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Understanding the difference between SIBO, SIFO and IMO 

Small intestinal bacterial overgrowth (SIBO) and small intestinal fungal overgrowth (SIFO) are conditions where there are too many bacteria or fungi in the small intestine.

Another related condition is Intestinal Methanogen Overgrowth (IMO), which occurs when there are too many methane-producing archaea in the gastrointestinal (GI) tract.

Microbes are divided into different groups, and methanogens belong to the kingdom of archaea, so IMO is the correct term for an excess of methane-producing microbes in the gut.

Diagnosing Small Intestine Overgrowth

The most common diagnostic tests for small intestine overgrowth include breath testing and small intestinal aspiration cultures to identify certain microbes like archaea, aerobic and anaerobic bacteria, and fungi.

What Are These Microbes?

  • Archaea: Archaea are a type of microbe similar to bacteria but with some differences. They can live in extreme environments, like hot springs or very salty water. In the gut, some archaea produce methane gas. When too many of these methane-producing archaea are in the small intestine, it can lead to Intestinal Methanogen Overgrowth (IMO).

  • Aerobic Bacteria: These bacteria need oxygen to survive. They live in parts of the body where oxygen is available, like the small intestine. If too many aerobic bacteria grow in the small intestine, it can cause Small Intestinal Bacterial Overgrowth (SIBO).

  • Anaerobic Bacteria: Unlike aerobic bacteria, anaerobic bacteria do not need oxygen to live. They thrive in parts of the body with low or no oxygen, like deeper in the intestines. Overgrowth of these bacteria in the small intestine also contributes to SIBO. Anaerobic bacteria from the large intestine can also migrate into the small intestine due to various factors such as disrupted migrating motor complex (MMC), ileocecal valve dysfunction, decreased gut motility, structural abnormalities, reduced gastric acid secretion, and compromised immune function. These disruptions allow bacteria originating from the large intestine to multiply in the small intestine, leading to symptoms like bloating, pain, and malabsorption.

  • Fungi: These are organisms like yeast and molds. In the small intestine, fungi like Candida can sometimes grow too much, leading to Small Intestinal Fungal Overgrowth (SIFO).

How They Relate to Small Intestine Overgrowth

In a healthy gut, there is a balance of different types of microbes. But sometimes, this balance gets disturbed, and certain microbes grow too much. When this happens in the small intestine, it can cause various problems:

  • SIBO happens when there's an overgrowth of aerobic and anaerobic bacteria.

  • SIFO occurs when fungi grow too much.

  • IMO is when there's too much methane-producing archaea.

These overgrowths can lead to symptoms like bloating, gas, stomach pain, and diarrhea. Diagnosing these conditions accurately helps doctors treat them effectively, restoring balance to your gut.

Diagnosing SIBO, SIFO and IMO

Small Intestine Aspiration and Cultures

The current gold standard for diagnosing SIBO and SIFO involves aspirating fluid from the small bowel, followed by culturing and counting bacteria and fungi.

Samples are collected from the upper small intestine (specifically the duodenum or jejunum) using an endoscope. During the endoscopy, a sterile catheter is inserted alongside the endoscope to suction 3–5 mL of small bowel content, which is then sent to a microbiology lab for aerobic, anaerobic, and fungal cultures. 

This culture and sensitivity testing helps tailor pharmacological treatment for SIBO patients and is the most reliable way to diagnose SIFO. However, regular microbiology labs can't culture archaea to diagnose IMO, so breath testing is currently the only way to diagnose it.

Unlike breath testing, which is relatively quick, non-invasive, and can be done without sedation, small bowel aspiration is time-consuming, expensive, and invasive.

It often involves an endoscopy procedure with sedation, which carries its own risks. Moreover, even with careful sample collection techniques, the culture may miss overgrowth depending on the specific area sampled and the risk of contamination with oral bacteria.

Breath Tests

Quantifying gasses produced by the gut microbiome through breath analysis (such as hydrogen, methane, and hydrogen sulfate) is the most affordable, non-invasive, and widely available test for diagnosing hydrogen-predominant SIBO and IMO.

Hydrogen and methane are unique markers for gut microbiota since human cells do not produce these gasses. This allows standardized protocols for diagnosing and treating gut microbiome-related disorders.

The presence of these gases in exhaled breath indicates the fermentation of carbohydrates by gut microbes, their movement from the gut to the bloodstream, and their expiration through the lungs.

When performing a breath test, a patient may be given a sugary solution to drink. In patients suspected of having SIBO or IMO, the bacteria and archaea will begin to ferment the sugar after ingestion.

This fermentation process produces gases, and changes in methane, hydrogen, and hydrogen sulfate levels in sequential breath samples will indicate the presence of IMO or SIBO.

Although breath testing is widely used because it's easy to administer and well-tolerated, it can give false-positive or false-negative results, making it an imperfect tool for diagnosing SIBO and IMO.

Due to these limitations, doctors may treat SIBO based on symptoms alone, using the patient's response to antibiotics to help confirm the diagnosis.

However, clinical symptoms alone are not always reliable for diagnosing SIBO. Breath testing remains useful for patients with symptoms and no other diagnosis found through endoscopy or imaging, especially if other conditions could lead to SIBO.

The use of breath testing for diagnosing SIBO and IMO is an area of scientific research that is constantly evolving. As more research is conducted, new standards may emerge.

For now, breath testing remains one of the tools healthcare professionals use to gain insight into their patients' health.

To learn more about SIBO and digestive health click here.

As your Gut Loving Dietitian, I possess the expertise to provide personalized advice and effective gut health solutions.  With virtual consultations available throughout BC, Canada, take the step today to address digestive concerns and establish a harmonious relationship with food. 

If you're curious about whether you have SIBO, IMO, or SIFO, I provide referrals and requisitions for breath tests.

Book a FREE discovery call or reach out via email to get tested and start your journey to better gut health. 

Written by: Matthew Riccardi, 4th Year UBC Dietetic Student 


Rezaie, A., & Rao, S. S. C. (2023). Chapter 15 - intestinal bacterial, fungal, and methanogen overgrowth. Handbook of gastrointestinal motility and disorders of gut-brain interactions (Second ed., pp. 205-221). Elsevier Inc.

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