As a herbalist I prefer to start with herbal antimicrobials, especially ones that won’t knock your beneficial gut flora around too much.

Cinnamon is a favourite but the herbalist’s materia medica is full of targeted herbal antimicrobial plants.

Other herbs include oregano leaf (the oil is far too strong in my experience and can negatively impact the beneficial microbiota) and fresh garlic.

cinnamon is a great herbal medicine to treat methane SIBO constipation SIBO methane dominant SIBO natural treatment options
Cinnamon is a good herbal medicine to reduce methane SIBO overgrowths

Berberine containing herbs are often the first choice for many naturopaths and functional medicine practitioners. While berberine can help to knock back bacterial overgrowths and has a role to play in parasite infections (think giardia and entamoeba histolytica) it may have a negative long term impact on the beneficial gut flora.

Improve your gut microbiome and minimise bacterial overgrowths

This last treatment aim can be layered over your SIBO treatment approach or it can come in after you are feeling better and you SIBO symptoms have been eliminated.

Here we want to improve your gut flora (keeping pesky bacterial overgrowths in the rearview mirror) reduce inflammation, keep your gut motility firing and heal and seal your gut. This process can be complicated and depends on where you are at and how long you have been unwell.

There are handy little equations (it takes 3 months to heal if you have been unwell for a year) but I don’t think that holds much water. This is the true value of natural medicine. It takes you as a person, with individual needs, into account and doesn’t try to fit you into a protocol or an equation.

There is no one size fits all when you are approaching methane dominant SIBO (or any other gut health issue) but we can take these broad treatment aims and tailor them to you specifically.

If you are looking for support in your natural treatment of methane SIBO then head over to our appointments page and book a time that works for you. Remember I consult with patients locally and online too.

If you have had any experience with SIBO or any other gut health issue then be sure to leave a comment in the section below!   

Article References and Resources

  1. Small intestinal bacterial overgrowth syndrome
  2. Methanogens, Methane and Gastrointestinal Motility
  3. The importance of methane breath testing: a review
  4. Small Intestinal Bacterial Overgrowth: A Comprehensive Review
  5. Small intestinal bacterial overgrowth recurrence after antibiotic therapy.
  6. Small Intestinal Bacterial Overgrowth: A Comprehensive Review 
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  1. The graph that you show for your methane dominant SIBO has an enormous level of baseline methane. It looks like this is a high colonic methane rather than a methane SIBO? At minimum the person did not follow the test prep diet, so there was a lot of fermentation happening in the colon that made the baseline methane very high.

    This might still be a big problem, but it is not SIBO methane….

    1. Well spotted P One.

      The graph with elevated methane levels may very well be a bloom of methane producing microbes in the large bowel. That’s why it is so important to combine the SIBO breath testing with a snapshot of the large bowel microbiome (DNA based stool testing like Ubiome helps as does MICROBA here in Australia).

      As the graph shows a rise in methane of 12ppm in the first 90 minutes it would still classically be diagnosed by methane dominant SIBO but I would be suspicious too.

      Thanks for the insight!


  2. What does someone eat who is
    1. Type 1 Diabetic
    2. Has MCAD (almost every food gives me a minor reaction, some major)
    3. Has Methane-dominant SIBO with acid reflux and heartburn
    4. Intestinal Permeability
    5. Vegan (and won’t compromise on this)

    High carb food is a no (diabetes), food high in histamine is a no (MCAD), and obviously foods that trigger Methane production are a no. Foods that are low in histamine (Apples for example), are a no on the low fodmap, and it makes starting a protocol for healing almost impossible.

    1. Hey Vic, thanks for taking the time to leave a comment!

      This would be a case by case answer as it is more complex than most. My hunch would be to start targeting the methane dominant SIBO immediately which in theory would help with your leaky gut and histamine reactions. As for diet I would explore the safe carbs (more on the whole foods side) while monitoring blood sugar regulation and FODMAP sensitivity (was the breath test glucose based or lactulose for the sugar?).

      It would very much be a process but I would expect everything to start improving with successful treatment of the SIBO.

      Acid reflux, heartburn or GERD (GORD here in Australia) symptoms can be managed during treatment with demulcent herbs in powder form, but that would depend on what you tolerate. Slippery elm or marshmallow root are key herbs here but they can sometimes flare a SIBO picture so again taking it slowly is important.

      Let me know if that helped at all.


  3. Hey Todd,
    I have had high methane dominant sibo for a few years as well as blastocystis. My symptoms are awful – 1 bowel movement per week, exhaustion, eczema, dehydration, low vitamins (Even though I supplement with high quality). I have tried 4-6 months of antimicrobials and it didn’t reduce the sibo, blasto or my symptoms. I think I have a sensitivity to salicylates. I feel like I’m sensitive/reactive to basically everything. I have a very clean diet.

    What do you think about an elemental diet for SIBO? My system feels terribly weak (made weaker from the antimicrobials, I think). I don’t know how to rebuild, or whether I should treat the blasto as well. Thank you in advance!

    1. Hi there Sas.

      Thanks for taking the time to share your experience. I would recommend looking into ways to improve your elimination (bowel movements) before going after the methane producing bugs with antimicrobials. It is best to be having a bowel motion once per day as a minimum as the symptoms you are describing could very well be from the reabsorption issues (due to the constipation).

      I have only come across the elemental diet in the literature. Here in Australia we don’t have good access to this as an intervention (the product isn’t available as far as I am aware). Have you come across partially hydrolysed guar gum in your readings? It is incredibly effective at increasing gut transit time and improving bowel movements. It’s a real life saver for many people with methane dominant SIBO!


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