Intestinal Methanogen Overgrowth (IMO)

Intestinal Methanogen Overgrowth, or IMO (E-Mo), is when methane-producing archaea are found in the intestines. These pesty microorganisms can cause a host of digestive symptoms that often go undiagnosed or wrongly diagnosed as Irritable Bowel Syndrome without diarrhea (IBS-c) among other diagnoses. Naturopathic Physicians have been treating digestive issues for years but a specific name was not agreed upon until recently. In the past, the diagnosis of SIBO or Small Intestinal Bacterial Overgrowth was used as a blanket diagnosis. However, it did not take into account organisms that are not bacteria and can be located throughout the digestive tract, not just isolated to the small bowels. As of October 2023, there is an established ICD-10 Diagnosis code for IMO. The K63.829 code now firmly establishes this condition as an official medical diagnosis and prevents certain providers from claiming “it isn’t a real diagnosis” anymore.

Who Can Have IMO

While anyone can have IMO, research has found some groups of people have a higher predisposition than others. Individuals who have a diagnosis of IBS are more likely to have IMO. This is because IBS is a diagnosis of exclusion, meaning that the doctor couldn’t find a cause for the patient’s digestive complaints. While we don’t have much statistical evidence on the prevalence of IMO/SIBO we do have a fair amount on IBS. It turns out that about 70% of IBS sufferers have IMO/SIBO (1).

Other risk factors that can cause SIBO are: Anatomical/structure pathologies inside the intestinal tract like diverticula, strictures, blind loops like short bowel syndrome (SBS), adhesions from abdominal surgery, and fistulas (more common in Inflammatory Bowel diseases). Motility disorders of the digestive tract as a result of gastroparesis, Celiac disease (CeD), or other diseases that can affect the migrating motor complex (MMC). Metabolic diseases such as Type 2 Diabetes Mellitus, or hypochlorhydria or low stomach acid. The elderly population has an increased risk. Other diseases such as Liver and kidney diseases, pancreatitis, Crohn’s disease, celiac disease, malnutrition. Medications such as antibiotics and medications that suppress stomach acid production such as proton pump inhibitors and H2 blockers (2).

What IMO Does

The high levels of archaea in the intestines can cause malabsorption, preventing the body from properly utilizing nutrients. Because food is not breaking down properly in the digestive tract, it causes a number of digestion issues as the body processes. This could be food rotting in the stomach, food not being removed from the body, or numerous other issues listed below. Archaea, like bacteria, like to eat carbohydrates. When there is an overabundance of carbohydrates in the intestines that are not absorbed into our body these microorganisms are going to consume these carbohydrates. and thus these carbohydrates are going to ferment.

This fermentation of these carbohydrates is going to cause damage to the intestinal tract cells causing a “leaky gut” or a malabsorption syndrome. IMO organisms create methane gas as a byproduct. The main organism in the human body that causes IMO is Methanobrevibacter smithii. This organism we now understand takes hydrogen gas (H2) from Ruminococcus and Chrisensenella organisms and consumes it to make its methane gas. This methane gas (CH4) causes damage to some of the nerves in the intestines which further reduces transit time/motility which in turn causes more damage and symptoms. This, combined with the list factors listed in the paragram above, will cause IMO. All of which leads to the classic symptoms of IMO.

Bacteria and Sugar

Since your blood type is just a carbohydrate aka sugar this sugar can be located throughout your body (not just on your red blood cells) and on the foods that you eat. This sugar is also found in high abundance in 80% of people’s digestive tracts. This is a result of a gene mutation called FUT2. This gene secretors blood type antigens ie your blood type sugar inside the digestive tract. This sugar is then consumed by the normal commensal bacteria that live there.

These bacteria, like everyone else, like a free meal. This is why certain probiotics work better (in my opinion) than others. If you have a mutation in the FUT2 gene you don’t secrete your blood type sugars and hence the bacteria don’t regularly get a free meal. When a meal is finally present, the starving bacteria are going to consume it quickly and stuff themselves. This will lead to a lot of flatulence, eructation, and trips to the bathroom as the bacteria break down their meal and expel their byproducts into our digestive systems.

Symptoms of IMO

One of the clear differences between IMO and SIBO is how the body’s digestive symptoms change. While both disorders can cause belching, flatulence, stomach pain, heartburn, anxiety, fatigue, and gas, IMO causes constipation while SIBO usually causes diarrhea. However, because both are based on specific bacteria or archaea, they can cause different symptoms in different patients.

IMO patients can have any combination or severity of digestive symptoms. Including those previously mentioned, they can also include nausea, fatigue, joint or muscle pain, and skin conditions.

Diagnosis

A diagnosis of IMO takes a couple of steps to procure. First, the patient’s symptoms have to line up with those listed above. Second, the patient needs to take a hydrogen and methane breath test that shows a high reading of methane-producing archaea. The old gold standard of testing IMO was an endoscopy with a culture. This procedure is expensive and was notoriously inaccurate as you can only test what you can culture and we do not have the technology to culture everything. This is also one of the reasons why it is not advisable to diagnose IMO/SIBO with a stool test/culture only.

This breath test has become the “gold standard” for testing SIBO and IMO, with one of the keys being preparation. Beginning 24 hours before the test, the patient needs to switch to a clean diet. Patients can have turkey, chicken or fish that is only baked or boiled, and seasoned with only salt and pepper. The patient can also have white rice, cooked and seasoned in the same fashion. For the last 12 hours before the test, the patient needs to fast. During this 12 hour period, the patient can only have water and their prescription medications. The test also requires that patients don’t exercise or smoke for at least one hour beforehand. Patients also need to stop taking any PPIs, antimicrobial medicines, and any substance that can be used to induce a bowel movement such as magnesium or coffee.

Taking the Test

When the patient walks through the door, they will provide a baseline sample for the breath test. They will then be given a sugary drink (usually Dextrose or Lactulose) that feeds the microorganisms in the gut. Afterward, we will ask them to provide another breath test sample every 20 minutes for the next 2-3 hours. The test monitors the sugary drink as it travels down the digestive tract, and if there is a colony of microorganisms that feed on the drink, there will be a spike in the breath test results.

If the hydrogen level reaches 20PPM (parts per million) over the baseline number, then the doctor can safely diagnose SIBO. When looking at the CH4 levels, if they are above 10PPM the doctor can diagnose the patient with IMO. If neither level spikes and there are still SIBO/IMO symptoms, then there could be a hydrogen sulfide (H2S) producing bacteria that should be tested for. The TrioSmart breath test can detect H2S gas and be used to diagnose Intestinal Sulfide Overproduction (ISO).

DDX

Doctors need to rule out other conditions to diagnose IMO. A hydrogen breath test can rule out SIBO as those bacteria only produce hydrogen and carbon dioxide, not methane.

A hydrogen and methane breath test can either diagnose or rule out SIBO and IMO, as these gases are only produced by microorganisms in the human digestive system. About 70% of all IBS cases are SIBO/IMO cases. Other medical conditions need to be ruled out if the breath test comes back negative, such as inflammatory bowel disease (either ulcerative colitis or Crohn’s disease), collagen-based disorders such as Ehlers-Danlos syndrome, cancer, Celiac’s disease, parasitic infections, Small Intestinal Fungal Overgrowth (SIFO), post-infectious IBS, a Helicobacter pylori infection, and more.

Allopathic Treatment

The standard allopathic treatment for IMO is a regime of antibiotics to flush the system. The standard antibiotics used are rifaximin and either neomycin and/or metronidazole as the treatments of choice. Rifamixin is unique in that it isn’t absorbed directly into the bloodstream. This allows it to have a stronger impact in the small intestinal tract. Patients undergoing neomycin and metronidazole treatments should be closely monitored for side effects.

The thought process is that this removes the cause, and can allow good bacteria to repopulate the vacated space. However, antibiotics function as a nuclear warhead, wiping out everything in the gut. This can lead to the removal of good bacteria as well, taking the gut longer to recover and regulate.

Natural Treatment

Despite being a relatively new diagnostic term, Personalized Natural Medicine (PNM) has already created a system of treatment for IMO. It begins with talking to the patient about a full hydrogen and methane breath test. PNM offers a full, comprehensive breath test in the office that is covered by most major insurances.

PNM’s standard treatment protocol for IMO includes a high dose of a chemical from Garlic called allicin, Biome Clear, and a herb called Quebracho colorado. By killing some of these methane-producing archaea and flushing them out, we are able to treat the problem at its source.

Bacteria Die-Off Reactions

While patients may experience discomfort at first as the archaea release methane when they are killed, this is replaced with proper digestion relatively shortly in most cases. Because the archaea are no longer consuming hydrogen during this kill-off phase, patients can note an increase in their hydrogen levels. This protocol also allows the good bacteria to remain unperturbed, allowing for minimal disruption in the digestive tract.

Once the killing phase is completed, then we begin a repopulation, healing, and prevention phase of treatment. A patient will always be asked to perform a follow-up breath test. If a patient has a positive result, then the treatment plan will change accordingly and the patient will undergo another round of treatment. Once the test comes back negative and symptoms have abated, then patients are recommended to perform a follow-up breath test every 3-6 months to ensure the microorganisms have not returned.

Diet

One of the key components of PNM’s treatment is diet. We use a SWAMI diet, which uses genetic information, lab markers, the SCD and Low FODMOD diets. These combined with other measures create a personalized, digestive-based diet for all of our patients.

Potential Complications

With any form of testing or treatment potential complications can present themselves. With testing following the prep diet and fasting for 12 hours can be a challenge. Patients can skew the breath test results if they don’t properly follow the prep diet. Some people will have reactions to the sugary drink provided at the start of the test. Depending on the type of sugar used (Dextrose/Lactulose) there can be some upset, gas, and diarrhea. Naturopathic Physicians will offer one of two main sugars used for this test as they do different things. Dextrose only feeds the bacteria in the first 3 feet (or so) of the digestive tract while Lactulose is an alcohol-based sugar that feeds microorganisms from mouth to anus.

Treatment can yield some symptoms as well. Dieoff reactions can cause your digestive symptoms to become worse over time. A host of different natural agents can help prevent or manage any digestive symptoms. Other times, patients will have to change treatment plans multiple times to find the right cure. This includes using antibiotics, elemental diets, different rotations of herbs, and finally, specific microbiome testing to ensure there are no other bacteria causing digestive issues.

Related Bacteria

IMO can be tied directly to Methanobrevibacter smithii, which is the most prominent archaea in the gut. This microorganism is responsible for breaking down complex sugars and produces methane as a by-product. Research has shown a direct correlation between high levels of methane in the gut and constipation. (3) By flushing out some of these bacteria, and therefore reducing the levels of methane, it is possible to alleviate some of these digestive symptoms. The other two bacteria lines that play a direct role in IMO are Ruminococcus and Chrisensenella organisms. These two bacteria lines make hydrogen gas that is then consumed by M. smithii which makes methane gas.

Citations

2. Small Intestinal Bacterial Overgrowth: a Comprehensive Review Andrew Dukowicz-Brian Lacy-Gary Levine – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099351/

3. Review Article: Inhibition Of Methanogenic Archaea By Statins As a Targeted Management Strategy For Constipation and Related Disorders K Gottlieb-V Wacher-J Sliman-M Pimentel – https://www.ncbi.nlm.nih.gov/pubmed/26559904