Constipation Methane SIBO Treatment: 2019 Guide

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, constipation methane SIBO is an extremely complex GI condition and one that can be more challenging to treat.

This post is targeted to methane dominant SIBO. If you’re looking for more comprehensive small intestinal bacterial overgrowth 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 methane 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, this 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 SIBO and 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. This is the methane SIBO and constipation connection.

While you might think SIBO and constipation is preferable to diarrhea, 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, diarrhea 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 and constipation.

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 SIBO 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 >10ppm at any point during the test if constipation is the dominant symptom, or >12ppm if constipation is not present.

Constipation Methane SIBO Test

Did you know that I and my colleague Mikaela specialise in organising and interpreting SIBO breath tests as well as restoring proper microbiome balance and GI function to those with IBS symptoms?

Methane SIBO Treatment

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

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 its 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 SIBO sufferers, when used on its 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 methane SIBO treatment.

Natural Herbal Antibiotics for Methane SIBO

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

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 methane SIBO and not all antimicrobials can kill off all types. The best way to overcome this is through the use of two different herbal antibiotics 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 herbal antibiotic tends to diminish with successive rounds of SIBO treatment.

Most SIBO treatment 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 methane SIBO 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.

Biofilm and Methane SIBO Treatment

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. I have written a whole blog post on biofilms here. 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 natural herbal antibiotic methane SIBO treatment protocol should include the use of a biofilm disrupting agent.

My current preferred natural biofilm disruptor is Biofilm Defense by Kirkman Labs. I typically prefer blends for treating biofilms and have had success using the unique matrix-dissolving enzymes in Biofilm Defense. As with all supplements, I recommend only using this kind of product under the guidance of a skilled functional practitioner, however they are available on Amazon and iHerb.


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 producers such as 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 SIBO and 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 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. Healing SIBO is a journey. If you are ready to begin yours, please head to the Work With Us page to learn more about how we work online with clients in many countries to treat SIBO and other root causes of IBS symptoms.