How to Treat Constipation-Causing Methane SIBO

Methane SIBO is it’s own special kind of overgrowth. One day it might even get it’s own name. But for now, understanding how it differs from the more common hydrogen form of SIBO is critical to developing a treatment protocol that addresses its well established defences. From chronic constipation and obesity, to false negative test results and antibiotic resistance, methane SIBO is an extremely complex GI condition and one that is particularly difficult to treat.

This post is targeted to methane-dominant SIBO. If you’re looking for more comprehensive SIBO information, check out my SIBO series articles: 1. Overview, 2. SIBO Testing, 3. SIBO Treatment.


Why is Methane SIBO different?


It’s not technically bacteria, but single-celled organisms called archaea, that are responsible for the methane form of SIBO. But, ‘SIAO’ just doesn’t have the same ring to it, I guess. The specific species of archaea is methanobrevibacter smithii. And if you have an overgrowth of this critter, you most likely have a bacterial overgrowth as well.

Why? When you eat fibre, the bacteria in your gut ferment it and produce hydrogen. And what do archaea feed off? Hydrogen! It is only once the archaea consume the hydrogen that they produce their own by-product: methane.

So, to support a large amount of archaea (i.e. an overgrowth), you need to be producing sufficient hydrogen to feed them. Which, if you’ve tested positive for methane SIBO, generally means two things:
1. You also have an overgrowth of bacteria (SIBO) which produce excess levels of hydrogen.
2. Even though you have an overgrowth of hydrogen-producing bacteria, excess hydrogen levels may not show up on your testing as the archaea consume the hydrogen and produce methane instead.

Methane SIBO Constipation


The Methane Constipation Connection


So, even though archaea help reduce the amount of hydrogen gas in our small intestine, the methane they produce can have its own negative effects. As with hydrogen in the small intestine, methane gas will also cause abdominal bloating, plus a much bigger problem; it slows down transit time which leads to constipation.

While you might think constipation is preferable to diarrhoea, and symptomatically in the short-term you might be right, constipation caused by these methanogens can create a vicious cycle of SIBO that is harder to break than the traditional SIBO-D, diarrhoea type. This was my issue, and the cause of lots of my healing struggles, so let me explain some more.

You see, methane slows transit time and causes constipation, and constipation allows more bacteria to grow, which causes more methane and more constipation… and so on, and so forth. A difficult cycle to break without the right treatment.


Methanogens and obesity


Higher levels of breath methane are also linked with obesity in humans. This is thought to occur via a couple of mechanisms. First, archaea have been shown to affect the amount of calories your body absorbs by increasing the capacity of gut bacteria to digest specific glycans. The more calories your body can absorb, the more weight gain you will likely experience.

And secondly, previous studies have demonstrated that methane gas slows small intestinal transit time, which may contribute to increased weight gain by increasing the amount of time during which energy is extracted from meals.

This is something that I experienced first hand, gaining over 10 kg in the space of two months before testing positive for methane SIBO (and then losing it again post-treatment). It’s also something I see a lot with my clients who have methane SIBO.


Testing for Methane SIBO


If you’re being tested for SIBO, make sure your practitioner orders both a hydrogen AND methane breath test. If you have archaea and they are consuming all the hydrogen (explained above), you will have a false negative on a hydrogen test – it will say there is no excess hydrogen gas production when really there is. Bottom line: you could be told you don’t have SIBO when really you do.

While the test interpretations aren’t always ‘black and white’ and are constantly changing, here are the methane numbers we are generally looking for on a three-hour lactulose breath test:
> A combined level of 12-15ppm within 100-120 minutes; or
> Methane measurements of >3ppm at any point during the test if constipation is the dominant symptom (this may be updated to >10ppm in the near future), or >12ppm if constipation is not present.

Methane SIBO Breath Test


Treating Methane SIBO


While I’ve written an entire blog on my approach to treating SIBO, here are the key things you need to consider when treating methane-dominant SIBO specifically. Basically, methanogens are tough critters to kill and you need to work with someone who specialises in SIBO.


Why you need to treat hydrogen SIBO as well


Cutting the food supply to the archaea is an important step in the process. And because archaea feed off hydrogen, this means reducing hydrogen-producing bacteria is critical. After all, the archaea may only be thriving because they have so much hydrogen to consume because of a more traditional bacterial overgrowth.

That is why I generally recommend using antimicrobials that target both bacteria and archaea in the small intestine. This means reducing fermentable carbohydrates and fibre in the diet initially is also a good idea.

Keep in mind though that archaea are hardy and can survive for a while without hydrogen, so killing their food source on it’s own is unlikely to be enough.


Antibiotics for methanogenic archaea


A lot of methanogenic archaea are unfortunately resistant to the majority of antibiotics that are commonly used against bacteria. So the antibiotics that a lot of practitioners would typically use to clear out bacterial infections tend to be ineffective with these types of archaea.

Even the most commonly used antibiotic for SIBO, Rifaximin has reported success rates of around 30% in methane-producing subjects, when used on it’s own. What is promising however, is that the combination of Rifaximin and Neomycin together has produced success rates of up to 87%. So, if you live in a country where these antibiotics are affordable and where doctors are sufficiently aware of current best practice, then antibiotics are still an option for methane-dominant SIBO.

It’s also worth noting that Rifaximin and Neomycin are considered to be narrower in spectrum to more commonly prescribed antibiotics and are not as well absorbed outside the GI tract. That basically means they are less likely to wipe out your gut flora to the extent that other antibiotics might. But with that said, antibiotics definitely aren’t my preference for first line treatment..


Natural Antimicrobials


My preferred first-line approach involves using natural antimicrobials (botanicals). Not only do I find them less aggressive, they have also been shown to be at least as effective as antibiotics in clinical trials for SIBO.

Two important principles to keep in mind when using antimicrobials to eradicate methane SIBO are:
1) Combine to kill – there are varying types of bacteria and archaea that can cause SIBO and not all antimicrobials can kill off all types. The best way to overcome this is through the use of two different herbs for maximum effectiveness.
2) Rotate to avoid resistance – bacteria and archaea are smart and will adapt quite quickly. While not as common as antibiotic resistance, the effectiveness of a given herb tends to diminish with successive rounds.

Most protocols last around 30 days per cycle and vary by the type of SIBO you have. Depending on methane gas levels, more than one round of treatment may be required. In terms of specific herbs, a lot of the research comes from livestock where methane production is a significant environmental concern. So, while not perfect, it does give us some science to back up what we see clinically. My preference for methane SIBO is to use blends and combinations that involve allicin, oregano, neem and/or berberine.




An estimated 75% of bacterial infections, and possibly higher in archaeal infections, involve biofilms. Biofilms are colonies of microorganisms that are protected by an extracellular matrix – which we think of simplistically as a protective home for the infection to live in. This protective home makes the infection up to 1000 times more resistant to antibiotic therapies and therefore, more difficult to kill. This is why a comprehensive antimicrobial SIBO treatment protocol should include the use of a biofilm disrupting agent.




After antimicrobials (or in some cases at the same time), it is often advisable to use a prebiotic, called partially hydrolysed guar gum (PHGG), to help feed good bacteria that are anti-inflammatory, improve transit time and restore balance to the small intestine. Feeding the good guys, such as anti-inflammatory butyrate and bifidobacteria, and encouraging the right balance of flora is an important part of the long-term healing journey. There is obviously a delicate balance here and prebiotics are something that needs to be introduced slowly.

As with many complicated conditions, there is a subset of methane SIBO clients who seem to thrive on prebiotics during and after treatment and those that become very symptomatic, something that is not yet well understood but will hopefully become clearer over time. It just highlights the point that what works for some people, can make things worse for others (and visa versa).


Managing constipation in the short term


We know that methane-dominant SIBO causes constipation. So, while we are treating and healing from our SIBO, what can we do about managing the constipation that comes with it? Simple. We do exactly the same thing that we do for constipation while we are healing any  root cause of IBS-C. We can use magnesium and vitamin C in combination, vitamin C flushing and enemas most commonly. CLICK HERE to access my Constipation e-Guide for all of the detail about these constipation-clearing strategies. The key thing is that the bowel is kept clear as we kill off the overgrowth, so waste, dead bacteria and archaea and the toxins they produce are being removed from the body.


For more SIBO treatment details…


Remember, this isn’t everything you need to treat SIBO, it’s just the highlights of what’s unique to the methanogenic archaea type of SIBO. For my comprehensive post on the latest SIBO treatment options check out this post. It covers off a lot of what we skipped here including:
> SIBO diet considerations
> Lifestyle factors to consider in SIBO treatment
> Specific probiotic strains for SIBO
> The Elemental Diet
> Supporting digestion and detoxification during treatment
> Use of prokinetics and the migrating motor complex
> The importance of healing the gut and addressing root causes to avoid relapse
> And lots more...


Final thoughts on treating Methane SIBO


SIBO, and particularly methane SIBO, is an extremely complex condition. I really encourage you to not waste years of your life taking the trial and error approach. Ask for accurate testing and treat using the most up-to-date science so you can get back to your vibrant and healthy life. I truly hope that the information in this post is helpful so when you commence your healing journey it is a real partnership between you and a practitioner that you trust to help guide you through the process.



Bella Lindemann

Bella is a Certified Functional Diagnostic Nutrition® Practitioner who specialises in working with women with gut infections and associated chronic digestive complaints, fatigue and food sensitivities.

  • Frank Accardo

    July 14, 2017 at 1:55 pm Reply

    Were you prescribed these two antibiotics to treat your SIBO-C? And, if so, did they make you sick? I’m pretty sure I’m suffering from the same thing, but the Neomycin scares me.

    • Bella Lindemann

      August 12, 2017 at 8:17 am Reply

      Hi Frank – I personally did not use antibiotics for SIBO and instead used a combination of natural antimicrobials. This is a similar approach to the one I take with clients currently. Antibiotics can definitely have negative side effects but these are currently considered the best type of antibiotics available for SIBO.

  • Michael Lucero

    July 29, 2017 at 10:55 am Reply

    Hello, one of the biggest problems I have is being able to find the right test for methane bacteria. I have already come up negative on a lactalose breath test but I want somthing sprcific for methane. Which test can I take for this and where.can I take them?
    Thank you,
    Mike Lucero

    • Bella Lindemann

      August 12, 2017 at 8:13 am Reply

      Hi Michael, I typically use Biohealth laboratories in the USA and sibotest in Australia and internationally. If you’d like to book in a consultation ( we can review your health history and past testing and get a methane breath test ordered for you.

  • Anon Ymous

    August 7, 2017 at 9:00 pm Reply

    Hi Bella. My 30 yr old problem is breath that smells like poop. I suspect that it is m. smithii overgrowth as suggested by this article:

    My dental health is impeccable and for brevity I’ll just suffice to say that it is not an “imagined” problem as my GI’s seem to infer…. (I’ve been fired from a job for the problem).

    I’ve given up on hopes for a cure.

    • Bella Lindemann

      August 12, 2017 at 8:22 am Reply

      There is a strong connection between the bacterial health of our intestines and our mouth, which can have an impact on our breath. I would recommend working with a practitioner to identify the specific root cause of your gut dysfunction, develop a tailored treatment protocol and would expect the secondary symptom of bad breath to correct itself over time. This is definitely something that can be fixed so don’t lose hope, and reach out via email if you would like more support. Bella

  • Donita Stoecker

    October 5, 2017 at 1:56 am Reply

    My email doesn’t work on this phone so could you please comment back to me on here please and ty

    • Bella Lindemann

      October 5, 2017 at 3:48 pm Reply

      Hi Donita, I’m am unable to provide personalised health advice outside of a consult sorry. Feel free to book a consult under ‘work with me’ but sounds like you are getting the support you need from a naturopath already. Kind regards, Bella

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