Methane dominant small intestinal bacterial overgrowth, often called methane SIBO or more recently intestinal methane overgrowth (IMO), is a common finding in patients struggling with constipation, bloating, flatulence, burping, and sometimes even reflux or heartburn.
This particular form of SIBO can be especially tough to treat. As a clinical herbalist working in a busy practice, I’ve seen my fair share of resistant methane cases. In fact, due to its stubborn nature, methane SIBO can make up over half of the cases I work with, especially patients who have been searching for answers for years without relief.
For most people, a combination of targeted herbal medicines (mainly tinctures), prebiotics, probiotics, and select nutrients helps reduce microbial overgrowth and resolve symptoms. The goal is to get the bowels moving, improve gut transit time, and reduce bloating.
But there’s a certain subset of patients, thankfully small, who are resistant to standard treatments. These are the ones who have been through antibiotics, multiple herbal protocols, and even the elemental diet, sometimes several times, with little to no improvement in their methane levels on retesting.
Today, we’ll dive into how I tackle these tougher-to-treat cases with more advanced methane SIBO treatments — when to pivot to new strategies and when to stay the course and adjust the herbal protocol.
If you’re looking for a broader overview of SIBO and how to approach it, be sure to check out our free ebook linked below.
Today we will cover some of the approaches I take with these patients to work through the methane 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.
- Methane SIBO and Diet
- Biofilm Busters to treat methane SIBO
- Prokinetic Herbs to get the gut moving
- Support bile flow to treat stubborn methane SIBO
- The Elemental Diet to treat methane SIBO
- Strong Herbal Antimicrobials for Methane SIBO
- Consider Overgrowths other than methane like SIFO
- Are Treatments Failing You for Methane SIBO?
- References and Resources
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.
When we are not seeing the results I would expect in the treatment of methane SIBO or intestinal methane overgrowth 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).
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.
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.
If you are dealing with a tough to treat methane SIBO case then biofilm disruptors can play a role in treatment. I like to save these for ‘as needed’ cases that aren’t improving with herbs.
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.
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.
Check out my article deep dive into prokinetic herbs here – Prokinetic Herbs: Herbal Medicine for Gut Motility
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 stubborn 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 but it is worth pointing out that they are older studies on animals or in-vitro (8, 9).
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.
Focusing on bile flow can help to bring down treatment resistant methane SIBO and improve constipation. Clinically I have seen this be the missing piece in treatment dozens of times.
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
2025 UPDATE – I have been recommending the elemental diet less and less to my treatment resistant patients for a few reasons. I’ve seen to many failures with this approach and combined with the hassle and the cost of the therapy I can’t justify recommending it frequently. I’ll update you here if that changes!
Strong Herbal Antimicrobials for Methane SIBO
Starting with the gentler approach of shifting the terrain back to balance and reducing the methane overgrowth with moderate antimicrobials works most of the time but when it fails I have no problem recommending a short and sharp strong herbal antimicrobial program for 4-8 weeks.
I can justify this approach in a few different ways.
- Patients start to discuss the combo antibiotic program and I have yet to see this work reliably. Strong herbal antimicrobials may disrupt the microbiome balance but it’s nothing compared to combo antibiotics often recommended as frontline conventional treatments for methane SIBO.
- We just need results. This was a tough realisation to come to. But what about the beneficials in the gut, what about antimicrobial resistance? So many reasons not to use strong herbal antimicrobials but the fact is they work for the right patient and they get results when nothing else has worked.
So what herbs would I turn to?
Top of the pile at the moment for treatment resistant methane SIBO would be
With this approach the proof is in the symptom improvements over 4-6 weeks. If you haven’t seen the needle move and aren’t feeling significantly better with strong herbal antimicrobials after this period it’s unlikely it’s the missing piece that will get you better and probably time to move onto a different approach.
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)
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 Mosaic Labs 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
2025 UPDATE – I have been using the Mosaic Labs OAT test in every tough to treat patient for the past few years and it’s changed my practice. I have come to see fungal overgrowths as a massively under recognised condition and can frequently go hand in hand with tough to treat or significantly elevated methane SIBO cases. More on that soon!
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, strong antimicrobials 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
- Archaeal Biofilms: The Great Unexplored
- Methanogenic flora is associated with altered colonic transit but not stool characteristics in constipation without IBS
- Breath methane in functional constipation: response to treatment with Ispaghula husk
- Relationships between transit time in man and in vitro fermentation of dietary fiber by fecal bacteria
- Relations between transit time, fermentation products, and hydrogen consuming flora in healthy humans
- Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity
- Inhibition of methanogenesis by human bile
- A possible role for bile acid in the control of methanogenesis and the accumulation of hydrogen gas in the human colon
- The effect of porcine bile acids on methane production by rumen contents in vitro
- Small intestinal fungal overgrowth
33 comments
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.
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
Seamus
homerick@aol.com
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!
Best,
Todd
What do you do if it is a motility problem and herbal prokinetics aren’t working?
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.
Great input! Targeting methane directly can really help. So glad you are seeing improvements :-)
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.
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!
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.
Hi Todd,
I have recently been diagnosed using a lactose/hydrogen breath test as having methane dominate SIBO. I feel like all I do now is read and study on this condition. I bumped into your site and have enjoyed reading all your input.
I have learned the classification of methane dominate SIBO, or SIBO-c has changed to more accurately reflect that no bacteria are involved. I wonder if you would consider changing your classification to reflect IMO as an search marker for those of us who struggle to learn everything we can about this particular diagnosis. These pesky critters can be hard to deal with. I especially have had a difficult time with anxiety…
I recently read a paper from 2017 that said woman drinking 1 glass of alcohol a day could promote symptoms of overgrowth. Great, so that 5/6 oz of wine I had everyday wasn’t good. : (
Anyway, I just wanted to say. Thank you, great information…let’s all keep learning.
Bonie
I have been dealing with stomach issues for years. My issues have gotten so bad I have constant symptoms. I’ve been to several GI doctors and no one has an answer. I recently heard of this and feel this may be the reason for all my issues. I need desperate help!
Lorrie, I’d find available functional dr near you.
I was diagnosed w/methane sibo, unfortunately I did NOT know where to start. After seeing 2 regular drs I found a functional. The regular docs don’t know anything about sibo, the functional is thinking of having me “try” HER own herbal meds for 3 months. After I explained my symptoms she seemed confused. I found another functional. Seems much more reliable. Anyway, finally got blood, breathe and stool test. With sibo IF your dr doesn’t order stool test, blood AND breath RUN away
Hi Todd, how are you ?
I have 28 y/o, from Chile. After one year of GI issues post food poisoning, I discovered the world of SIBO in reddit, while looking for answers. At hospitals, ER, ‘everything is fine, it’s just in your head, maybe a mild gastroparesis from the foodpoisoning but that’s RARE’. I investigated, checked by my own with breath test, sent my poop to US (diagnostic solutions lol), and boom: Methane Sibo, SIFO, and Blastocystis Hominis, plus other things, like very low elastase-1.
Right now, really underweight, very confused, overwhelmed, lost my job, parties, friends, my life because of this. Depression is hitting hard.
Good news is that we have a lot of plants here in Chile, but nobody knows how to work with them for this issue (SIBO). I was prescribed rifaximin + metronidazole, and I consider that like a suicide (in the condition that I am right now). I was even thinking on rifaximin + some herbs, like an alternative.
Wanted to ask you I can work with you, even if I live in Chile, for you to help me with thinking in a possible plan. I can try here in Chile to find the plants, herbs, extracts, products.
This completely took my life away, and I want it back </3
Thank you,
Andrea
Hola Andrea, estoy en la misma que tú.
Si quieres nos ponemos en contacto, te dejo mi correo:
m.antonio3@gmail.com
Hi Todd
My question is does having chronic Lyme disease and a positive diagnosis for methane SIBO mean that the lyme is creating the MEthane overgrown?
Thankyou 🙏🏼
Hi Ruth, thanks for your comment. Many of my lyme patients have methane overgrowths. I suspect that the lyme is causing the slow motility and constipation and this leads to methane overgrowths as you suspected.
Hope that helps!
Best,
Todd
hi todd! i have stubborn methane sibo. i am trying to improve motility time with magnesium and motility complex. now i am going on the elemental diet. my question is..do i take neem, cloves, berberine, oregano, interphase plus and allicidin all at once and at the same time as doing the elemental diet? Also do i take digestive enzymes only on introduction of the food again?
i am really suffering and only just realized it was sibo. i have had this issue for so long and not known it. I thought it was normalto feel that way after eating.
Hi Ariel, thanks for the comment. It depends on the case but I would recommend just the elemental diet on its own for most that go this route, not a combo with herbs too.
Todd–thank you very much for this information. It’s truly something to work with. I have seen bits and pieces of this, but never an order or plan. So one is left guessing, trying, and often failing. Life does get pretty tough with unresolved symptoms, but you are offering us hope, here.
Hi Hannah, thanks for the great feedback. I hope you find the support you need!
Thanks Todd for all the great info you provide. In regard to improving motility/transit time for methane sibo. In the process of treating transit time with ginger, artichoke, etc. is it possible to experience die off symptoms as transit time is improved?
I have had methane SIBO for years with on and off debilitating flare ups and have still failed to find a doctor or practitioner to help guide me through it. I’ve cut out dairy and gluten permanently. But to end a flare up, I basically just starve myself, only eating proteins/kale/spinach until my symptoms subside but after 2-4 weeks back on a normal diet, symptoms reoccur. I’ve been told the route cause of my issues are anatomy based, with a very torque and redundant colon, with sluggish motility, so there’s no way to eliminate SIBO completely unless I cut FODMAPS.
More than 10 years ago, near perfect digestion.
Then, I was given Pantoprazol for 10 months. And the problems started.
Bloating, gas, constipation, blurred vision, nausea…
I’ve tried many many things, diet, antifungals, antibiotics, natural products,… but it always gets less effective.
Last year, I finally got the breath test for SIBO, positive for hydrogen and methan.
As I have had many rounds of antibiotics before, I was sent to a “SIBO expert” who did a duodenal aspirate and found nothing.
Since, I have had a couple more rounds of antibiotics, they always helped but temporarily.
I do a new breath test in 2 weeks.
– could the duodenal aspirate be a false negative? (made too high?)
– how do I deal with the recurrence? Could biofilm breakers help? I see some with digestive enzyms.
I had had a pancreas insufficiency for 8 years, general symptoms improved a tiny bit after it got resolved (pancreas infection of unknown nature)
– how do I kill methan SIBO with natural products or essential oils that I can buy OTC?
– how do I support and cleanse my liver?
Follow holistic health by Shelia! She can help you!
hi, i did approx 8wks of low fodmap and took Sibotic for methane SIBO; diagnosed w a breath test. Felt better for about 2wks. As I started to introduce fodmap foods back w the guidance of a dietician, I started experiencing bloating and abd pain, and constipation. I started Xifaxin 6 days ago along with a probiotic; yeast based, and just started a prebiotic; biota boost. I have been taking a prokinetic at night and magnesium. Not sure if I am overdoing it and not sure the best time to take the probiotic and prebiotic. I am taking the probiotic typically in the morning approx 2hrs before or after the antibiotic, Xifaxin. I have been taking the prebiotics at night w the motility activator. any add. suggestions or advice would be appreciated. thank you
Hey there!
I’ve recently done the elemental diet to get down my hydrogen levels (it was originally at 139) and methane levels (sitting at 30). After the three-week diet, my hydrogen levels have normalised but my methane level is sitting at 11 (just one above the range).
I can’t tell if that is a normal consequence of my hydrogen levels coming down. My naturopath did mention something about the methane just being a part of having the high hydrogen numbers. Not entirely sure whether to start another herbal protocol.
I have Methane Sibo with costipation with 3 or 4 bowel movements each day usually after meals & sometimes Diarrhea. I have lost 20 lbs. I was on Rifaximin & Neomystin 2 years ago which helped a little for a short time.
My neurogastro dr wants to start me on it again because my methane is very high. I have been on a low fiber diet because high fiber foods have a laxative effect. I am 80 yrs. old.
I have had Methane Sibo with Diarrhea for 3 yrs.
I eliminate after most meals & more.
I am on a low fiber diet.
My neurogastro dr put me on Rifaxamine & Neomystin 2 years ago which helped a little, maybe 5 months.
He wants to start me on the 2 antibiotics again because my recent breath test was high methane.
Please advise if possible.
Hi Todd
SIBO results above says “Increases of methane greater than 12ppm over the lowest preceding value within the first 100 minutes are indicative of bacterial overgrowth. Levels between 100-120 minutes are considered borderline See additional interpretation” – what about methane results after 120mins (i.e. some tests run for 3h) – I thought that an increase in methane over 10ppm at any point during the test means MIO?
methane breath test interpretation is all over the map at the moment. There isn’t great consensus. Increase of 10-12ppm in some labs/studies, levels of 10ppm or above in others. To me methane levels have become very subjective and case by case. The big question is ‘how is methane impacting your gut?’ Then take treatments from there!
Hope that helps!
Todd your information is spot on for those of us who’ve fought methane sibo for years. It’s ALL about motility. Please know you’re doing a wonderful service to so many. Keep spreading the word. I have felt best when I used ginger, clove and aloe Vera to keep things moving. Other things that truly help include mag citrate and florastor probiotic. If things are moving even my supposed “food allergies” don’t even affect me at all. And my mood is amazing when the methane isnt proliferating. We in the U.S. truly appreciate you for sharing this excellent information.
Hi Todd
Do you have experience with aromatograms that allow you to exactly determine the inhibitory activity of herbs/essential oils against microorganisms (bacteria or fungi) isolated from the sample taken eg skin, stool? It’s common to test for antibiotics in an antibiogram but (not yet) so common to test for natural remedies and I don’t know why.