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.

byron herbalist todd mansfield gut health specialist

Need help with your digestion?

Hi, my name is Todd Mansfield. I am a clinical herbalist with a special interest in all things gut health.

If you are looking for digestive health support consider working with me. I see people online as well as in person from my clinic in Byron Bay.

More booking information here.

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 have read this far and tried many of the options above with little success be sure to check out my advanced methane treatment guide or if you live in Australia or New Zealand consider working with me here at Byron Herbalist.

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!


  4. My symptoms are bloating, excessive burping and chronic gastric pains after eating meat or veggies. I use to eat and go to bathroom within the hour after every meal. Then October 19, 2019, I suddenly couldn’t eat crying due to gastric bloating and gas within 10 minutes of consuming food. The concerning thing was I cannot pass gas I must burp and and burp for a 1/2 hour or more because of continuous build up of gas, sweating and fatigue these episodes was lasting over an hour. I don’t know what will set it off. I did the process of elimination to determine what sets the bloating and gas build up and it is anything. I can drink any liquid but protein drinks. Matter of fact I hardly eat at all. I had several test, cat scan, upper and lower GI and endoscopy. No INS, H pylori, no Crohns; stomach looks great. I had Roux-en-Y bypass about 8 years ago. Since I am basically in a fasted state I was wondering does fasting starve off bad bacteria.
    Pre/probiotics make me bloat and have gas pains. I am 3days away from completing my second round of xifaxan but this round I am using hydrolized guar gum. I also take HCL with Pepsin to help with digest proteins with some help. But again I rather fast and starve the bacteria overgrowth since I am already in the process.

  5. Hi I am unsure whether I have SIBO Methane dominated. Since January 2020.
    I have Severe bloating which is now nearly continuous, was intermittent at the start.
    I can look 7 months pregnant. Sometimes abdomen is hard as a rock. I look awful to say the least. I have no pain. No cramps or rarely. The last five days I have monitored I am emptying my bowels once a day.
    I have had ultrasounds, no fluid or ovarian cancer, blood test no celiac disease, stool test no parasites or bacteria, Breath test for Helibacter Pyori. SO researching my symptoms do sound like the SIBO but with the Methane. I have just engaged a gastroenterologist who says stay on Nexium but I believe my system is not digesting my food properly due to low acid so have started on Apple Cider Vinegar. That makes sense to me. Am I on the right track? thanks so much. Kind regards. JULIE .

  6. Hi Todd
    I have just found your website and thought it was very helpful regarding understanding what SIBO is all about. I have the methane variety and so wondered which diet specifically you would recommend – you mentioned FODMAPS but didn’t really seem to endorse it completely. Are there key foods to eat and not eat during the die-off phase? As I understand it, removing ALL fermentable foods it not the way to go with methane SIBO. I am currently on the SIBO 2 phase diet, but it is not specific for methane dominant SIBO. Any pointers would be very welcome ,thankyou.

    1. Hi Julie,

      From what you have described there may very well be a SIBO picture here. With the 60 minute consult and a full workup I would be more confident in recommending a SIBO breath test.

    2. Hi Barry, thanks for sharing your experience. I don’t believe that a low FODMAP diet will ‘cure’ SIBO and mainly use it to improve symptoms while directly treating SIBO.

      The number one approach for methane SIBO and LIBO is to move your bowels and increase gut transit time. Each patient reacts differently but the name of the game is to find the perfect balance of fibre and the ratios (soluble and insoluble) that keeps the bowels moving without causing the rebound constipation from the methane production.

      Hope that helps!


      1. Thanks Todd
        I am starting soon on Atrantil a natural product produced by Dr Ken Brown a gastroenterologist in USA
        My local gastroenterologist is virtually just prescribing one antibiotic and won’t give me breath test as says not accurate.
        The bloating is severe !!
        So fortunate so far as no pain.
        I made my own Kefir and drank it for years that may have contributed not sure. I’m no longer taking it just in case.
        While I await delivery of Atrantil I’m taking digestive enzymes and apple cider vinegar with meals.
        I was on Keto diet , but stopped that when overseas for 3 months.
        I totally believe that our gut is our second brain ! But mine is obviously unbalanced.
        I will make sure thanks to your advice to have the 5 hour gap between meals. I may restart strict Keto but think I overdid the meat and dairy !
        Thanks will let you know Re Atrantil if works.
        What is your opinion of antibiotics?
        I would rather not really take them .

  7. Hi! I’ve been struggling with Sibo for a number or years now and every test has come back as hydrogen dominant. However, all my systems are consistent with methane production. Have you ever seen this and any suggestions? I also do not seem to tolerate Berber one.

    1. Hi Dana, Yes I have seen this. The specific symptoms for SIBO subtypes do vary and aren’t set in stone. While berberine is a good approach there are many many other herbal antimicrobials that I use all the time. In fact I generally hold off on the berberine unless it is needed. I always use prebiotics and probiotics for my SIBO patients too!

    2. Hi, can you share a probiotic brand/ product that has reuteri DSM 17938? I only could find BioGaia and it doesn’t seem that great. Thanks!

  8. have done the breath test and have methane dominant silo Ihave severe weight loss also have candida IBS diverticular Got it by taking a broad spectrum antibiotic have been advised to take fibre and gumbi gumpbihave been assured this will cure silo and IBS Your thoughts?have been ill for five months

  9. Was on low food map for far t oo long and struggling to introduce high food maps in a bit of a mess worried about restoring my microbiome to good health

    1. Hi Hanni,

      The fibre will help to increase your gut transit time (a mainstay approach for methane SIBO). As long as it is tolerated I would take a similar approach. FODMAP restriction can be necessary for symptom control but transitioning off of it as soon as possible is ideal. Some need to stay on it longer than others.

  10. Hi Tod,
    My daughter has had issues for over 12mths now all starting with constipation Bloating, gas And weight gain she has seen Nautropath’s dieticians specialists And tried so many supplements had stool tests showing up high in Firmicutes and other inflammatory bacteria
    I have being convinced she has Methane SIBO as her symptoms seem to be accurate with that and have read methane producing SIBO can also be the reason for weight gain and the reason for not being able to loose weight
    Her diet is good and has plenty of exercise she has started having Qenda which defiantly improved bowel habits and also just started Atranil
    Her bloating and issue with weight is her main concern so any other suggestions would be great as it’s being a never ending cycle.
    Thank you

  11. When all the symptoms are pointing towards methane sibo like trapped gas, fatigue, constipation,reaction to fodmaps is doing breath tests still needed?

    I had h pylori for a long time which probably contributed to my sibo.Now having got rid of h pylori am still dealing with sibo c and hardly findind a diet that works even bi phasic diet has limited sucess as anything that doesnt digest well feed sibo and in morinings my stomach is very slugish to start working so it doesnt matter if it’s lowfodmaps or not.

    Am from a third worlds country so this testing and all is hardly doable with all the testing,retesting and high shipping costs which am unsure if it would reach the lab in time.

    Does pommgranate peel works well for both types of sibo or just the herbs you recommended .Thanks

  12. Do you ever recommend grape seed extract for SIBO. My symptoms indicate I have the Methane dominant type. A breath test is not an option for me, is there any other test you might recommend,i.e. blood work? My biggest issue is trying to gain weight. Thanks

  13. I have noticed that Todd has not responded since May, is there a problem that he is not available to answer comments? Thanks

    1. Hi Celilia,

      Sorry on the absence. My practice has been very busy recently and I didn’t have a spare moment to keep up with anything but client care. I have made more space in my week and will be here more frequently keeping up as best I can.



  14. Out of the blue, about 3 yrs. ago, I began exhibiting symptoms of bloating, distension, & abdominal discomfort intermittently. It was on a par with having over-indulged in a really large Thanksgiving dinner and feeling as though I was going to explode. Over time the symptoms began to increase and eventually became chronic. I also was experiencing excessive belching, some flatulence, and while I was not having diarrhea or constipation, as I have a regular BM every morning, my stool was a pale tannish color.

    I was given a multitude of tests by a gastroenterologist but nothing proved conclusive until I was given the ‘Breath Test.’ Results came back as positive for the methane strain of SIBO. A two-week regimen of Xifaxan was prescribed and had no affect whatsoever. By happenstance, a couple of months later I was prescribed Bactrim for a different issue but it worked wonders at relieving the pain & discomfort in my belly. The relief lasted about 2 1/2 mths., at which time Bactrim was prescribed again. Once again it relieved the discomfort for about 2 mths. A 3rd round was prescribed when the symptoms returned but had little affect, which I suppose means I am becoming immune to Bactrim. I am loathe to try any more antibiotics as I do NOT want to develop C. diff or anything worse. I would appreciate any input you may have as my Dr.s seem to be at a loss for further treatment, other than antibiotics.


  15. I have so many questions I do not know where to begin….I was born with Gastroschisis, have pcos, no gallbladder and now recently diagnosed with methane dominate Sibo. I am feeling very lost, overwhelmed, and confused by all the food choices I cannot have or what I have read I should not eat. I would love ANY help in this area!! Please

    1. Hi Jennifer,

      I have found that dietary restrictions can help with the symptoms of methane SIBO but doesn’t do much to treat the actual overgrowths. Here I use select herbs, prebiotics and probiotics too. Treating the symptom of constipation can help move the needle too if it present.



  16. I have never been officially diagnosed with SIBO by a doctor, but I did a microbiome test in January and again in June of this year, that resulted in diet and supplement recommendations that would suggest methane SIBO is present.
    My one main continual issue is excess gas production. I have a bowel movement every day, sometimes twice a day. My diet is very clean, almost vying on the side of restrictive since I’m follow the diet recommendations from the company who did the biome testing combine with the SCD diet. But I still can’t seem to overcome the excess gas production after I eat. Foods like apples and eggs are a few of the worst offenders, and I will be suffering from bloating and very smelly and excessive gas for hours after eating them, so they’re avoided all together. I took berberine for 12 weeks and noticed no difference. I used Atrantil for 4 months, but the reduction of gas comes right back without the Atrantil and I don’t think taking a supplement like this for my whole life is a good fix. I use Iberogast every day on an empty stomach once in the morning and right before bed to encourage small intestine motility. So I’m wondering if the PHGG would help to eliminate the constant struggle with gas production? Any thoughts?

    1. Hi Daisy, Thanks for the comment. PHGG is a mainstay in my treatment approach of methane production. You have to go low and slow and there appears to be some excess gas production while your microbiome adjusts to the extra soluble fibre. In the vast majority of people this tends to resolve after a month or two of supplementation. Best, Todd

    2. Hey Todd, how does treatment differ when IMO is not causing constipation (very high levels of methane)? I have tried multiple rounds of antibiotics and herbs such as berberine, neem, Allicin, oregano. Elemental diet didn’t improve things either. My stomach has been persistently bloated for 7 months with constant belching and a white tongue – a desperate 24 year old here!

  17. Hi Todd. I have Hashimoto’s hypothyroiditis and have been able to reduce my peroxidase antibody result from 425 in Jan 2020 to 287 today. I tested for and have Epstein Barr Virus that has become active (early antigens came in at 133). I have done a Mediator Release Test for food sensitivity and have eliminated those foods from my diet (wheat, dairy, soy, oranges and a bunch of other less reactive foods), and have been taking lomatium disectum to get at the EBV. My TSH has also fallen from 15 to 8, so I’m making progress. I have methane-dominant SIBO based on a glucose breath test. Reference methane at 35, went up to 41 in 20 minutes and then stayed elevated between 25 and 35 for the entire three hour test. I started on Oregano oil, Candibactin BR, and Allicillan. Does that make sense to you?

    1. Hi Timothy, Great work on the hashimoto’s numbers and your approach to the EBV treatment too. You seem to be in good hands. I frequently see methane levels that start high and stay steady throughout the test. I interpret these (cautiously) as elevated methane production in the large bowel which I recommend treating for most patients.

  18. Hi Todd,

    Just realized I do not have SIBO given the small increase from an elevated baseline. So, never mind…thanks.

  19. Hi Todd, very interseting site you have about SIBO! Don’t know if you can help me a litte bit further. First of all sorry for my bad Engelish – didn’t use it so much more lately. Since 2013 I’ve those IBS -D symptoms and I got this diagnose. It all started very acute ( maybe an infektion ) .Symptoms are: often loose stool /bloating/ distention. Test shows these ‘tings’: Blastocystis spp, Beta-defensine too high, secretoir IgA too low, too much fett in the stool. Took Precossa (=Saccharomyces boulardii) and Bactrim- effect: Blasocystis was still there. Took than Gabroral ( = Paromomycin) – effect: Blastocystis was gone! But it doens’t changed my symptoms. So followed LOwFodmap without any effekt, or minimal. Took a stool test ( Gut pathogen profile) and they found that Entrebacter Cloacea was too much, that, so they say: is Potential Pathogen. And a few weeks ago a SibO test ( Breath), which shows a level of methane which is too high, peak 60, and hydrogan very low (3). They say I’ve SiBO methane (but there’s little doubt if it is in the small or the large bowel- borderline). Is there a relation between high methan level and enterobacter cloacea? And as I’v read here on your site methane ‘bacteria’ ( Archae) needs hydrogen( as fuel), so that could explain the low level of hydrogen? Also, you say her above: “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.” – what does it mean in my case? Symptoms I’ve are the SiBo hydrogen ( loose stool) and not methane ( obstipation), anyway they found high level of methane. Litte bit confused now. Maybe I’v a hydrogen dominant sibo? What about treatment? I’m taking now Allicin from Garlic, and Neem, also following a diet ( but not that strictly )which is called : Fast Tact Diett ( by Norman Robillard- heard of it?). Effect is, right now, I’m getting more obstipated , still have som bloating. Took also three days one capsule of Oregano oil…after the third day my symptoms ( almost 10 times in one day loose stool) became very wrose in two days, so I’v quit with it. Hope you can get me some orentation……Kind regards form Norway.

    1. Went throught my history, and after reading you artikel about treatment of Blastocytis, and found that I took first Saccharomyces boulardii CNCM I-745 (Precosa) in july 2018, and Paromomycin (Gabbroral) in August 2018. At the end of September 2018 a stool test, and they didn’t find Blastocystis anymore. So, if it was a result of Precosa or/and Gabbroral, isn’t sure. Anyway, as said above, my symptoms are not gone…

      1. Hi Martin, Thanks for the comment. I often find this. People do all this work to eradicate blastocystis and when they finally do they only feel marginally better, if at all. The ecosystem balance is where I tend to focus trying to feed up beneficials while selectively reducing less friendly microbes with targeted herbs!

  20. Hi Todd!
    Thanks for the very interesting article! I did a test myself and had a very high methane baseline, despite having done the preparatory diet correctly… I read you wrote it can be due to methane producing bacteria in the large bowel rather than due to SIBO. But it there a way to treat it ? In what way is it different than trading SIBO ?
    I have been taking oregano and other herbal supplements for a few weeks but there doesn’t seem to be much improvement…
    Thanks a lot for everything you do 😉

    1. Hi Lea, my approach to methane in the large bowel is similar to the small bowel. Focus on increasing gut transit time, actively reduce the methane producing bug with targeted antimicrobials (high tannin herbs are great here) and normalise bowel movements. A few weeks is too short an intervention for most. I tend to see improvements at the 4-6 week mark which lets me know I am on the right treatment track. If no improvements have been seen there I will generally swap out the herbs! Best, Todd

    1. Hi Todd
      Would you mind sharing which high tannin herbs you use for methane SIBO? Would you start the PHGG at same time?

      1. high tannin herbs include cinnamon, green tea, pine bark and pomegranate husk. PHGG can be a bit of an art to weave into methane SIBO treatments but is very helpful if it doesn’t cause constipation. Hope that helps!

  21. Hi Todd, every food, supplement and medicine burns my gut. Gas rises up and burns my throat nose and eyes. All my mucus membranes are burning

    I haven’t had a normal bowel movement in two years Without a coffee and only twice a week.

    Microba testing showed high hydrogen sulphide producers. I have salicylate intolerance so I can’t use herbs. A yeast allergy which makes probiotic selection tricky. Phgg makes me itch. Can’t tolerate Protein and fat. Beans, grains, histamine, sulfites (so no lactulose). I’ve been gridlocked like this for 2 years. How do I find the door in pls when my body is rejecting everything? I can’t tell if the burning is something to do with my gut or MCAS. Either way the gut is the root cause. I now have malnutrition and can only eat Choko and white Rice without burning.

    1. Hi Sue,

      Thanks for sharing your experience. It sounds like your case is quite complex, particularly with the H2S producers and the gut damage associated with these bugs. I would start looking at the possibilities of an elemental diet to take the burden off of your digestive system. The more unwell patients are the longer it seems to take to be able to build them up enough to tolerate the herbal medicine that will make the difference.

      Hope that helps!



    2. I have very similar symptoms for the past 7 months. My entire GI system is inflamed. React to gluten, dairy, soy, histamine, oxalates, salicylates, all herbs, drugs and vitamins. Diagnosed with mild gastritis, but have severe GI problems (constipation). Microbiome testing shows elevated methane producers. Doctors will not test for SIBO via breath test in USA/NY. I have Xifaxin, but have not taken it yet since I am not clearly diagnosed with SIBO. It is very difficult to live like this (constant symptoms, fatigue, brain fog, constipation, diarrhea, food intolerance symptoms, MDs only want to run endsocopies and colonoscopies. I asked for the antibiotic. I’m afraid the colonoscopy prep will screw up my microbiome more than what it is now. Been to many doctors and naturopaths, but not much progress. Has Gut Zoomer testing (nothing pathogenic, but wrong balance of intestinal flora).
      Have elevated stool SIGA whatever that means?
      Anyway, you are not alone if that helps?

  22. Hi Todd ! As said before-very interesting to read here. Just one question: Is the treatment the same for Methane dominant with constipation , and Methane dominant with loose, and often, stool ( say : diarrhea )?

    1. Hello Todd Tks for yr reply. I can’t tolerate elementals. Was put on novalac allergy formula to deal with my histamine/salicylate intolerance. (I can only eat 3 foods) the formula is high sulphur and glucose syrup which appears to be high fructose corn syrup and therefore sulfites which I react to. I am now much worse and suspect my H2S Sibo has swung over to methane. Through my own experimentation I am now tolerating molybdenum and B2 to try to clear transulfation pathway. Have u ever treated anyone with herbs who is salicylate intolerant and wd tiny doses of artemisia be any benefit pls?

  23. I have methane sibo, but I have diarrhea. I don’t know how to heal myself. All articles about methane talk about constipation.

    1. This is an unusual presentation but not unheard of. Track your gut transit time with sesame seeds or corn. If it is delayed (over 24 hours) then the methane is still slowing everything down. Most of the anti-methanogenic herbs should help too, just skip the laxative approach.

  24. Hello Todd,
    I have high methane and hydrogen on a glucose test but was tested negative on a lactulose test. Does this indicate the specific place in my intestines that the overgrowth is occurring?
    I would like to try the probiotic you recommended (lactobacillus reuteri dsm 17938) but I have histamine issues. Have you noticed that your clients with histamine issues have responded poorly to that probiotic?
    Thanks so much for a wonderful amount of info on methane sibo.

  25. Hi Todd, I have methane dominant SIBO and did 6weeks of antimicrobials, which brought my methane down by half (66->29) but my hydrogen up by a lot (4-> 26). Is that unusual? Could I just do another round of antimicrobials (Allimed+Neem) or will that keep bringing my hydrogen up?

  26. My naturopath diagnosed me with both methane and hydrogen SIBO a few years after my 2nd c-section. We are fairly certain that is what caused the SIBO. If I were to have microneedling done to break up the internal scarring of the c-section scar, could that improve motility, therefore making it harder for SIBO to become present?

    1. Unfortunately I don’t have experience with the microneedling approach. I generally refer out to visceral manipulation osteopaths (there are a few good ones here in Byron Bay) and sometimes use castor oil packs to help with generally good results. The methane side of things can be a real challenge in certain patients.

  27. What do you do with the oregano leaf? How do you prepare/consume it? For how long? Also, how many cloves of garlic to use? For how long?

  28. Hi Todd,

    Excellent information, I had a recent breath test diagnosis was IMO and really need your help on a recommended probiotic that offers the right strains for me? Thanks John USA

  29. Hi Todd,

    What herbal antimicrobials do you recommend for lactating mothers who have methane dominant SIBO?

    I react badly to fresh garlic, instead I am having an Allium Sativum extract three times a day, iberogast before every meal, cold pressed pomegranate juice, and I also have the seeds.

    Is there anything else I can add that won’t negatively effect my milk supply or harm my baby?

    Tyler 🙂

  30. Hi, is Saccharomyces Boulardii i-745 good for knocking out methane…I believe I read that it one of your other articles but it is not mentioned here. Also, can you recommend a brand for L. reuteri DSM 17938…I’m in Canada and can only find BioGaia that doesn’t seem very good. Thanks!🙏

        1. I just got florastor and it says duration of use is one week on the box. I know everyone is unique but generally how long do you stay on the probiotics… until symptoms clear? Can you stay on them for longer periods?

      1. Hey again, started l reuteri for methane and symptoms are flaring right away also leaning more towards constipation which this is supposed to help…is it normal in the beginning for symptoms to flare when starting a probiotic as the terrain adjusts?

        1. The main use is around leaky gut and regenerating/regrowing the gut lining but it is also anti fungal, reduces other bacterial overgrowths and also promotes Treg function among many other things! A great probiotic if tolerated 🙂

  31. Hey Todd,

    can you help me with my glucose test results? I did a lot of research on the internet and I think due to what I read test results show methan sibo positive.

    Before drinking glucose my ch4 level was at 19ppm. I did the prep for the test right. Just had some rice for lunch the day before testing.
    At min 15 20ppm, 30-45min 18ppm, 60min 16ppm, 90min 15ppm, so no increase. Havent had symptoms during nor after testing.
    0 H2 production the whole testing.

    thanks for your help and all the best


    1. Hi Peter, this could be LIMO (methane in the large bowel). It isn’t severe but some patients are quite sensitive to methane gas production in the gut. I would track your gut transit time and assess you for constipation and bloating before going after the methane producing bug first.

      Hope that helps!

  32. Hello Todd,

    I have methane SIBO and histamine tolerance also. I have microscopic collitis as well and after a round of Rifaximin treatment, I need to use probiotics. Probiotics either flare my SIBO or histamine allergy. I tried BioGaia last time for methane SIBO, but that triggers histamine allergy. VSL#3 also causes allergy, and Bifidobacterium Longum which blocks histamine increases my SIBO. Could you please recommend a probiotic?

  33. Dear Todd,

    indeed, IMO (Methan SIBO) is very challenging for those who have it. It can take years after try and error. I suffer myself.

    The thing we need to keep in mind, treatment is not well studied yet. Therefor you find contrary approaches. Mark Pimentel Sayscut fibre and do a low fermentation diet plus using antibiotics. Others say, like you, and I agreed with it, we need to make the bowl movement first. This is a thin line, hydralized gear gum for an example doesn’t help me at all, but I like the taste. Flaxseed is too heavy creating gas.

    There are days, whatever I eat, whole day of gas traveling around . So it can’t be the food alone, because the same food on other days doesn’t do it that intensed.

    I really hope there is a treatment plan for all of us, as it is, it will not work. There must be other factors to consider, it neither food alone nor taking some pills…

    Unfortunately there are no experts in Germany,.

    Have a nice day and keep up your good work

  34. Can Lyme disease (or other tickborne infections) be the root or underlying cause for SIBO? Have you found this to be common — or even possible — in your practice or research?

  35. re: ‘Can Lyme disease (or other tickborne infections)’ from my experience of getting what is now known to be Lyme Disease in 1962 (tick complete with a thick circular rash)- it was the antibiotics that slowly steadily brought me to this problem. My dad, a physician gave me (perhaps) too many of the wrong kind of antibiotic. I had never mentioned the tick to him. Maybe they did not have the appropriate antibiotic then. I also had some kind of trigger in Mexico where i lived with an episode of Diarrhea. Some say it could be food poisoning that introduces an imbalance. This is a tough problem to solve and yet i persevere.

  36. Wonderful to see a practitioner who understands that if you get it all moving and reduce the bacteria, it will clear up.

    As a wellness practitioner and Colon Hydrotherapist, I have so many clients who come in who have been treated with anti-fungal’s and antibacterials by MD’s, and ND’s only to arrive back in the same place again.

    Thank you so much for putting this commonsense advice out there, so the world can heal itself!

  37. Hey I am 23 and was diagnosed with methane sibo, have constipation and pain in my gut every morning. I did a round of antibiotics and it was not helpful. I can almost feel the stool in my gut every morning but have difficulty emptying. I have tried eliminated as many foods that seem to make it worse to find some relief but haven’t. I also feel i am becoming intolerant to more foods and recently got seborrheic dermatitis on face all of a sudden. Any advice ? thank you!

  38. I live in US, I would love to be your patient, thanks for the wonderful information, you benefit so many of us, I have methane SIBO symptoms for 10 years but diagnosed recently, if you ever work with patients here, I will be so grateful!

  39. I love your videos and blog and wish that I could be treated by you–but live in the U.S.

    I have a history of methane sibo or IMO–positive breath test– I think it is in the small bowel because when it recurs I get intense bubbles in my throat that make it hard to breath and cause LPR in a very painful and intense way–when better managed this goes down significantly. I also have MCAS and react to high histamine foods and take DAO enzymes and supplements to manage hives and dysautonomia and POTS symptoms.

    I am currently in a predicament–I am terrified to treat my SIBO/IMO with anything because I had a very bad case of c diff last summer. It almost killed me but I was able to get a fecal matter transplant and it resolved leaving a lot of gut symptoms in it’s wake. I have been doing much better–but feel the methane sibo returning in full force. I want to try something like the Atrantil or similar or maybe a bovine serum immunoglobulin or something–but I see many reports of people taking Allicin or an herbal antimicrobial and having a c diff relapse. I wonder if you have any recommendations for people with a c diff history to look into. I feel terrible and am supposed to start graduate school soon–desperate for relief but do not want that desperation to drive me to do something that could cause the c diff to return–that was absolute hell and has taken me a full year to recover from.

    I take LDN and a ginger and artichoke supplement to try to help with motility and dandelion and marshmallow root tea for my throat. Plus mast cell stabilizers.

    Any advise would be hugely appreciated!

    Thank you for your content!

  40. Hi Todd,

    You mentioned Bifidobacterium lactis HN019 is potentially a good strain for dealing with SIBO, but is there a specific brand you recommend?

    I’ve not had any luck finding that strain alone – i.e. it always comes with several others and I know one needs to be careful about adding in a lot of different strains as they can sometimes make things worse.

    Any information would be greatly appreciated.


  41. I have dealt with methane sibo for years until a low fodmap diet seemed to help. I fell off the diet wagon this summer and a recent poor choice of lunch for two days in a row of yogurt top it off has sent my body back into GI stasis mode. I have bad breath now and also the smell/gas in coming out of my pores. I was reassigned to a different job which is extra stressful and I am deeply embarassed about my offending odors. What can I do to jumpstart back to health? I am exercising again and going low carb. I am trying to find something to move my bowels more frequently and to treat this, fast!

  42. From your article, it sounds like I may have LIBO (10 ppm methane at baseline, then 0 until 2 1/2 hours later 7ppm, good prep I feel). However, unlike others I am not constipated (normal once a day stools) and transit time seems fine based on your “corn test” :). My issue is at least 1 or 2 times a week my stomach is uncomfortable most of the day, and bloating (not distended). Does it still sound like a methane issue, or something else? Recent colonoscopy normal. Not sure where to turn to fix this! Thank you for your help!

  43. Is there any difference between partially hydrolyzed giar gum and just ‘hydrolyzed guar gum’?

  44. Fantastic resources here, thank you Todd. I have methane dominant SIBO and have successfully been speeding up my digestion with Magnesium, Psyllium Husk, PHGG and Turkey Rhubarb. Also taking Rock Rose and Sac Boulardii. I would like to ask, is it a good thing to go from constipated with solid stools to having diarrhea? I don’t mind the diarrhea as a side effect if I am on track to faster digestion and reducing methane, but should I be concerned by it and adjust supplement volume?

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