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Dealing with Bloating, Constipation and Other IBS Symptoms? The Root Cause May Be Methane SIBO

If you're struggling with chronic bloating, constipation, and other IBS symptoms like flatulence, abdominal pain, and diarrhea, you've probably tried a whole host of remedies to make your digestive system happier. Maybe you upped your fiber intake or started carrying a water bottle so you could keep yourself optimally hydrated. In desperate times, you might even have used over-the-counter or prescription medications like laxatives. However, none of these treatment options will resolve your issues if you don't identify the root cause producing your problems. One explanation to consider is a condition called methane SIBO. 

Here's what you need to know.

What Is Methane Sibo?

Methane SIBO is an extremely complex GI condition that's also highly difficult to treat. The hardest thing about treating hydrogen-dominant SIBO is that it often reoccurs. Methane-dominant SIBO, on the other hand, tends to stay gone once it's been dealt with, but it can be incredibly stubborn and treatment-resistant.

Before getting into the specifics of methane SIBO, let's cover some basics about the gut microbiome so you can get a better handle on how this gastrointestinal disorder disrupts the status quo. 

Maintaining the right balance of bacteria in your digestive tract is absolutely crucial. When too much bacteria accumulates in the small intestine, this can produce that all-too-familiar collection of GI symptoms. Experts refer to this condition as small intestinal bacterial overgrowth (SIBO). As scientists have learned more about the microbiome, they've begun to suspect that SIBO could be related to irritable bowel syndrome (IBS)

How Common Is SIBO?

It can be tricky to get reliable statistics on the number of people who have SIBO. One way to get a sense, according to experts, is to look at the rates of SIBO among patients with IBS, which range between 30% and 80%. 

According to Dr. Hazel Veloso, a gastroenterologist at Johns Hopkins University in Baltimore, the common opinion among medical practitioners used to be that SIBO is quite rare. But now, physicians have found that it's a frequent underlying cause of IBS.

Increased knowledge of SIBO has led to more effective treatment. An absolutely essential part of developing an effective treatment plan, however, is differentiating between methane-dominant SIBO and the more frequently occurring hydrogen-dominant SIBO.

Methane-Dominant SIBO vs. Hydrogen-Dominant SIBO

It can be hard enough to diagnose hydrogen-dominant SIBO, due in part to the misattribution of top symptoms such as:

  • Diarrhea
  • Gas
  • Bloating
  • Abdominal pain
  • Cramping
  • Food intolerances
  • Fat malabsorption
  • Skin rashes

Methane-dominant SIBO is even more difficult to catch. While some symptoms of methane-dominant SIBO overlap with those of hydrogen-dominant SIBO, there are important differences, and the treatments used for one will not necessarily work for the other.

Perhaps the most significant difference in terms of symptoms is that it's rare for hydrogen-dominant SIBO to cause constipation, while that's one of the top symptoms associated with methane-dominant SIBO. 

As we'll go over in more detail in the next section, higher methane gas levels mean a slower transit time for food through the digestive tract. Individuals with methane SIBO also tend to have bloating more often and for longer periods than those with hydrogen SIBO. One theory to explain this is that gas gets trapped along with partially digested food in the digestive system. 

Another telltale indication of methane SIBO is unusual weight gain—more on that to come, but the basic idea is that the same imbalances that led to high methane gas levels also cause the body to take in more calories from the food we eat.

What Is Methane SIBO?

What Causes Methane SIBO?

Each time you eat foods that contain indigestible fibers, gut bacteria ferment them, producing hydrogen. Then, single-celled organisms called archaea feed off hydrogen, producing methane. The body expels excess methane via flatulence or exhalation.

If methane levels rise too high, unpleasant symptoms like bloating, constipation, abdominal pain, and more can occur. Gastroenterologist Allen Lee, M.D. of the University of Michigan and other experts can't say for certain why high methane levels cause these issues for some people but not others, but they think factors include:

  • Diet
  • Genetics
  • Illness (particularly GI infections and autoimmune conditions)
  • Medication use

Though methane SIBO is not a new disease, physicians have massively increased their understanding of what conditions make someone more likely to develop it. According to Dr. Jack A. Di Palma, a professor of medicine as well as the director of the gastroenterology division at the University of South Alabama College of Medicine, doctors used to think SIBO occurred due to scleroderma (a disease that causes progressive hardening of your skin and connective tissues) or post-surgical structural problems. Now, they realize that the kinds of medications a person takes—for instance, antibiotics or narcotics—can throw off the balance of gut flora. 

The small intestine keeps its bacteria population balanced via two main mechanisms: well-timed passage of food (clinically, this is called motility) and acidity. So, if something affects motility, as opioid painkillers such as Vicodin do, or acidity, as proton-pump inhibitors (PPIs) do, then that puts someone at increased risk for methane SIBO. 

There are three main areas that causes of methane SIBO fall into:

  1. Physical abnormalities
  2. Digestive defects
  3. Impaired motility

Physical Abnormalities

The most common physical abnormalities associated with methane SIBO are: 

  1. Scar tissue created by past GI surgeries, like a cesarean or hysterectomy 
  2. Dysfunction of the ileocecal valve (ICV)

The ICV valve links the small and large intestines. If it's not able to close properly, bacteria from the large intestine may be able to travel into the small intestine where it can cause all types of problems, including SIBO.

If scar tissue creates obstructions in your intestines, it can become very difficult for digested food to make its way out of the body. The longer food lingers in the small intestine, the more likely it is that an overgrowth of archaea will occur.

Digestive Defects

Your digestive system is a fine-tuned machine, and when one part of it isn't working to full capacity, issues can get big, quick. 

Some symptoms that indicate a digestive defect include:

  • Belching, gas, or bloating within an hour of eating a meal
  • Acid reflux
  • Bad breath
  • Feeling of excessive fullness after eating
  • Visibly undigested food in stool

To diagnose a defect, doctors cross-reference your symptoms with levels of different markers of digestive function, such as:

  • Hydrochloric acid (HCL)
  • Pancreatic enzymes
  • Bile
  • Secretory IgA (sIgA)

Impaired Motility

High levels of methane gas slow motility, but in many cases of methane SIBO, there's another reason that the time it takes food to move through the intestines has increased. Some examples include:

  • Brain injuries: Both direct head injuries as well as whiplash injuries can cause changes to the autonomic nervous system that result in delayed gastric emptying. 
  • Hypothyroidism: When the thyroid isn't performing at full capacity, slower intestinal transit time can result. 
  • Chronic inflammation and infections: Systemic inflammation and infections can have a cascade effect; however, those that affect the GI tract itself are the most problematic. 

Can Methane SIBO Cause Other Health Issues?

The purpose of the archaea in the small intestine is to decrease the amount of hydrogen gas. As we explained earlier, having too much hydrogen gas in the small intestine produces the seriously unpleasant constellation of symptoms associated with hydrogen-dominant SIBO. However, too much methane gas can be just as bad, though in different ways.

Some people, clinically termed "methane producers," have overactive intestinal methanogens. According to one study, those individuals are more likely to have GI issues like irritable bowel syndrome and chronic constipation. 

The study authors think methane might slow down the transit time for food in the digestive tract. This, in turn, causes constipation. And chronic constipation has been linked to the overgrowth of bad bacteria in the small intestine. More bad bacteria equals more methane equals more constipation, and thus a cycle is created that can be almost impossible to break.

Along with chronic constipation, severe cases of methane SIBO can cause additional problems, including:

Let's talk more about weight gain linked to methane SIBO. Scientists have found that the presence of high levels of methane on a breath test often corresponds with obesity. They think this connection stems from two factors: first, that the archaea responsible for producing methane also shift your body into a mode in which it absorbs more calories, and second, that (as we've established) it slows transit time, which can also increase the number of calories the body takes in. 

Let's break both those ideas down a bit more. 

Researchers have found that the archaea can change the way your gut bacteria digest a certain kind of carbohydrate, which subsequently increases the number of calories you absorb. And the more calories you absorb from the food you eat, the higher the odds you'll gain weight. 

Studies also show that methane gas slows the time it takes food to move through the small intestine. The longer the amount of time spent there, the more calories can be extracted. Again, the more calories taken in, the more opportunity to accrue extra pounds.

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

How to Know If You Have Methane SIBO

If your primary care physician suspects your symptoms may stem from methane SIBO, they will probably refer you to a gastroenterologist. 

To diagnose methane SIBO, most gastroenterologists use breath testing to immediately distinguish between methane-dominant SIBO and hydrogen-dominant SIBO, so long as they analyze the results to look for both methane and hydrogen abnormalities. Otherwise, someone with methane-dominant SIBO may get a false negative. 

There are two different breath testing options: the lactulose breath test and the glucose breath test. Doctors tend to prefer one or the other, but both are quite accurate. Dr. Hazel Veloso, a gastroenterology faculty member at Johns Hopkins University, opts for the lactulose breath test more often as she finds the glucose breath test results in more false positives. However, Dr. Stephanie Hansel, a gastroenterologist at the Mayo Clinic feels glucose breath testing is a better option for most patients and only uses lactulose breath testing for those with diabetes.

The methane numbers observed on the breath test help doctors get a better sense of what might be causing a patient's symptoms. If a person has a rise of more than 10 ppm of methane over from the lowest previous value within 90 to 120 minutes of the administration of the test, they most likely have methane SIBO. However, if someone has baseline measurements of more than 10 ppm that remain elevated, that points to the presence of archaea in the large intestine, which corresponds to a slightly different diagnosis (IBS-C positive methane).

Other Tests Used to Confirm a Methane SIBO Diagnosis

Some doctors like to follow up a breath test with other diagnostic tests, such as an advanced stool analysis and a microbiome assessment.

As we've already discussed, the symptoms of methane SIBO, such as bloating and chronic constipation, overlap with those of many other infections and gut imbalances. If doctors stop after a methane breath test, they could miss the presence of other conditions that may also require treatment. 

Another issue is that not all methane producers experience unpleasant symptoms caused by elevated methane levels. Although their symptoms may correspond to methane SIBO, and a breath test may register high levels, other imbalances may be the more significant reason behind the symptoms. That means the most effective treatment for their symptoms will differ from the baseline protocol for methane SIBO.

Treating Methane SIBO: The First Step

Once doctors have made a clear diagnosis, they'll come up with a treatment plan that takes into account your health history and current medications. The first goal will be to eliminate known risk factors, such as the use of PPIs.

According to Dr. Richard W. McCallum, professor and founding chair of the department of medicine at Texas Tech University Health Sciences Center, between 25% and 30% of people around the world are taking PPIs, which are known to contribute to SIBO. Maintaining an acidic environment helps your small intestine prevent the overgrowth of bad bacteria." If you go on a PPI for a few months or maybe years, then you've really taken away a major defensive unit,” Dr. McCallum said.

If the use of PPIs can't be completely discontinued, Dr. McCallum suggests switching to an alternate-day dosing schedule. Another option could be the use of less potent antacids, like calcium carbonate or H2 blockers. Or you could try what he described as "an old trick out there with the alternative medicine and homeopathic world"—a daily spoonful of apple cider vinegar.

How to Successfully Treat Methane SIBO

The Best Way to Deal with Methane SIBO

Let's get the bad news out of the way first: doctors haven't found a way to cure SIBO. The current goal of treatment, as Dr. McCallum put it, is this: "We're aiming at minimizing the bad days and trying to maximize good days by identifying risk factors, problems, and areas where we can intervene.”

Treating methane-dominant SIBO has its own considerations. Methanogens can be very hard to kill, and to achieve the best results, you'll probably want to work with an expert in this type of SIBO.

Treating methane SIBO involves at least four considerations:

  1. Optimizing your diet
  2. Limiting the presence of methane-producing microbes
  3. Supporting the health of your gut microbiome
  4. Managing symptoms

1. Optimizing Your Diet

Adjusting your diet can help you get your SIBO symptoms under control in the short-term while also setting you up for long-term improvements. Without access to raw materials from food that they feed off, the bacteria and archaea that cause excess gas production begin to die off. So, what kinds of foods do they like?

Fermentable Fiber

Archaea feed off hydrogen, and hydrogen-producing bacteria feed off fermentable fiber. Cutting out foods that contain fermentable oligosaccharides, disaccharides, monosaccharides, and polyols—known collectively as FODMAPs—can be a valuable part of a SIBO treatment plan. 

It can be quite difficult to avoid high-FODMAP foods, since some of them can be found in so many different dishes—for example, onions, garlic, and wheat. Other high-FODMAP foods are beloved, tasty, and otherwise good-for-you foods like apples, peas, watermelon, and several kinds of mushrooms.

According to Dr. McCallum, doctors don't expect you to cut these foods out forever. “As I tell my patients, only someone living in a monastery could stay on the low-FODMAP diet. It's meant to be a guide." By going without high-FODMAP foods, patients can learn what their sensitivities are and build a long-term, sustainable diet that fits their needs.

Decreasing FODMAPS means decreasing fiber, which can be problematic for individuals with methane-dominant SIBO, as it can make constipation worse. To prevent this, it's important to adapt the low-FODMAP diet to allow for higher levels of fiber and polyphenols that can encourage a healthier transit time and lower methane levels.

Some powerhouse foods that can fulfill this role include:


Researchers have found that isoflavones, polyphenolic compounds found in foods including soybeans, can decrease the production of methane and hydrogen gas. Some low-FODMAP foods that contain isoflavones are:

  • Tamari
  • Tempeh
  • Miso

2. Limiting the Presence of Methane-Producing Microbes

Methane SIBO can be caused by several different kinds of archaea, and not all antibiotics and antimicrobials effectively eradicate them all. This means that in many cases, the most successful treatment plan involves the use of more than one antibiotic or antimicrobial. 

If you have to undergo multiple rounds of treatment to get your SIBO symptoms under control, it can be a good idea to rotate the treatments used so that the archaea do not become resistant.


Unfortunately, the antibiotics commonly used to treat hydrogen-dominant SIBO don't work as well for methane-dominant SIBO. For instance, the top treatment for hydrogen SIBO—rifaximin (sold under the brand name Xifaxan)—only has a success rate of 30% for methane SIBO.

Because of this, some doctors feel the best option for methane SIBO is a combination of rifaximin and neomycin, which have a success rate of 87%. The problem with this approach is that neomycin kills off many types of beneficial bacteria, negatively altering the composition of the gut microbiome in ways that can be permanent. It can also damage the intestinal membrane, which makes you more susceptible to other diseases. So, using neomycin to wipe out SIBO can create new health issues that are equally, if not more, serious.

Rifaximin has not been linked to the same adverse side effects, but remember, it's not all that effective either.

Long story short, it's definitely worth exploring alternatives to antibiotics. 

Herbal Antimicrobials 

Herbal antimicrobials can be a good alternative to antibiotics. Clinical trials have shown they can be just as effective, and they won't do lasting damage to your digestive tract. 

Most treatment plans for methane SIBO will run on a 30-day cycle. If you have especially high methane gas levels, you may need to go through more than one round of treatment. 

Three herbal treatments backed by scientific findings and clinical experience are:

3. Supporting the Health of Your Gut Microbiome

Both prebiotics and probiotics can be valuable tools for fortifying the health of your microbiome. However, they can also make symptoms worse for some people. 


In addition to their general digestive benefits—nurturing the good bacteria in the gut—a few prebiotics can reduce methane levels, making them an extra-good option for people with methane SIBO.

Partially hydrolysed guar gum (PHGG), for example, has been found to:

  • Feed anti-inflammatory bacteria
  • Speed up transit time
  • Decrease methane levels

So, supplementing with PHGG can help you reduce methane production and rebalance your gut microbiome. 

Another prebiotic, galacto-oligosaccharides (GOS), also reduces methane levels, but it can cause SIBO symptoms to worsen for some people. 

In fact, as with fiber overall, prebiotics may be problematic for some SIBO sufferers. Some people with methane SIBO get incredible relief from prebiotics while others compare ingesting prebiotics to throwing gasoline on the fire, which is why it's important to introduce them slowly and keep a close eye on the body's response.


There's a wealth of data that shows probiotics can help clear up chronic constipation. However, not all probiotics are created equal. Different products and different formulations have their own unique effects. 

For example, Bifidobacterium lactis can improve transit time, which can bring major benefits for individuals with methane SIBO. Another strain, Lactobacillus reuteri decreases beneficial methane production as well as hydrogen production, making it a powerhouse for treating SIBO. But Bifidobacterium infantis (the strain found in the popular probiotic brand Align) can actually increase methane levels, which obviously would make things worse. 

As with prebiotics, you'll need to start with small doses of strains known to have good outcomes for your particular symptoms and carefully assess their effects.

4. Managing Symptoms

As you work to address the underlying issues causing your symptoms, you'll also want to incorporate treatments that help to manage those symptoms in the short term. The precise details will vary based on your symptoms, but typically it will be important to look for ways to encourage healthy digestion. Keeping your small bowel as clear as possible while you kill off overgrowth ensures that waste, dead archaea, and their byproducts get flushed from the body as quickly as possible.

Here are some products that can help facilitate healthy digestion:

  • Stomach acid boosters: Supplementing with hydrochloric acid (HCL) can help speed up digestion for those who naturally produce low levels of this important digestive compound. However, dosing needs to be carefully monitored because HCL has the capacity to increase hydrogen production when doses get too high.
  • Digestive enzymes: As with HCL, boosting your levels of digestive enzymes can be quite helpful if you don't produce enough of these on your own.
  • Herbal bitters: These work in a similar way to digestive enzymes, helping to break food down thoroughly, which prevents it from fermenting in the gut and generating excess methane gas. 
  • Pancreatic enzyme and bile boosters: These compounds can help correct imbalances.

Healthy digestion also depends on overall lifestyle factors such as adequate sleep and stress reduction. If the body spends most of its time in an activated state due to fatigue or excessive stress, it directs blood flow away from the GI tract and into the muscles as part of an evolutionary response designed to help us flee from physical danger. This isn't as useful when facing modern threats like an overly demanding work schedule, but the body does it anyway. A consequence of this diverted blood flow is that parasympathetic tone in the enteric nervous system (ENS) decreases. 

Any methods you find to relieve stress—such as meditation or yoga—will likely improve your digestion. It can also be helpful to develop a relaxation ritual you can run through right before you eat. 

What to Expect from Methane SIBO Treatment 

While treating SIBO improves your heath in a long-term sense, the immediate effects may make you feel worse, not better. When the archaea in your small intestine die off, they release endotoxins including lipopolysaccharides (LPS) that trigger an inflammatory response from the immune system. 

This can cause a new set of symptoms, such as:

  • Headaches
  • Skin rashes
  • Fatigue
  • Anxiety
  • Depression

It can also make your GI symptoms worse. 

To some degree, you just have to stick with it and trust that the outcome will be worth it. However, there are some strategies you can put in place to minimize your discomfort, including:

How to Prevent Methane SIBO Relapse and Protect Your Digestive Health 

While methane SIBO does not have the same relapse rates as hydrogen SIBO, that doesn't mean you should take your gut health for granted after a successful course of treatment. The specific best practices for protecting your digestive health will depend on the specifics of your diagnosis, your response to different treatments, and your overall health history. 

That said, there are some general considerations that will likely be relevant as you wrap up active treatment and enter into the recovery phase.

Reestablishing Diet Diversity

If you've been following a low-FODMAP protocol, you may be able to begin gradually reintroducing foods that were off-limits. As you do, pay special attention to foods known to nurture beneficial bacteria.

Since your body may have low levels of those good bacteria, you'll want to start with small servings of those foods to build up beneficial microflora bit by bit while minimizing symptoms like bloating and gas. 

Repopulating the Gut Microbiome

Both probiotics and prebiotics can speed up the process of repopulating your gut with good bacteria. Often, individuals who have had bad responses to these supplements prior to or during treatment will not have that issue in the recovery phase. 

Remember, having a strong population of good gut bacteria keeps troublemakers like archaea from getting out of hand.

Restoring Optimal Digestive Function

If you have been dealing with chronic constipation for a long period of time, your body will need extra support to get into the rhythm of regular, unassisted bowel movements. One way to give your gut some extra love is to add our Belly Bliss Smoothie to your daily routine. This smoothie recipe, created to facilitate gut health, features fiber-rich blueberries that help combat constipation, hydrating coconut milk that nourishes the gut lining, and anti-inflammatory cinnamon and vanilla, both of which increase nutrient absorption. 

Focus on These 3 Things to Make the Most of Your Recovery from Methane SIBO

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