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Tests to Check for Bacteria in the Intestinal Tract

Different types of bacteria, known as enteric pathogens, can cause intestinal disease. In order to diagnose an infection, the clinical lab must differentiate between the bacteria causing the disease and the bacteria that are normally found in the intestines. To do this, labs rely on bacterial cultures, immunology tests, special stains and carbohydrate use tests.

  1. Bacterial culture

    • Bacterial cultures are still the gold standard (most reliable) test to identify bacteria from a stool sample. A small portion of the stool sample is placed in petri dishes with different kinds of nutritional media. This helps identify the kind of bacteria in the intestine depending on their nutritional needs and what dishes they grow in.

    Immunology tests

    • Some tests for bacteria in the intestinal tract involve the use of antibodies specific for certain bacteria species. A bit of the stool sample is placed on a glass slide and the antibody solution is added to it. If the bacteria for which the antibodies are directed is in the sample, clumping will occur.

    Special stains

    • Different bacteria stain different colors and are of different shapes when seen under the microscope. The classic stain is the Gram stain. Most "good" bacteria in the intestines are Gram-negative, staining pink. Many of the "bad" bacteria in the intestines, like Clostridium, are Gram-positive, staining purple.

    Carbohydrate utilization

    • Different bacteria use different types of carbohydrates (sugars). Carbohydrate utilization (use) tests help both test for the presence of bacteria in a stool sample and to identify what bacteria those are. Small samples of stool are placed in tubes with different carbohydrates. As the bacteria use the carbohydrates, their waste products change the acidity in the tubes, causing a color change.

    Molecular biology tests

    • The next generation of tests for any kind of bacteria, intestinal or otherwise, involve what is called "molecular biology." This is testing for the presence of the bacteria's genetic material. There are many times when the bacteria will not grow in the petri dishes because they are mishandled at the time of collection. Molecular biology tests only require the genetic material to be in the sample, not viable bacteria.

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