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The underlying causes of chronic fatigue syndrome are multifactorial. A growing amount of research suggests that imbalances in the digestive system may play a part in a subset of patients (read our articles ‘Chronic Fatigue Syndrome: What You Need to Know‘ and ‘Digestive Health In Chronic Fatigue Syndrome‘ and ‘Small Intestine Bacterial Overgrowth: Causes‘). This article discusses testing for small intestine bacterial overgrowth (SIBO).

Some research suggests that 81% of people with chronic fatigue syndrome, 84% of people with fibromyalgia, 54% of people with hypothyroidism and up to 78% of people with IBS have small intestine bacterial overgrowth (although these numbers have also been found to be lower in other studies).

“We have to embrace complexity”: This quote from a paper discussing gut peristalsis (the mechanisms we have to move food and the stool through the digestive system) really resonated with me.

The digestive system is no exception to this rule and the vast majority of clients we work with have digestive imbalances.


One method for testing small intestine bacterial overgrowth is the Hydrogen breath test which are widely used to explore what’s going on in functional gastrointestinal disorders.

In a nut shell, glucose hydrogen breath test is more acceptable for diagnosis of small intestine bacterial overgrowth whereas lactose and fructose hydrogen breath tests are used for detection of lactose and fructose maldigestion respectively. Lactulose hydrogen breath test is also used widely to measure the orocecal transit time for GI motility.

Basic Principle of Hydrogen Breath Test

Bacteria in the bowel generally produce hydrogen gas on fermentation of carbohydrates. In bowel, bacteria can only do this when dietary carbohydrates are not absorbed in small intestine and stay as undigested material as it travels along the digestive tract into large intestine. Though some of the hydrogen gas produced by the bacteria is expelled as flatus or in making other molecules such as sulphides, acetate and short chain fatty acids but most of the gas is absorbed across the lining of the large intestine into blood stream. The gas is then transported to lungs via the blood stream and from blood it is exchanged into the airways of lungs and breathed out. The only source of hydrogen gas in the breath can be from bacterial fermentation in the bowel. The same applies to the gas called methane which is exhaled by some people and not all. The bacteria in their large bowel make methane from the hydrogen. The amount of hydrogen and methane gases breathed out from the lungs can be easily measured by taking a breath sample, and measuring by a breath-testing machine.

Types of Hydrogen Breath Tests

I am not going to discuss al of the options or discuss any in detail. But I do want to highlight some key points.

1. Glucose hydrogen breath test

Arguably, the best breath test for detecting small intestine bacterial overgrowth.

2. Lactose hydrogen breath test

“Lactose intolerance depends not only on the expression of lactase but also on the dose of lactose, intestinal flora, gastrointestinal motility, small intestinal bacterial overgrowth and sensitivity of the gastrointestinal tract to the generation of gas and other fermentation products of lactose digestion.”

3. Fructose hydrogen breath test

“It has been reported that prevalence of fructose intolerance (FI) in patients with functional GI disorders (FGID) range between 38 and 75 %.”

“2 studies reported a prevalence of fructose malabsorption in functional dyspepsia or unexplained GI symptoms of 40-55% and 73%, respectively. Therefore, it seems to be reasonable to perform routine fructose H2 breath tests in patients with unexplained abdominal symptoms who have had an unremarkable medical check-up including laboratory tests, physical examination, ultrasound and endoscopy and in the absence of “red flags” (e.g., unintended weight loss, rectal bleeding, fever, severe diarrhea or vomiting, persistent pain in the upper or lower right abdomen, family history of inflammatory bowel disease or colon cancer.”

4. Lactulose hydrogen breath test

“Of the 2,390 patients with IBS-like symptoms, 848 (35%) were symptomatic lactose malabsorbers and 1,531 (64%) symptomatic fructose malabsorbers. A combined symptomatic carbohydrate malabsorption was found in 587 (25%) patients. Out of 460/659 patients with early significant H2 increase in the lactose and fructose test who underwent a glucose breath test, 88 patients had positive results indicative of small intestine bacterial overgrowth.”

Small Intestine Bacterial Overgrowth Testing: Conclusions


There are several ways to get information about SIBO but breath testing seems to be the best approach. As well as testing to confirm the overgrowth we need to consider what causes it in the first place. Other testing, such as stool or urine may give us some indication, often we can’t say for sure. As you will see in our article on treating SIBO, sometimes only time will tell.