Gut Testing

Gas? Bloating? Generally “dodgy” digestion? Or perhaps food creates digestive problems. Find out about hydrogen-methane breath testing and how testing can help find the cause of your gut distress.

How Does Gut Testing Work Using Breath?

Hydrogen methane breath testing is a non-invasive diagnostic tool used to identify causes of gut dysfunctions particularly those related to carbohydrate malabsorption and small intestinal bacterial overgrowth (SIBO). This test plays a crucial role in identifying the underlying causes of gastrointestinal symptoms and can help guide appropriate treatment strategies.

By analysing the breath for the presence of hydrogen and methane gases (neither of which can be produced by humans), healthcare providers can gain valuable insights into your digestive health and make informed decisions about your care.

The process of hydrogen methane breath testing begins with a prep diet, then consuming a specific substrate, such as lactulose, glucose or fructose, each of which has different absorption potential in the intestines.

If bacteria in the gut break down these substrates, they can produce hydrogen and methane (and sometimes other) gases. These gases are then absorbed into the bloodstream and are rapidly exhaled through the lungs. By measuring the levels of these gases in the breath at specific intervals after taking the substrate, the test is a measure of your ability to digest and absorb certain carbohydrates, and may give clues that indicate bacterial overgrowth in the small intestine.

Carbohydrate Malabsorption causes Gut Dysfunction

Another important use of hydrogen methane breath testing is to identify carbohydrate malabsorption. People with symptoms such as bloating, flatulence, abdominal pain, and diarrhoea may undergo this test to determine whether their symptoms are related to an inability to properly digest certain carbohydrates.

Elevated levels of hydrogen or methane in the breath can indicate malabsorption, helping pinpoint the specific carbohydrates causing the issues. This information is crucial for developing personalised dietary plans that minimise symptoms while a treatment regime is implemented with a goal to correcting the problem and improving overall gut health.

Small Intestinal Bacterial Overgrowth (SIBO)

Hydrogen methane breath testing is instrumental in diagnosing SIBO. SIBO occurs when there is an abnormal increase in the number of bacteria in the small intestine, leading to the fermentation of carbohydrates and subsequent production of hydrogen and methane gases.

By analysing breath samples, elevated levels of these gases can confirm the presence of SIBO and trigger further investigation (to find the cause) and personalised treatment plans accordingly. Treatment may involve the use of antimicrobials,  probiotics, dietary modifications, and other targeted therapies aimed at restoring healthy, balanced gut microbiota.

Moreover, the ease of conducting hydrogen methane breath testing means that monitoring of treatment efficacy and the assessment of disease progression is possible. By conducting follow-up tests after implementing therapeutic interventions, your healthcare provider can evaluate changes in gas levels to determine whether the treatment plan is effectively addressing the underlying gut dysfunction.

Adjustments to the treatment protocol can be made based on the results, ensuring that you receive the most appropriate and personalised care.

10 Signs You Might Have SIBO

What are the Limitations of Breath Testing?

It is important to note that hydrogen methane breath testing is not without limitations. Interpretation of test results requires expertise. There are many factors, such as diet, use of antibiotics and certain other medications, and a range of conditions that can affect gastrointestinal motility, influencing the accuracy of the test.

False positives (predicting a problem that doesn’t exist) and false negatives (missing a problem that is truly a problem) are possible. This emphasises the need for comprehensive clinical evaluation and a holistic approach to care.


In summary, hydrogen methane breath testing serves as a valuable tool in the diagnosis and management of gut dysfunction, including carbohydrate malabsorption and small intestinal bacterial overgrowth.

By providing insights into your ability to digest certain carbohydrates and the prediction of the presence of abnormal bacterial populations in the small intestine, this testing method helps clinicians develop personalised treatment plans that address the root cause of your gut symptoms.

While it is not a standalone diagnostic tool, when used in conjunction with a thorough clinical assessment, hydrogen methane breath testing can significantly improve outcomes and quality of life.


How is SIBO Treated?

Clinical studies have shown improvement in IBS (Irritable Bowel Disease) patients who are treated for bacterial overgrowth.  Naturally, those suffering from these symptoms should see their health care practitioner or contact our office for a comprehensive evaluation. In some cases, testing is not necessary.
The standard treatment for SIBO in the USA is an antibiotic called rifaximin. Because this drug is not well absorbed throughout the body, it mostly stays in the gut and is very effective against the bacteria that cause SIBO. Some of our clients choose this type of treatment.  However, Rifaximin is a very expensive drug (around $1000/course) and is not funded in New Zealand. Research has revealed that response rates using botanical treatments are about the same as using antibiotics. Furthermore, relapse rates tend to be higher in those who choose antibiotic treatment.  If using antibiotics, following our guidelines is important to get the gut in good shape again and minimise the risk of reinfection. 

It is important to be aware that those who are susceptible to SIBO may be prone to recurrence. Management of SIBO is very individual, however we follow the following principles:

  • Increase stomach hydrochloric acid (HCl) and digestive enzymes.  These are your normal gut defenses against bacteria
  • Break up biofilm.  This is a mucous layer in the intestine that harbours bacterial  In the normal gut this is useful to protect your good bacteria, but is counter-productive in a SIBO gut.
  • Eradicate or out-compete the overgrown bacteria
  • Restore the normal gut flora/defenses.
  • Repair the damage!

A diet low in carbohydrates and free of refined flours, sugars and alcohol is important, but we do not recommend anyone undertake dietary restrictions without guidance. Many people find that a low FODMAP diet can reduce symptoms, but this diet is intended for short-term use only and is not recommended to be done without proper supervision. 

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