Methane SIBO Treatment

Small Intestinal Bacterial Overgrowth (SIBO) is a complicated gut condition characterized by abdominal pain, diarrhea, bloating, and constipation.

Recently, it has been discovered that a variant of SIBO — methane SIBO — exists and that its treatment and symptoms differ slightly from the “classic SIBO”.

In this article, we’ll take a look at what methane SIBO is, why it happens, and what treatment options patients have.

What is SIBO?

SIBO occurs when bacteria invade the small intestine.

Normally, the small intestine is almost empty of bacteria (compared to the large intestine, which has large numbers of bacteria). This is because the small intestine is mobile (it keeps on contracting and pushing food down the gut) and contains bile (a chemical that helps you absorb fat).

Both mobility and bile make sure that any bacteria that grow in the small intestine are washed down into the colon.

If this process is impaired due to some reason, bacteria start proliferating in the small intestine, producing gas and interfering with nutrient absorption. This leads to a variety of symptoms, including:

● Abdominal pain after a meal
● Diarrhea
● Weight loss
● Gas
● Indigestion
● Constipation
● Cramps
● Bloating

Since the small intestine is the major location of nutrient absorption, SIBO can lead to a number of nutritional deficiencies, including:

● Vitamin B12 deficiency — this causes muscular weakness, tingling and numbness in hands and feet, and central nervous system damage and mental confusion in advanced cases. It can also lead to anemia.
● Calcium deficiency — SIBO leads to fat malabsorption. Excess fat binds calcium, reducing its absorption. This manifests as osteoporosis, which means weakened bones.
● Lactose-intolerance — SIBO can damage gut lining, which makes lactase dysfunctional. SIBO patients can therefore become intolerant to dairy products.
● Other nutritional deficiencies, including vitamins A, D, E, K, zinc, and iron deficiencies.

What is methane SIBO?

You can think of methane SIBO as a complication of the “classic” or hydrogen SIBO.

When patients develop SIBO, bacteria in the small intestine produce an excess of hydrogen gas. Single-celled organisms called archaea (specifically methanobrevibacter smithii) feed on this hydrogen.

This leads to an overgrowth of archaea, and these organisms produce methane gas. All methane SIBO patients have underlying hydrogen SIBO because you need an excess of hydrogen gas for archaea to proliferate.

Recently, the term Intestinal Methanogen Overgrowth (IMO) has been proposed to replace methane SIBO but hasn’t been widely accepted yet. Archaea are not exactly bacteria and can proliferate in the large intestine too, so “Small” Intestinal “Bacterial” Growth might not be an appropriate term.

What are the symptoms of methane SIBO?

Symptoms of methane SIBO include constipation, bloating and gas, and weight gain.

Constipation is a dominant symptom in these patients because of the overproduction of methane gas, which has been shown to reduce intestinal transit time.

Weight gain occurs because archaea are obesogens, which means they help the body extract more nutrients from diet.

How is methane SIBO diagnosed?

Methane SIBO is diagnosed using history, physical examination, and breath tests.

Your doctor’s appointment begins by the doctor asking you questions about your symptoms and their duration. The doctor will also ask you about any pre-existing conditions that you have and the medications you take for them.

This is followed by physical examination, where the doctor might listen to or gently feel your abdomen.

If methane SIBO is suspected, the doctor will order breath tests.

There are two types of breath tests — hydrogen breath test and methane breath test. Both are needed to diagnose methane SIBO.

During a breath test, you’re given a sweet drink. You’re required to blow into a tube after consuming the drink, which helps measure the amount of hydrogen (or methane) in your breath.

If hydrogen and methane increase by more than a certain amount after consumption of the drink, this means there are excess gas-producing bacteria in the small intestine.

If breath testing doesn’t provide a clear diagnosis, your physician may order a stool culture or an intestinal fluid aspirate (where fluid from the small intestine is drawn out) to look for bacteria.

How is methane SIBO treated?

Treatment of methane SIBO involves bacterial eradication, nutrient supplementation, and preventing relapse.

Bacterial eradication can be done using antibiotics and dietary modification. While a low-FODMAP diet can be used to starve bacteria in hydrogen SIBO, it may not be very effective for methane SIBO because it reduces the intake of fiber, which can worsen constipation.

Doctors generally recommend eating a well-balanced diet and taking smaller meals in SIBO. An elemental diet, which involves consuming pre-digested nutrients, can also be very helpful for SIBO. For specific dietary advice for methane SIBO, it’s best to consult a doctor.

While the bacteria that cause hydrogen SIBO can be easily killed off with antibiotics like rifaximin, metronidazole, and ciprofloxacin, archaea are often resistant to these.

A combination of neomycin and rifaximin has been shown to be very effective against archaea, but neomycin is a broad-spectrum antibiotic that can kill healthy gut bacteria too.

Some practitioners advocate for the use of herbal antimicrobials like Neem and Oregano to kill archaea. They are less aggressive than antibiotics and have been shown to be effective.

If you are severely malnourished due to SIBO, your doctor may also give you intramuscular injections of vitamin B12 to prevent deficiency. Oral vitamins, calcium, and iron supplements may also be needed.

Both bacterial eradication and nutrient supplementation treat the symptoms of SIBO and not the cause. To prevent relapse, it’s important to begin treatment for the root-cause of SIBO. There are many causes behind bacterial overgrowth, including:

● Short bowel syndrome — where the small intestine fails to absorb nutrients either because of surgery or congenital abnormalities
● Small bowel diverticulosis
● Blind loop syndrome — where bacteria grow in a bypassed segment of the small intestine
● Crohn’s disease
● Ulcerative Colitis
● Irritable Bowel Syndrome
● Diabetes mellitus
● Scleroderma — where the small intestine becomes immobile, allowing bacteria to proliferate


SIBO leads to overproduction of hydrogen, which is utilized by archaea to produce methane, leading to methane SIBO.

Treatment of methane SIBO involves eradication of archaea (as well as abnormal bacteria), nutrient supplementation, and treating the root-cause of SIBO.

Medically Reviewed by Onikepe Adegbola, MD PhD

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