Mastering Methane SIBO: Your Ultimate Guide to Relief

Grace Clark-Hibbs

March 21, 2024

We often hear about SIBO in the generic sense – like it’s a one-size-fits-all diagnosis. But it’s more nuanced than that. In fact, there are three known types of SIBO – methane SIBO, hydrogen SIBO, and hydrogen-sulfide SIBO – and each type should be approached a little differently.

In this article we’ll dive into what methane SIBO is, how it compares to the other types, some possible root causes, and (most importantly) how to find relief.

No stone goes unturned here, let’s dig in!

What is SIBO?

SIBO, or small intestinal bacterial overgrowth, is defined as a condition in which there is an altered number and type of microbes in the small intestine. (1, 2

A “normal” or “healthy” small intestine should be almost sterile, with very few microbes living in it, because this is where the majority of our food is digested and absorbed. This makes our small intestine a great feeding ground for bacteria and other microorganisms, allowing them to grow out of control. 

If left untreated, this overgrowth can result in uncomfortable gut issues (like bloating, constipation, diarrhea, and gas), nutrient deficiencies, and even damage to the mucosal lining of the digestive tract.

To learn more about SIBO in general, including more info on the other types of SIBO (hydrogen and hydrogen-sulfide), check out our comprehensive article here.

What is methane SIBO?

Methane SIBO is often considered the “second phase” of SIBO. 

Phase one occurs when overgrown bacteria produce hydrogen from fermenting carbohydrates in the small intestine. This is followed by phase two, which occurs when the methane-producing microorganisms consume the hydrogen and produce methane as a by-product.

Until recently, the term “methane SIBO” has been used to describe the type of SIBO that is usually characterized by slow motility and constipation, which is caused by methane-producing bacteria. 

As we’ve learned more about this condition, we’ve learned that the type of microbes responsible for producing methane in the gut are actually called archaea and are not bacteria at all. (3)

Archaeons are similar to bacteria in that they are microorganisms that make up part of the human gut microbiota, but they are evolutionarily different. Research has also shown that these archaeon can overgrow in areas outside of the small intestine. (3

Because of these two discoveries, scientists and medical professionals have shifted towards using the term intestinal methanogen overgrowth, or IMO. For the purposes of this article however, we will continue to use the more well-known term, methane SIBO.

Why does it cause constipation?

As previously described, methane production has been directly linked to slow gut transit time, which leads to constipation. To put it simply, the longer it takes for food to move through the digestive system the less frequent bowel movements will be. 

One mechanism to explain this experience is that methane appears to trigger a pathway that blocks acetylcholine from binding to the appropriate nerve cell receptors along the digestive tract. This blockage results in the muscles of the GI tract not contracting and releasing as they should, which leads to slow gut motility and constipation. (3, 4)

Methane SIBO symptoms

Symptoms can vary from person to person, but the most common symptoms of methane SIBO include: (1, 3)

  • Constipation (hard, pebbly stools and/or less than 1 complete bowel movement per day)
  • Incomplete emptying (when you have a bowel movement that isn’t satisfying or it feels like you didn’t get everything out)
  • Bloating
  • Trapped gas
  • Foul/methane smelling gas
  • Food sensitivities
  • Abdominal pain
  • Nutrient deficiencies (like B12)
  • Fatigue
  • Brain fog
  • Probiotics make symptoms worse at first
  • Undigested food in stool 

Less common symptoms include:

  • Rashes
  • Strong body odor (sometimes described like a “barnyard smell”)
  • Dark circles around the eyes

What are the root causes?

Developing methane SIBO or IMO is completely dependent on how the gut was colonized at the very beginning of life. This is because the microorganisms that make up a newborn’s gut are quickly changing in their early days of life and are influenced by a variety of factors. 

These factors include the mother’s diet, how the baby was delivered (C-section vs. vaginal birth), whether their breast fed or formula fed, if the mother or infant have taken antibiotics, and whether there are pets or siblings in the home. (5)

As we learned earlier, methane in the gut is produced by archaea, but these microorganisms don’t show up until about 3 years of age and don’t show up for everyone. This means that not everyone has the capability to produce methane or to develop methane SIBO.

One study found that about 47% of patients who tested positive for SIBO had methane dominant SIBO. (6)

Now, just because you have archaea present in your gut doesn’t mean you’re going to develop methane SIBO. Diet, lifestyle, and other medical diagnoses also play an important role. Other potential root cause include: (1, 7, 8)

  • Limited diet, especially if it’s low in plant fibers
  • Low stomach acid
  • Slow gut motility
  • Chronic stress (including not getting enough sleep)
  • Chronically overexercising
  • Not eating enough
  • Poor digestion (i.e. low enzyme secretion, poor bile flow, poor detoxification)
  • Blood sugar imbalances
  • Poor meal hygiene (i.e eating too quickly, not chewing enough, eating while distracted, etc.)

Additional risk factors include: (1, 9, 10)

  • Migrating motor complex (MMC) abnormalities 
  • Ileocecal valve dysfunction (the valve between the small and large intestine)
  • Diabetes
  • Adhesions (abdominal trauma, endometriosis)
  • Gallbladder removal
  • Structural issues (bowel resection, fistulas)
  • Gastrectomy
  • Hypothyroidism
  • Drug side effects (like proton pump inhibitors – Nexium, Prilosec – and hormonal birth control)
  • Chronic alcohol consumption

How to test for methane SIBO

The gold standard for SIBO testing is a small intestine aspirate and fluid culture. The process involves collecting a sample of fluid from the small intestine, however it’s rarely used because of how expensive and invasive it is. (1)

The most common way of testing for methane SIBO, and SIBO in general, is a glucose or lactulose breath test. These tests involve the patient ingesting a glucose or lactulose solution and collecting exhaled air samples over 2-3 hours. These samples are analyzed for the presence of hydrogen and methane gas at various times post ingestion. (1, 4)

A positive methane SIBO breath test should yield greater than or equal to 10 ppm (parts per million) methane gas in 90 minutes or greater than 10 ppm at any time during the collection process.

How do you get rid of methane SIBO?

The overall process for getting rid of methane SIBO or IMO involves first identifying and starting to address the root causes, establishing some foundational diet and lifestyle habits, and simultaneously killing off the “bad” microorganisms and replenishing the “good” ones.

The final, and possibly most important, step is the repair phase. This is the phase that makes sure the SIBO does not return. The focus is on continuing to develop a diverse and thriving microbiota, making sure the gut lining is healthy and sealed (i.e. no “leaky gut”), and ensuring the foundational habits are still in place. 

Methane SIBO is a little more challenging to treat because multiple steps are involved in its development, which means treatment takes longer. It can also be more challenging to increase transit time versus slow it down (i.e constipation vs. diarrhea).

It won’t be possible to address the methane production until the bowels are moving and fully emptying consistently and this can take some troubleshooting. 

Treatment options:

There are three treatment options for methane dominant SIBO that we’ll cover in this article. These include antibiotics, herbal remedies and natural approaches, and how to use probiotics and motility agents in the treatment process.


Rifaximin is the primary pharmaceutical used to treat SIBO today because it has the most research to support its effectiveness. It’s a GI-selective antibiotic, meaning it stays in the gut and is not absorbed systemically. It also does not appear to negatively impact the “good”, or healthy, bacteria in the gut. (11) A round of rifaximin treatment usually lasts about 7-10 days depending on the dose. (12

However, the efficacy of rifaximin on long-term elimination of SIBO, especially methane dominant SIBO, is low. One study found that up to 40% of patients with SIBO-like symptoms did not feel better after a round of antibiotics. (1

And another study found that 47% of participants (35 out of 80) had a recurrence of their SIBO nine months after a week-long treatment of rifaximin. (13

Herbal remedies and natural approaches:

There are a wide variety of herbal treatment options available and the combination of these herbs should be customized to the specific needs of the client. They are also more broad-spectrum than antibiotics. Meaning they can get rid of bacteria, viruses, fungi, and parasites, which is helpful for clients who struggle with more than one type of overgrowth. Treatment length will vary depending on the types of herbs being used, but will typically last between 4-12 weeks. 

The most common herbal supplements for SIBO include Candibactin-AR and Candibactin-BR (used together) and Biocidin. Each of these are made of a different blend of herbs that include antimicrobial herbs such as garlic oil, oregano oil, red thyme oil, and berberine. (14)

Methane SIBO requires an additional layer of support. Atrantil is commonly used for methane SIBO because it helps eliminate the hydrogen that gets consumed and turned into methane. It also helps get rid of the archaea in the small intestine all together. Peppermint, quebracho extract, and horse chestnut are the primary ingredients in Atrantil. (15)

These supplements are recommended as part of an overall SIBO treatment protocol that includes addressing the root cause, targeted supplements, and diet and lifestyle recommendations.


Probiotics can’t be used to treat methane SIBO, or any type of SIBO for that matter, on their own but they can be excellent tools in the toolbox. In fact, they can be especially helpful for addressing the underlying, or root, causes.

At its core, SIBO is an imbalance of “good” and “bad” gut bugs, where the “bad” are outnumbering the “good”. So, repopulating the beneficial bacteria via probiotics and food is one of the things a thorough SIBO treatment protocol will include.

One of my mentors, Dr. Heather Finley, MS, RDN, LD, likes to refer to the whole gut microbiota as a garden, the healthy gut bugs as flowers, and the overgrown gut bugs as weeds. In an active SIBO infection, the garden hasn’t been tended to in awhile and the weeds outnumber the flowers. 

So in order to get the “garden” into shape (i.e. get rid of the SIBO), we have to go in and pull the “weeds”, making room for the vibrant, beautiful “flowers” to grow and flourish. This usually includes planting some new “flowers” in the form of probiotics, so there’s a nice variety – each one bringing their own special flare.

Research shows that probiotics can be effective at reducing SIBO symptoms and can help reduce some of the long-term impacts of a SIBO infection. They have even been shown to enhance the impact of various treatment methods, including prescription antibiotics. (1)

That being said, the type and dose of probiotic matters. One study found that probiotics triggered an increase in symptoms including bloating, gas, and brain fog. And another study found that one month of probiotics actually increased methane production as measured by a lactulose breath test. (1)

Given these conflicting results, additional research needs to be done in order to understand the role probiotics should play in SIBO treatment. This is why it’s important to work with an experienced practitioner to make sure you’re not making the situation worse.

Motility agents

Similar to probiotics, motility agents can’t get rid of SIBO on their own, but they can help address the constipation and slow motility that often accompanies methane SIBO. 

It’s common to get stuck in a vicious cycle where the slow motility leads to fermenting carbohydrates, which leads to the hydrogen-producing bacteria to grow, which leads to archaea consuming hydrogen and producing methane as a byproduct, which leads to even slower motility. 

infographic explaining each step of how methane SIBO develops, called the methanogen overgrowth cycle

If you find yourself stuck in this cycle, a great place to start is by using natural motility agents, such as ginger. Try drinking ginger tea 2-3 times per day between meals. This will also increase your daily hydration, which is an important piece of constipation and motility as well.

Lifestyle approaches to support treatment

An effective SIBO protocol should always include recommendations around lifestyle. This is for a variety of reasons, but a big one is because stress is such a common root cause. If you’re not ready to invest in support, implementing some or all of these strategies is a great place to start.

Some examples of lifestyle approaches that will support treatment include: 

  • Intentionally addressing stress daily
  • Implementing good meal hygiene (i.e. allow 20 min to eat a meal, chew food to applesauce-like consistency, don’t eat while distracted or on-the-go)
  • Taking 4-5 deep breaths before starting to eat
  • Getting 8-9 hours of sleep every night
  • Getting 5-10 minutes of daylight on your face each morning to regulate circadian rhythm
  • Supporting the body’s natural detoxification pathways by:
    • Sweating
    • Daily complete bowel movements
    • Staying hydrated

Can you treat methane SIBO with diet alone?

It is not possible to treat methane SIBO with diet alone. Once the microbes have infiltrated the small intestine, they will continue to grow and cause problems until they are removed with antibiotics or herbal antimicrobials. 

That being said, there are a few “SIBO Diets” that have gained popularity in the SIBO treatment world, so we will go into what they are, why they’re recommended, and what role they can play in the treatment process.

The Low FODMAP Diet

The Low FODMAP Diet is the most well-known diet recommended to help people who struggle with IBS or any sort of uncomfortable gut symptoms. FODMAP is an acronym for a group of sugars, or carbohydrates, that are not completely digested or absorbed in the intestines. 

This can cause things to slow down in the small intestine and eventually ferment when they reach the large intestine. All of this can lead to extra water being pulled into the gut and excess gas being produced by fermentation, which can cause abdominal discomfort and even pain. (16)

The Low FODMAP Diet was developed as an elimination diet, which means high FODMAP foods and ingredients are removed from the diet for a set period of time (usually 2-6 weeks). Then the same foods are slowly reintroduced (usually over 8-12 weeks) in order to identify which specific foods are triggering the symptoms. The whole process should be supervised by a health professional who specializes in it.

The reintroduction phase is probably the most important part of the diet plan but unfortunately, this diet is often presented to anyone who struggles with gut issues as a “forever diet”. They are also not given much support as they navigate this huge lifestyle change. This can leave people feeling confused, very limited in what they can eat, and frustrated when their symptoms don’t go away completely.

Since between 40-80% of people with IBS also have an abnormal SIBO breath test or increased bacterial counts (11), the Low FODMAP Diet is not going to help everyone. 

It can, however, be used to help relieve some discomfort in the short-term, but it will not get rid of overgrowth on its own. This is why it is so important to work with a practitioner who is familiar with both IBS and SIBO.

The Bi-Phasic Diet

This diet plan was developed by a prominent doctor in SIBO research and treatment, Dr. Nirala Jacobi. It was created as a two-phase diet plan that was intended to be implemented alongside an antibiotic or herbal antimicrobial treatment protocol.

Phase 1 is intended to “starve” the overgrown bacteria and lasts 4-6 weeks. The idea is to start relieving symptoms and reducing the bacterial count before any antibiotics/antimicrobials are introduced. Most forms of carbohydrates and sugar are eliminated in this phase.

Phase 2 of the diet starts when the antibiotics/antimicrobials start and lasts another 4-6 weeks. This phase is slightly less restrictive so that any remaining bacteria can grow a little bit before being eliminated by the antibiotics/antimicrobials.

Similar to the Low FODMAP Diet, the Bi-Phasic Diet is intended to be followed short-term while under the supervision of an experienced practitioner. It’s also not a treatment plan on its own. To learn more about this diet plan, head over to our comprehensive article.

The Specific Carbohydrate Diet

This diet was originally developed in the 1920s to help children with celiac disease. It then became mainstream in the 1980s when it was marketed as a diet that could improve inflammatory bowel disease (IBD) symptoms.

It involves eliminating a select group of carbohydrates from the diet, including grains, grain products, some legumes, added sugars, processed meats, canned vegetables, starchy vegetables, and some spices like curry, garlic, and onion. (17)

Again, the idea is to eliminate these foods for a set period of time and then to slowly reintroduce them, one thing at a time, to see what the individual triggers are. The Specific Carbohydrate Diet may help with symptom relief, but it can not be used to treat methane SIBO on its own and should only be followed under the supervision of a healthcare professional.

Elemental Diet

This is a meal-replacement diet that contains all the essential nutrients for survival broken down into their simplest forms. For example, proteins are in the form of amino acids, carbohydrates are in the form of short-chain maltodextrins, and fats are in the form of short-chain fatty acids. 

The elemental diet requires you to only consume powdered, predigested nutrients mixed with water for 2-4 weeks and nothing else. The idea is that the nutrients will be completely absorbed at the beginning of the small intestine and not be available to feed any of the bacteria downstream – essentially “starving” them out.

This is the only diet plan listed here that has been specifically studied as a treatment option for SIBO, however the recurrence rate after returning to a normal diet is not well documented. If even one bacteria remains in the small intestine after treatment, it will multiply and cause a relapse as soon as regular food is eaten again. It’s also very expensive (~$50 per day) and not a realistic option for many.

What foods should you avoid with methane SIBO?

There are no specific foods you need to avoid if you’ve been diagnosed with methane SIBO, but there are foods that may aggravate your symptoms in the short-term. 

Foods that can slow down motility even more include:

  • Dairy (especially cheese) 
  • Alcohol
  • Raw vegetables and fruit (focus on soft, very well cooked vegetables)
  • Gluten-containing grains (start by switching to sprouted grains or sourdough before completely eliminating gluten)

A better approach to take is to ask yourself, “what can I (comfortably) add to my diet to help my gut in the long-term”. It may be hard to think about adding in new foods right now, but a diet that is full of variety, especially plant variety, is what leads to a healthy gut that is resilient to overgrowth.

Are there side effects of treatment?

Side effects of treatment are minimal, but can involve a set of symptoms commonly referred to as “die off symptoms”. 

Die off symptoms are not experienced by everyone and will often include things like increased bloating, gas, and changes to bowel movement consistency and frequency. They can also include flu-like symptoms such as chills, headache, low energy/fatigue, and mild fever.

That being said, there are two things to consider when deciding between antibiotic and herbal remedies. First is the impact antibiotics may have on the healthy gut flora. Rifaximin is believed to be a targeted antibiotic and therefore have minimal impact on the “healthy” bacteria in the gut, but the existing research cannot definitively confirm this. 

Second is the possibility of developing antibiotic resistance with multiple rounds of antibiotic treatment. While these are not traditional side effects, they are effects that can happen as a result of treatment. 

If you’d like to learn more about SIBO die off symptoms and how to prevent them, check out this article.

How do I prevent a methane SIBO relapse?

The number one way to prevent a relapse is by addressing the root cause or causes. As discussed earlier, these can include low stomach acid, chronic blood sugar imbalances, slow gut motility, hormonal imbalances, chronic stress, etc. 

Next, is to make sure the treatment protocol ends with a repair phase. This is essential to preventing a relapse because it’s not enough to just remove the overgrown microbes, it’s also important to reverse the damage that was done.

This includes continuing to build the gut immune system, continuing to support any issues with digestion (i.e. low stomach acid, poor enzyme secretion, sluggish gallbladder, etc.),  supporting the gut lining, and repairing any “leaky gut”. 

The repair phase will also include promoting overall bacterial balance through long-term dietary and lifestyle recommendations. These will include:

  1. Having a diet that is full of variety, especially plant variety (shoot for 30 different plant foods in a week).
  2. Consuming probiotic- and prebiotic-rich foods to promote short chain fatty acid (SCFA) production. SCFAs are the byproducts of probiotic bacteria consuming prebiotic fiber and have anti-inflammatory effects in the body.
  3. Daily stress management strategies. Start with meals and expand from there. For example:
    1. Make sure you’re allowing time to eat in a calm and relaxed environment.
    2. Set an alarm at 4 different times throughout the day in which you intentionally tune into how you’re feeling and ask yourself what you need. This doesn’t have to take long, even a few minutes a day of this practice will make a huge impact.

Lastly, it’s important to understand how to manage and troubleshoot your symptoms going forward. For example, do you know what to do when you’re feeling constipated? What about when an unexpected stressful life event happens – do you have strategies in place so you don’t fall back into old patterns?

infographic that explains the four essential steps for preventing a methane SIBO relapse

Work with your practitioner to identify what strategies are the most effective for you and have those in your back pocket, ready to go when needed.

Still stuck?? Try this…

First thing’s first, get support.

If you’ve been on several rounds of antibiotics or herbal antimicrobials and your SIBO keeps coming back, it’s time for a more comprehensive and holistic approach. This may include additional testing, such as stool testing, tissue mineral analysis, and/or hormone testing.

It may also include supporting and retraining the nervous system, which is a common missing piece for many. If you’re consistently in a state of “fight or flight”, your body won’t be able to put enough energy towards healing your gut. 

Finally, the healing process may involve having some difficult conversations with yourself about what is causing the most stress in your life – is it a difficult job or an unhealthy relationship? Are there bigger changes that need to happen in your life in order to fully heal? These are questions that only you can answer.

Final thoughts

In general, methane SIBO develops after something triggers the gut motility to slow down. This leads to carbohydrates fermenting in the intestines, which leads to bacteria consuming the fermented carbs and producing hydrogen gas. 

Finally, microorganisms called archaea will consume the hydrogen gas and produce methane as a byproduct. The presence of methane slows down gut motility even more and perpetuates a vicious cycle that can be challenging to break.

The key to getting rid of methane SIBO for good is identifying and addressing the root causes, taking a holistic approach to treatment (i.e. not just taking a round of antibiotics or antimicrobials), and working with a health professional who is experienced with SIBO. 

If you’ve been struggling with SIBO, bloat, constipation or other IBS symptoms and need some insight into your root causes, check out my Why Am I STILL Bloated Quiz!

pinterest image with a woman leaning against the wall with her other hand holding her stomach in pain

Remember: this post is for informational purposes only and may not be the best fit for you and your personal situation. It shall not be construed as medical advice. The information and education provided here is not intended or implied to supplement or replace professional medical treatment, advice, and/or diagnosis. Always check with your own physician or medical professional before trying or implementing any information read here.

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Grace sitting

Hi, I’m Grace!

A registered dietitian & gut health expert based in Portland, OR with my husband & orange tabby, Tony.


And I’ve been in your shoes!


As someone who has struggled with my own severe, chronic, & painful bloat & constipation for over 15 years, I understand what it’s like not to get answers from conventional medical support.


This is why I’ve made it my mission to help everyone who feels held back & defeated by their gut find freedom from their embarrassing symptoms FOR GOOD!

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Why am i STILL bloated?!?


Uncover the root cause of your persistent, uncomfortable bloat with this 10 Question Quiz!

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