Virulence factors gut microbiome (qualitative)

The laboratory looks in the stool for genetic features (genes) of bacteria that research has linked to disease-causing properties, for example making toxins. Such genes are also found in healthy people without symptoms. Which features are tested differs per laboratory and is not standardized.

• Presence of bacterial genes that research has linked to disease-causing properties. This is not a diagnosis of an intestinal infection and not a test for a specific pathogen.

For the GP, an abnormal value in the gut flora is usually no reason for further tests or treatment. With symptoms, the GP looks at the symptoms themselves and, if needed, arranges tests according to the guideline, for example for celiac disease, bowel inflammation or a gut infection. According to international experts, the result is not a basis for a diet, supplements or antibiotics.

Gut flora testing describes which bacteria are in a portion of stool. It has not been shown that the result helps in making a diagnosis or choosing a treatment, in people with or without symptoms. According to the guideline on irritable bowel syndrome, there is no test that can confirm this condition. An international group of experts concluded in 2025 that there is not enough evidence to use gut flora testing in healthcare, that there are no fixed healthy reference values and that there is no generally accepted definition of dysbiosis. According to the MDL Fonds (Dutch digestive health foundation), too, we do not yet know exactly what a healthy gut flora is; the result is therefore a description, not a medical judgment.

• The composition differs greatly from person to person and can change from day to day; a second portion of stool can give a different result.
• Diet, antibiotics, acid-reducing medicines, laxatives, probiotics and a recent gut infection affect the result.
• Methods and reference values are not standardized; results from different laboratories or methods cannot be compared with each other.
• Stool mainly shows the bacteria in the last part of the large intestine, not those in the small intestine or on the gut wall.

Because there is no fixed definition of an abnormal gut flora, there are no figures on how common it is. Bowel symptoms without a clear cause are common, though: according to the guideline, irritable bowel syndrome affects about 4 in 100 adults in the Netherlands (by the strictest criteria).

The result is a description of your gut flora at one moment, with no established medical significance, whether or not you have symptoms. The test is not needed to stay healthy and does not explain bowel symptoms. With bowel symptoms, the GP usually finds the cause through questions and a physical examination, supplemented if needed with targeted blood or stool tests, for example for celiac disease or bowel inflammation. With blood in the stool, unexplained weight loss or new bowel symptoms after the age of 50, this test is no substitute for an examination by the GP.

• Porcari S, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol 2025;10:154-67 (open-access versie, Wageningen University & Research)
• FMS Richtlijnendatabase: Prikkelbaredarmsyndroom, module Diagnostiek PDS
• NHG-Standaard Prikkelbaredarmsyndroom (PDS)
• Thuisarts.nl: Ik heb het prikkelbare-darm-syndroom (PDS)
• MDL Fonds: Alles over je darmmicrobioom