625 S Fair Oaks Ave, Suite 360

Pasadena, CA 91105

Testing for Small Intestinal Bacterial Overgrowth

Small Intestinal Bacterial Overgrowth, known as SIBO for short, is an overlooked cause of mystery gut symptoms. It develops in a wide range of immune mediated conditions, including contact with toxic mold, Lyme disease, long COVID, and food poisoning-induced autoimmunity.

Causes and Symptoms

Though not commonly thought of as such, the gut is the largest immune organ in the body. In particular, the intestines are the densest region of immune cells, which includes collections of immune tissues known as Gut-Associated Lymphoid Tissue (GALT) and Mucosa-Associated Lymphoid Tissue (MALT). When damaged, the intestines lose the ability to create peristaltic waves, which is the coordinated sweeping activity that advances food and other materials through the digestive tract.

With the stasis, food material and microbes, including bacteria and fungi, may proliferate in the small intestine. The small intestine, the part of the digestive tract beyond the stomach, normally harbors low levels of microbes because of two factors: the neutralizing force of the stomach acid on microbes and the peristaltic wave efficiently transporting material out of the small intestine. Disruption of this clearance mechanism means that there is a nutrient source—the undigested food—and persistent microbe retention within the small intestine.

Common small intestinal bacterial overgrowth syndrome symptoms include:

1.     Gas and bloating: SIBO can lead to excessive gas production, which can cause bloating, belching, and flatulence. This is often more pronounced after eating certain foods, particularly food that are high in carbohydrates and sugars.

2.     Abdominal pain and discomfort: Many individuals with SIBO experience abdominal pain, cramping, and discomfort. This can range from mild to severe and may be relieved temporarily by passing gas or having a bowel movement.

3.     Diarrhea or constipation: SIBO can disrupt the normal digestion and absorption of food, leading to changes in bowel movements. Some people may experience frequent loose stools or diarrhea, while others may have constipation. Other fluctuate between these two symptoms.

4.     Malabsorption and weight loss: SIBO can interfere with the absorption of nutrients from food, leading to deficiencies in essential vitamins and minerals. This can result in weight loss, fatigue, and nutritional deficiencies.

Diagnosis — Detecting SIBO

There are two primary methods for measuring for small intestinal bacterial overgrowth syndrome.

The first is an upper endoscopywith collection of the small intestinal fluid for aspiration. This procedure is technologically like a colonoscopy but starting at the upper end of the digestive tract, entering the digestive tract from the mouth. This process allows for visualization of the mouth, throat, esophagus, stomach, and small intestine. At the small intestine, the fluid within there can be collected and later analyzed for bacteria.

This method for diagnosis has significant limitations. It is costly, invasive, and not widely available—as it is usually completed only got gastroenterology specialists. It’s also not necessarily accurate either. There’s an estimated 19.6% contamination rate of the aspiration sample, usually by bacteria in the mouth. There is limited reach of the further parts of the small intestine known as the ileum and jejunum.

Once collected, the microbes that are present might not grow in the culture and be mistakenly deemed absent. Bacteria-like organisms known as archaeons, which produce the gas methane, are not culturable at all and will be universally missed by

The most common test in clinical practice for SIBO is called a breath test. This non-invasive test involves first breathing into a bag and then consuming a sugar solution afterward. The sugar solution—either lactulose or glucose—is a food source for bacteria in the digestive tract. For the next two hours, at regular intervals of 15 minutes, the patient breathes into other collection bags.

The gas contents within the bags are then sent to a lab for analysis. The analysis focuses on the levels of one of three main gasses produced by the bacterial colonizers in the small intestine. The three gasses of interest of hydrogen, hydrogen sulfide, and methane. The levels of each gas and the rate at which they rise indicate different clusters of microbial growth.

The use of breath testing is typically preferable to endoscopic sampling for the diagnosis of small intestinal bacterial overgrowth syndrome. The presence of exhaled breath with hydrogen and methane are known as exclusive biomarkers of metabolically active gut microbes because these gasses are not produced by human cells. Breath testing is safe, simple, and non-invasive. It is widely accessible in clinics and frequently offers home testing options.

Breath testing has limitations as well. It is an indirect measure of microbial growth, using the gasses as a proxy for the presence of bacteria. The accuracy can be undermined by poor oral hygiene, antibiotic use, and promotility medications that improve the transit rate used one week before the test. Plus faulty test kits may use inappropriate cutoffs for gas levels. Another error is gas kits that calculate the combined levels of hydrogen and methane, rather than their individual levels.

Though all forms of small intestinal bacterial overgrowth syndrome testing have limitations, they have value. First, both forms of testing provide objective documentation of small intestinal bacterial overgrowth syndrome which is important because the symptoms are themselves nonspecific. Another important factor is the type of SIBO guides treatment. The optimal regimen of antibiotics differs between the different subtypes of small intestinal bacterial overgrowth syndrome.


Lim, Jane, and Ali Rezaie. “Pros and Cons of Breath Testing for Small Intestinal Bacterial Overgrowth and Intestinal Methanogen Overgrowth.” Gastroenterology & Hepatology 19.3 (2023): 141.

Shah, Ayesha, Uday C. Ghoshal, and Gerald J. Holtmann. “Unravelling the controversy with small intestinal bacterial overgrowth.” Current Opinion in Gastroenterology 39.3 (2023): 211-218.

Bures, Jan, et al. “Small intestinal bacterial overgrowth syndrome.” World journal of gastroenterology: WJG 16.24 (2010): 2978.