Constipation Methane SIBO Treatment: 2019 Guide

Methane SIBO is its 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 fat-loss resistance, to interpreting test results and choosing interventions, constipation methane SIBO is an extremely complex GI condition and one that is particularly difficult to treat.

Last Updated: July 2019

Here is what we are going to cover in this post:
> What is methane SIBO and the difference from hydrogen SIBO.
> The methane SIBO and constipation connection.
> Testing for methane SIBO and interpretation.
> What diet to use for methane SIBO.
> How is methane SIBO treated - the five different components.
> Methane SIBO herbal treatment considerations.
> Biofilms, prebiotics, probiotics, relapse prevention and lots more… 

As always, we’ve referenced peer-reviewed scientific journals where possible to illustrate the current research. We’ve also relied on our own clinical experience at The Functional Gut Health Clinic working with hundreds of clients who have tested positive for methane SIBO.

What causes Methane SIBO?

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. The specific species of archaea we hear about most, who resides in the GI tract is methanobrevibacter smithii. And if you have an overgrowth of this critter in your small intestine, you most likely have a bacterial overgrowth as well.

Why? When you eat fiber, 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. So they can remain hidden.

Methane SIBO Constipation

Methane SIBO Symptoms

The symptoms of methane-dominant SIBO are often a lot different to those of hydrogen-dominant SIBO. Here are the three main signs we look for to indicate whether a SIBO lactulose breath test for methane SIBO is warranted:
> Constipation: discussed in more detail below, methane gas slows down transit time and causes constipation in most of those who test positive for methane SIBO.
> Bloating and Gas: bloating is probably the most common and noticeable symptom of methane SIBO. While the archaea consume the hydrogen gas which might theoretically reduce total gas volume, our experience clinically is that methane SIBO clients tend to have more sustained bloating. This may be because of the slow motility (constipation) causing the gas to become trapped in the GI tract for longer compared to the more diarrhea-dominant form of SIBO.
> Unexplained weight gain: discussed in detail below, the archaea responsible for methane SIBO are also known as obesogens that help the body extract additional calories from our diet.

The Methane SIBO 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 SIBO 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. SIBO constipation is a difficult cycle to break without the right intervention.

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

This methane SIBO weight gain 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 we see a lot with our clients who have methane SIBO constipation. The good news is it’s fixable.

Testing for Methane SIBO

SIBO Lactulose Breath Test

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 only 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 SIBO test interpretations aren’t always ‘black and white’ and constantly evolving, here are the methane numbers we are generally looking for on a three-hour lactulose breath test:
- A rise of >10ppm over the lowest previous value within 90-120 minutes (depending on the level of constipation); or
- For high baseline methane measurements (>10ppm) that stay high, this may be more indicative of archaea in the large intestine (sometimes referred to as ‘IBS-C positive methane’)

Constipation Methane SIBO Test

Stool Analysis and Microbiome Assessment

When a client presents with the classic signs of methane SIBO, it is rare that we would only order a SIBO lactulose breath test. We would also typically recommend an advanced stool analysis and microbiome assessment for the following reasons:

1. SIBO symptoms overlap with other gut infections and imbalances: the symptoms of constipation, gas and bloating are common to many other GI imbalances and so only relying on a SIBO breath test could result in missing a whole range of other imbalances that need to be considered while addressing methane SIBO. This includes other methane producers like H.pylori as well as levels of beneficial bacteria known for keeping methane in check.

2. Not all methane producers are symptomatic: somewhere between 30-50% of the world’s population are thought to be methane producers, many of whom are not constipated or otherwise symptomatic. This means methane levels alone, may not be the sole reason for symptoms and dysfunction. Identifying or ruling-out other imbalances will help inform the most effective treatment approach to address the underlying root cause of symptoms in each client.

How to Treat Methane SIBO

While we’ve previously written a separate blog on our 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 specializes in SIBO and ideally this particular type of SIBO.

Methane SIBO Constipation Treatment Approach

1. Diet for Methane SIBO

Diet is helpful for two reasons. First, the right diet can help to reduce symptoms in the short-term and lay the foundation for healing. Second, restricting the food supply to the bacteria and archaea responsible for excess gas production is an important part of the methane SIBO treatment process.

While we customize our diet plans to each individual client, here are some of the general things we consider:

Fermentable fiber

Given that archaea feed off hydrogen, what do hydrogen producing bacteria feed off? The answer is: fermentable carbohydrates. This is why diets like Low FODMAP are often used to restrict fermentable fiber content for SIBO. However, for methane SIBO associated with constipation, reducing fiber will often exacerbate constipation. This is not something hydrogen-dominant SIBO sufferers generally need to consider. Less fiber in the diet also lowers Short Chain Fatty Acids (SCFA) like butyrate which have been shown to be inversely related to methane levels and enhance colonic motility.

It is for this reason that we can’t cut out fiber for methane SIBO and why diets like Low FODMAP can cause further issues if not properly adapted. It is important to try and increase fiber and polyphenols where tolerated to help feed up the beneficial bacteria associated with improved motility and methane reduction. Here are a few foods we like to incorporate and prioritize when tolerated:
> Flax seeds
> Berries
> Nuts and seeds
> Brown rice
> Quinoa
> Green tea.

Protein sources

Another consideration is the amount and type of protein being consumed. When reducing carbohydrates, many people replace it with increased quantities of fat and animal proteins. This can be problematic as recent studies suggest excess dietary fat promotes absorption of lipopolysaccharides (LPS). LPS are the endotoxins released by bacteria that can promote inflammation. So, increasing their absorption may contribute to various inflammatory disorders or at least an increase in inflammatory type symptoms. Reducing red meat and adding in vegetarian proteins as tolerated can help.

Soy isoflavones

Isoflavones found in soy products have been shown to reduce methane and hydrogen sulfide production. This is because hydrogen (the food for methane and sulfur-reducing bacteria) is consumed by equol-producing bacteria when a soy isoflavone known as daidzein is converted to equol. This means including lower FODMAP and fermented soy products like tamari, tempeh and miso if tolerated can be a helpful addition to a methane SIBO diet.

2. Eradication options

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 are typically used to clear out bacterial infections tend to be ineffective with these types of archaea.

Even the most commonly used antibiotic for SIBO, Rifaximin (Xifaxan) has reported success rates of around 30% in methane-producing subjects, when used on its own. However, the combination of Rifaximin and Neomycin together has produced success rates of up to 87%. Unfortunately, Neomycin is a broad-spectrum antibiotic known to cause damage to the microbiome. For the last fifty years, it has commonly been used in sterilizing the GI tract, permanently reducing the population of many beneficial bacterial strains. Medical research also demonstrates that neomycin can disturb the intestinal membrane, increasing the risk of other disease states. As such, it may be effective in wiping out SIBO but your gut may not easily or ever recover properly from the impact it has on the microbiome.

It’s worth noting that Rifaximin is considered to be narrower in spectrum to more commonly prescribed antibiotics and is not as well absorbed outside the GI tract. That basically means it is less likely to wipe out your gut flora to the extent that other antibiotics like Neomycin might. But because Rifaximin on its own has low success for methane SIBO and we don’t want to permanently damage the gut with Neomycin, antibiotics definitely aren’t our preference for first line treatment.

Natural HERBAL Antimicrobials

Our preferred first-line approach involves using natural herbal antimicrobials (botanicals). Not only do we 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.

Having treated methane SIBO constipation in hundreds of clients, our preference is to use blends and combinations that include the herbs listed below. We create individual protocols, personalized to each client that both combines and rotates through methane SIBO specific products.

While specific brands and dosages are being updated all the time, our preference for methane SIBO is to use blends and combinations that include the following main herbal ingredients.
> Allicin (Garlic) - Animal study
> Oregano - In vitro study
> Neem - Animal feed study

Elemental Diet

The Elemental Diet is another approach we often consider for particularly stubborn instances of methane-dominant SIBO. If various rounds and combinations of herbal antimicrobials or antibiotics haven’t been sufficiently successful, the Elemental Diet has pretty strong clinical evidence for reducing hydrogen, which we know is a fuel source for methane-producing archaea.

It is basically a liquid diet of predigested nutrients that are absorbed in the upper part of the small intestine. This effectively starves the bacteria in the lower part of the small intestine that is responsible for feeding methane SIBO. Given this also starves good bacteria, it is best used as a last resort and for a short period of time to avoid long term dysbiosis.

While it is possible to make your own, we tend to recommend Physicians’ Elemental Diet by Integrative Therapeutics as it contains a balance of macronutrients, minerals, essential vitamins and electrolytes that can be used as a sole source of nutritional intake for a two to three week period.

A note on SIBO biofilms

An estimated 80% of bacterial infections, and possibly higher in archaea 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 methane SIBO treatment protocol will generally include the use of a biofilm disrupting agent.

Did you know that Bella, Mikaela and Mark all specialize in Methane SIBO Constipation? At The Functional Gut Health Clinic, we specialize in ordering and interpreting SIBO breath tests as well as restoring proper microbiome balance and GI function for those with IBS symptoms.

3. Microbiome Support

Prebiotics for methane SIBO

After antimicrobials (or in some cases, at the same time), it is often advisable to use a prebiotic called partially hydrolysed guar gum (PHGG) that has been shown to reduce methane levels. PHGG helps 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 and Bifidobacteria, and encouraging the right balance of flora is an important part of reducing methane production and long term rebalancing of the microbiome.

Another prebiotic known as Galacto-oligosaccharides (GOS) has also been shown in animal studies to reduce methane levels. In clinical practice, we have found this best to be introduced toward the end of treatment to avoid symptom reactions.

Given many SIBO sufferers react negatively to prebiotics, 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 vise- versa).

Probiotics for methane SIBO

There is both clinical and scientific evidence for probiotics improving constipation outcomes. The challenge is that while certain beneficial bacteria families are helpful, the literature suggests strain, quantity and other ingredients all matter. Bifidobacterium lactis (HN019) strain has been shown to improve transit time while Bifidobacterium infantis (35624) using a product known as Align, actually increased methane levels. In another study, the probiotic Lactobacillus reuteri (17938) had a beneficial effect on chronic constipation via decreases in methane production (as well as hydrogen), including the complete eradication of methane in 11 of the study patients.

As with prebiotics, probiotics for SIBO can be a delicate balance to find. The right strains for the right clients can help significantly but use the wrong product, strain or quantity and you might make symptoms worse. This is an area of research that is constantly evolving, which highlights the importance of working with an expert team who are up to date on the latest science and clinical perspectives on SIBO treatment.

4. Digestive support

Managing SIBO constipation in the short term

We know that methane-dominant SIBO causes constipation. So, while we are eradicating and healing from 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 our 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.

Supporting digestion

Supporting digestion is important for those with constipation SIBO (SIBO-C). When gut function is compromised, short-term use of digestive support products can help keep the system running until balance is restored. The need for these products is assessed individually, but tend to include one or more of the following:

> Stomach acid support - Hydrochloric acid (HCL) can help kick-start digestion in those with low levels, but needs to be balanced against the fact that in high doses, the literature suggests that HCl appears to be a hydrogen donor.

> Digestive enzymes or herbal bitters - help break down food properly to avoid excess fermentation in the gut, thereby reducing excess gas production.

> Support for things like pancreatic enzymes and bile depending on imbalances identified on testing.

Another aspect of supporting digestion relates to rest and stress reduction. This is all about increasing blood flow to the GI tract, and increasing parasympathetic tone in the enteric nervous system (ENS). When the body is stressed it deprioritizes certain functions like digestion in favor of others like blood flow to muscles (to run!). Practically this means trying to be more relaxed, especially before eating, will help digestion. Things like meditation, breathing exercises and yoga can also reduce stress and improve digestion.

Detox and managing SIBO die off symptoms

As bacteria and archaea are killed off, they release endotoxins like lipopolysaccharides (LPS) into the GI tract that typically promote an inflammatory response from the immune system. We’ve written a detailed blog on the science of die-off and common die-off symptoms HERE but in short, the most common SIBO die-off symptoms we see clinically are:
> Fatigue
> Headaches
> Body aches and pains
> Skin rashes or reactions
> Mood symptoms (e.g. anxiety and depression)
> Increased GI upset.

Constipation SIBO Die Off Symptoms

As with other forms of die-off, the key to reducing the severity of symptoms is to:
> Reduce the rate of cell death by titrating in diet changes and supplements slowly.
> Reduce inflammation by getting sufficient rest and using antioxidant and anti-inflammatory supplements.
> Support detox pathways including the liver and using charcoal or clay binders as needed.

There’s lots more detail in our die-off post if you need more support with this.

5. Identifying and addressing your root cause of methane SIBO

While relapsing cases are a common challenge with hydrogen-dominant SIBO, methane SIBO is noted more for its stubbornness/difficulty to treat in the first place. Once its gone though, it tends to stay gone more often than not. Nonetheless, identifying and addressing any underlying root causes of methane SIBO is an important part of the long term gut healing journey. Here are the top root causes we look for, summarized into four main categories:

Physical obstructions

Physical obstructions can impair outflow through the intestines. This means contents, including bacteria are not properly moving through and out of the small intestine, potentially causing an increase in the number of bacteria or archaea (i.e. an overgrowth). The two most common we see in methane clients are adhesions from past GI surgery (cesarean, hysterectomy, etc.) and ileocecal valve (ICV) dysfunction. The ICV is the valve between the small and large intestine. If this is not working correctly and remains open, bacteria from the large intestine may be able to migrate into the small intestine and cause SIBO.

Digestive defects

Proper digestion is part of our body’s immune system and defense against bad bacteria and archaea. If our digestion is impaired, too much or the wrong kind of bacteria may make their way into the small intestine. Digestive markers we look for to assess digestive function include:
> Hydrochloric acid (HCL)
> Pancreatic enzymes
> Bile
> Secretory IgA (sIgA) for mucosal immunity.

We also look for certain symptoms to indicate impaired digestion and cross-reference these with the markers on testing identified above:
> Belching, gas or bloating within one hour of eating.
> Heartburn or acid reflux.
> Halitosis (bad breath).
> Aversion to high protein foods.
> Feeling of excess fullness after meals.
> Greasy or undigested food in stool.

Impaired Motility

While methane gas itself impairs motility, there are other common root causes that are often associated with methane SIBO:

> Migrating motor complex (MMC) autoimmunity - often associated with ‘post-infectious IBS’, this is the result of anti-CdtB and anti-vinculin antibodies attacking the MMC. It is very common in hydrogen SIBO but only affects a small proportion of methane cases.

> Head or whiplash injuries - brain injuries are associated with delayed gastrointestinal emptying due to changes in the autonomic nervous system.

> Hypothyroidism - an underactive thyroid is commonly associated with delayed intestinal transit time.

> Chronic infection - particularly other gut infections that cause chronic inflammation.


Certain medications have side-effects that can affect motility. Some of these include opiates, antispasmodics, immodium and proton pump inhibitors (PPI’s).

Preventing methane SIBO relapse

As discussed above, methane SIBO is generally less susceptible to relapse than hydrogen-dominant SIBO in our experience. It’s also important to understand that at this stage of the methane SIBO treatment process, everything is going to be individually tailored to your specific case, given your test results, response to various treatments, health history, symptoms, etc. That said, here are a couple of general ongoing considerations to incorporate for long-term methane relapse prevention:

Diet diversity and food reintroduction

Bringing back more diversity into your diet will help feed levels of beneficial bacteria and help nurture a more balanced and healthy microbiome. This often needs to be done in a gradual and intentional way, to avoid a flare in symptoms like bloating and gas. If you’re lacking the number or type of bacteria required to break down and digest certain fibers, introducing them slowly will give your microbiome a chance to repopulate these strains.

Introduction and increased use of probiotics and prebiotics

While probiotics and prebiotics can be used as part of the eradication phase, they are sometimes not tolerated well at that time. In these cases, we generally introduce or increase the use of prebiotics and probiotics after eradication. This is to help repopulate a diverse microbiome that keeps methane producing bacteria and archaea in check.

Continued digestive and motility support as needed to keep the colon clear until proper function is restored

If the cause of your constipation is methane alone, clearing methane SIBO will likely eliminate this problem. However, if your constipation was merely exacerbated by methane SIBO, then keeping the colon clear while we identify and rebalance additional root causes is of continued importance. For some clients who have been chronically constipated for years (or decades), the body needs a little bit of time and support to get into the flow of unassisted and regular bowel movements.

Explore additional root causes if methane levels are reduced but some symptoms remain

SIBO is only one of the many root causes for IBS type digestive symptoms. In many cases, we find additional infections and imbalances on advanced stool testing that also need to be addressed. Clients who’ve had a previous clear (negative) stool test will often find new pathogens showing up on retesting, likely because they have removed biofilms during SIBO treatment. It means those other infections were probably there all along, they just didn’t show up on testing because they were hiding in the biofilm. Where this occurs, it is important to address these additional root causes for long term symptom resolution and gut healing.

Why you might need to treat hydrogen SIBO as well

The archaea responsible for methane SIBO feed on hydrogen as a fuel source. The chemical formula for methane is CH₄, which is one atom of carbon and four atoms of hydrogen. That means if you are producing methane in high numbers, you were likely also producing hydrogen in even higher numbers, it was just being consumed by the archaea and turned into methane. The diagram below illustrates how for every one methane, you need four hydrogens (which don’t show up on SIBO testing).

SIBO hydrogen hides methane

That is why we generally recommend using antimicrobials that target both bacteria and archaea in the small intestine. Addressing hydrogen-producing bacteria means cutting the food supply to the archaea. After all, the archaea may only be thriving because they have so much hydrogen to consume because of a more traditional bacterial overgrowth.

Depending on the size of the bacterial overgrowth and the treatment approaches used, it is possible to be left with elevated hydrogen levels after treating methane. If this occurs, the next round of antimicrobials and diet intervention can be targeted specifically to the hydrogen-producing bacteria.

Work with our practitioners to treat Methane SIBO constipation

SIBO, and particularly the methane type, is an extremely complex condition. We really encourage you to not waste years taking the trial and error approach. Ask for accurate SIBO testing and treat using the most up-to-date science so you can get back to your vibrant and healthy life. We 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 methane dominant SIBO and other root causes of IBS symptoms.

For more SIBO treatment information...

We’ve also written a three part series on SIBO. They cover:
> 1. Overview of SIBO
> 2. SIBO Testing
> 3. SIBO Treatment

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Methane SIBO Constipation Natural Herbal Treatment

About author: Bella Lindemann, FDN-P

Bella Lindemann is the founder and lead practitioner of The Functional Gut Health Clinic. With her science degree, functional nutrition certification and extensive experience, she is a recognised expert in gut health and the science of SIBO. Having worked with hundreds of methane SIBO cases, including her own, she is passionate about helping her clients address this imbalance and take back control of their digestive symptoms.