Methane SIBO: Advanced Treatment Options

methane sibo natural treatments herbal medicine SIBO

Methane dominant small intestinal bacterial overgrowth, also known as methane SIBO or even SIMO (small intestinal methane overgrowth) is commonly seen in patients with constipation, bloating, flatulence, burping and sometimes even reflux and heartburn. This particular condition, as well as large intestinal methane overgrowth or LIBO/LIMO (sorry for the acronym overload, it does make life easier!) can be a tough condition to treat

In the majority of patients, an approach combining select herbs, prebiotics, probiotics and targeted nutrients helps to reduce this microbial overgrowth. The goal is to get the bowels moving, speed gut transit time and reduce bloating. There is a certain subset of patients, thankfully quite small, that are resistant to treatment of their methane overgrowth. These patients have been through antibiotic combinations, herbal treatments and even the elemental diet, sometimes a number of times, and their methane levels still won’t budge on retesting. 

For more info on SIBO in general check out our free ebook in the link below.

Today we will cover some of the approaches I take with these patients to work through the microbial overgrowth and all the symptoms associated with it. 

For a review on the general approach to treating methane dominant SIBO see SIBO: Methane Dominant Treatment Plan.

Image taken from: Archaea: Essential inhabitants of the human digestive microbiota showing the Archaea that have been found in the gastrointestinal tract. 

Methane SIBO and Diet

First off let’s cover diet. 

For the most part I don’t insist on a low FODMAP diet when treating my SIBO patients. As we progress down the treatment road and we are finding that symptoms are still persisting I bring in the low FODMAP diet. 

Often it isn’t every FODMAP that causes symptoms, just a handful. 

Major offenders are onion and garlic, dairy products, high fructose foods and finally certain legumes. This varies from patient to patient. 

But why wait to restrict FODMAPs? Why not jump straight into a low FODMAP diet first? 

Great question. First off I don’t find it is necessary for the majority of SIBO patients. Some practitioners disagree with me strongly but I have found that limiting all FODMAPs is unnecessary for a successful outcome in most patients. 

I can think of one patient that was on a self-imposed low FODMAP diet for 7 years. As soon as she consumed a high FODMAP food all of her symptoms came back. To me this simply indicates that there is a digestive imbalance that has not been corrected. When we started working together I recommended SIBO breath testing. Even after 7 years of strict low FODMAP eating her SIBO results were still positive. 

Summary – When we are not seeing the results I would expect in the treatment of constipation SIBO I start to discuss the need to restrict FODMAPs for symptom improvement while we treat the root cause (an overproduction of methane in the digestive tract). 

Biofilm Busters to treat methane SIBO

Biofilms have been getting a lot of press lately. For the most part I rely on herbal medicines to treat biofilms and prefer to formulate each and every herbal tincture different for each patient. Ofen I will change up the formula and the herbs throughout the course of treatment to get good coverage.

When herbal medicine, prebiotics and probiotics aren’t shifting the symptoms and methane gas levels aren’t coming down I will consider biofilm disruptors. 

What are biofilms?

I like to think of biofilms as little microbial cities. Different species of bacteria, fungi or the methane producing archaea can join forces, wall themselves off, and become extremely resistant to treatment. 

Does this sound like a difficult to treat methane dominant SIBO case or what? 

Unsurprisingly we can see below that these methane producing microbes that are the cause of methane dominant SIBO can and do form biofilms. The most common methane producing microbe in the human gut is called Methanobrevibacter smithii. Methanosphaera stadtmanae is the second most common methane producing microbe. These two archaeal bugs form biofilms as seen in the image below (1).

Image taken from: Archaeal Biofilms: The Great Unexplored

There are a few options including n-acetyl-cysteine or the proteolytic enzymes found in a range of products including interphase plus or kirkman labs biofilm defence. Here in Australia there is a new biofilm disruptor or biofilm buster from Bioceuticals Clinical range called Bio-film Clear. 

Image: Bio-Film Clear from Bioceuticals Clinical

It is important to take these before your herbal antimicrobials and preferably on an empty stomach so that the enzymes work on breaking down the microbial biofilm and not the food in your stomach.  

Summary – If you are dealing with a tough to treat methane SIBO case then biofilm disruptors can play a role in treatment but we have to be careful here because beneficial bugs live in biofilms too. 

Prokinetic Herbs to get the gut moving 

Methane production slows down gut transit time and causes constipation. We know this from studies on animals and humans (2) and also from my clinical experience. 

Image: Bitter orange peel is a new herbal prokinetic I have been using in my herbal medicine for methane SIBO

Speeding up your gut transit time can be the missing piece to bring down the methane SIBO bugs and keep them down (3).

This helps by reducing the methane gas and the symptoms it causes – bloating and distention, constipation, delayed gut transit time, reflux, burping, excess flatulence – the list could go on. 

In my approach to treating methane dominant SIBO I will focus on speeding up gut transit time straight out of the gate with different herbal medicines. You can check out this article for a deeper dive on prokinetic herbs

If we are having trouble bringing down the methane gas levels and improving symptoms I often double down on herbs, probiotics, prebiotics and fibres that can speed small and large bowel transit time.

The science doesn’t appear to be getting the attention it deserves but a few papers from the same research team have explored the connection between slower gut transit time and a more alkaline gut pH with higher methane producing bugs (4, 5).

Taking this research into account we want to speed up gut transit time and decrease gut pH to decrease methane producing bugs. I have also found this to be the number one way to improve bloating in methane SIBO patients. The important bit here is that it can take time and dedicated effort to get transit time down below 24 hours.

Summary – Speed up gut transit time to make the environment less favourable for methane producers. This also improves bloating when it is delayed.

Support bile flow to treat methane SIBO

Bile is produced in the liver and stored in the gallbladder. Everytime you eat something oily or fatty the gallbladder sends bile to the small intestine to emulsify and absorb the incoming fat laden food.

We know that methane can slow gut transit time (6).

But how does methane impact bile flow from the gallbladder? 

There is little data on whether methane gas does slow bile flow and gallbladder contractions but we do have some older research showing that bile itself can reduce methane production.

One study found that human bile significantly inhibited methane production. Taking it one step further, the same study showed that when they added cholestyramine, a bile acid binder, the effects were reversed. Finally, the authors reported on a case study of a ‘highly methanogenic’ (lots of methane) patient who had issues with bile flow. After a surgical procedure to improve bile flow the patient went from high methane production to no methane production in just three months (7).

These results have been seen in a few other studies (8, 9).

But it is worth pointing out that they are older studies on animals or in-vitro.

Still, understanding how methane impacts smooth muscle contractions in the gastrointestinal tract and how this may impact bile flow plus the fact that bile acids have been shown to reduce methane production makes focusing on bile flow an important aim in treatment resistant methane SIBO.

Summary – Focusing on bile flow can help to bring down treatment resistant methane SIBO and improve constipation. 

The Elemental Diet to treat methane SIBO

I am relying on the Elemental Diet more and more to treat challenging gut health cases. It certainly isn’t a cure-all and I have seen patients react to the liquid only diet. For this reason alone I tend to recommend a 2-4 day Elemental Diet trial. If my patient feels ok with the short trial and they see benefits and symptom improvements then we discuss the process of a 2-3 week Elemental Diet. 

Often the hardest bit is starting the process. I was recommending it enough that I had to trial it myself. I went 5 days on the liquid only diet with almost no problems. Sure I was hungry and I craved food. I did notice a drop in energy and I wasn’t quite as sharp mentally but all up it was more than bearable. 

I have one incredible case of a three week Elemental Diet lowering methane production by 82ppm by the 100 minute mark 

SIBO breath test showing extreme methane dominant SIBO 

SIBO breath test showing methane dominant SIBO now resolved – dropped by 82ppm after a 3 week elemental diet. 

Consider Overgrowths other than methane like SIFO

This part seems so simple but is often overlooked. I have to admit I have missed other forms of gut imbalance and focused exclusively on methane dominant SIBO in the past, sometimes with limited results. 

As of yet we don’t have clear research on fungal overgrowths in the small bowel. There have only been a handful of papers published on the subject. 

One paper found small intestinal fungal overgrowth in over 20% of patients with SIBO. They found the common symptoms associated with SIFO were (10)

  • Abdominal pain 
  • Gas
  • Bloating 
  • Flatulence 
  • Diarrhoea

Every symptom in that list bar the diarrhoea overlaps with methane SIBO. If both are present it can be hard to tell which is which. 

It can be hard to test for SIFO, and no the SIBO breath test will not screen for a fungal overgrowth unfortunately. 

I have been using the Great Plains organic acid test (OAT) in my practice recently and have been amazed at how common fungal overgrowths are. In my opinion it is the best way to test for fungal overgrowths in the body. You can read more on that with a great case study here – Candida Infections: Three Testing Options

Are Treatments Failing You for Methane SIBO? 

As we discussed, the methane producing microbes can be difficult to shift in a subset of people. Often swapping the herbal antimicrobial approach and including probiotics and prebiotics is enough to get symptom improvement. For people who have tried this then diet, biofilm disruptors, gut motility herbs and supplements and bile flow support can help. Also, consider other possible root causes like SIFO. 

Have you experienced tough to treat methane SIBO? If so, what has helped? Leave a comment below and share your experience. 

References and Resources

  1. Archaeal Biofilms: The Great Unexplored
  2. Methanogenic flora is associated with altered colonic transit but not stool characteristics in constipation without IBS
  3. Breath methane in functional constipation: response to treatment with Ispaghula husk
  4. Relationships between transit time in man and in vitro fermentation of dietary fiber by fecal bacteria
  5. Relations between transit time, fermentation products, and hydrogen consuming flora in healthy humans
  6. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity
  7. Inhibition of methanogenesis by human bile  
  8. A possible role for bile acid in the control of methanogenesis and the accumulation of hydrogen gas in the human colon
  9. The effect of porcine bile acids on methane production by rumen contents in vitro
  10. Small intestinal fungal overgrowth

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  1. Please help I was diagnosed with sibo last year 2021 after seeing a functional doctor, I kept telling him my symptoms and he said it sounded like sibo so he gave me a breath test and yes it was positive for methane sibo, he tried me on candibactin ar and br also gi revive, prebiotic and a mobility pill plus I was on a low fod map diet and gluten free diet but all have failed I can’t sleep at night because of my stomach waking me up every night I’m booted, gassy and constipated and just plain tired of feeling this way, this can’t be life, please help me.

  2. I have something similar; I did the SIBO methane breathing in tubes test and it confirmed that I have methane SIBO. I tried the antibiotics—2 including Refaximin and as expensive as they are, they did nothing.
    My only symptom is that I am awakened after an hour or so by ( what appears to be) gas trapped somewhere in my lower back/intestine ( Oh, and I have some constipation but do go to the bathroom every morning even if it takes a few minutes),
    Now I take Clonazapam and i sleep for maybe 4-5 hours and sleep sitting up on the couch the rest of the time
    After reading quite a lot about SIBo I believe my problem is a problem of motility.
    This Todd Mansfield site is wonderful and I am going to pursue further
    Very Best

    1. Hi Seamus, thanks for the comment! It definitely sounds like a motility issue, especially with the confirmed methane. Track your gut transit with whole sesame seeds or even beetroot. If it is much more than about 36 hours I would focus almost exclusively on this first.
      Hope that helps!

  3. My doctor has been treating me for SIBO (confirmed with a breath test) with a combination of things, including Interphase Plus, Biocidin and Olivirex. After a year and a half of treatment, And my symptoms coming back when I stopped the meds, she decided it was the methane that was the problem and we retested to confirm. My tests showed normal hydrogen, but high methane. I am now trying a combination of Interphase in the am, Biocidin and Olivirex, Motility Pro, spacing out my food consumption by 5hrs, and Allicillin right before bed (it upsets my stomach otherwise). It hasn’t been very long, but my symptoms seem better. Less bloating. Still some gas, but bearable.

  4. Po zjedeni 5 litrov medu za kratky cas som zacala mat obrovske problemy s plynatosťou ze sa to nedalo ani vydrzat. Gastrolekar mi zistil masivne premnozenu candidu. No ani lieky ktore mi dal mi nejako problem nevyriesili mozno na 20%. Po roku trapenia som to super vyriesila vysokopercentnym kvalitnym oreganovym olejom. Uzivala som este jablcny ocot 2 tyzdne raz za 2 mesiace,bulharske probiotika od firmy Daflorn, ktore hned odstranili zapal z creva a hlavne co mi pomohlo amazonske byliny v tinkture Amazonsky protokol od Peter Chobot od firmy Incabotanica, ktory zbavi telo od vsetkych patogenov. Raz do mesiaca este aktivne uhlie 3 dni na odstranenie odumretych zvyskov patogenov. Netreba ani zanedbat vycistit telo od pesticidov a tazkych kovov ktorymi sa bakterie a virusy, plesne zivia a dobre prosperuju.

  5. Hello! Thanks for your informative articles.
    I have had sibo and ibs for 4 years and am on my 3rd round of xifaxan and alinia. Nothing seems to be working sadly. I have both hydrogen and methane dominant results on my breath tests. I’ve been on a biofilm disruptor this past week to hopefully make this round work. What are your thoughts on alinia and Lovastatin for methane dominant sibo? Alternatively, candibactin AR and BR or oregano oil with coconut charcoal. I would really appreciate your input!

    1. Hi Dani, thanks for the comment. SIBO, particularly methane dominant, can be so stubborn in some! Depending on your symptoms I would explore gut transit, biofilms and have even resorted to combining xifaxan and herbal medicine (with prescribing Dr on board) to tackle the challenging SIBO cases. PHGG can be a game changer. Finally I am currently exploring the use of the phase 2 biofilm disruptors (or the script based bismuth thiols) for persistent methane overgrowths.

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