Stool Cultures: When They Are Ordered and Why

This Noninvasive Stool Test Is Used to Help Diagnose Digestive Disease

Some digestive problems, such as diarrhea, may go away on their own, but when they do not, a trip to the healthcare provider is in order. A healthcare provider will want to do some tests to see if there is an underlying cause for symptoms such as diarrhea, abdominal pain, and nausea or vomiting. A stool culture may be part of a number of tests that a healthcare provider will order that are designed to find out what is causing all the symptoms and is used to examine stool for harmful bacteria, parasites, or an overgrowth of the “helpful” bacteria that reside in the intestine. Thankfully, a stool test is noninvasive and, as tests go, fairly easy.

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Why It's Used

A stool culture is used to try to grow pathogenic bacteria from stool. These bacteria may cause gastrointestinal infections with symptoms such as diarrhea, blood, or mucus in the stool, abdominal pain, and nausea or vomiting. Bacteria that cause intestinal diseases such as cholera, typhoid fever, and dysentery can be detected by growing them in the lab. 

Other rapid tests have replaced stool culture for diagnosing many of these bacteria, as well as for detecting pathogenic viruses (like rotavirus) and parasites (like amoeba and giardia) that don’t grow in stool cultures. With so many different species of normal bacteria present in stool, it may make the detection of pathogens tricky.

This test may also be used in a standard work-up for ulcerative colitis, Crohn’s disease, or irritable bowel syndrome (IBS). Prolonged diarrhea can be a symptom of all three conditions.

How to Prepare for a Stool Culture

There are usually no preparations required for a stool culture; stool is simply collected in a sterile container and taken to a lab for testing.

The physician or another healthcare provider that orders the test will provide a sterile container to collect stool (along with any other items needed to complete the test, such as disposable gloves). Care must be taken to ensure the stool is not mixed with urine or with water from the toilet. A healthcare provider may give directions on the best way to take the sample. In the case of diarrhea, wearing a disposable glove and holding the sample cup under the bottom while using the toilet may work well to collect the stool.

The sample should be taken immediately to the lab because it must be put into a nutrient solution. (If not taken to the lab immediately, or collected at the lab, the sample should be refrigerated or kept cold.) Bacteria may be found with just one sample, but at times, up to three specimens from different bowel movements may be needed for testing to rule out infection or parasites.

How a Stool Sample Is Performed

After the stool is placed in the culture, it may take two to three days for any bacteria that is in the stool to grow. These bacteria can then be isolated and examined under a microscope so that they may be identified.

Potential Risks

This test is safe, painless, and relatively private if one collects the stool while using the bathroom alone. While many patients may feel embarrassed or uncomfortable presenting their stool to a lab, it is important to keep in mind that receiving stool samples is a standard part of the job for lab technicians and just business as usual for them. Putting the sample in a bag, such as a brown paper bag, to carry it to the lab can help alleviate some embarrassment.

Follow-up Necessary

Call your healthcare provider in a few days for the results. If a pathogen is found, the test result is positive or “isolated,” treatment may be necessary. The treatment needed will depend on the type of bacteria that was found. Most often, only one type of bacteria may be in the stool, but in some cases, there may be multiple pathogens. If no pathogen is found, which may be called a result of negative or “not isolated,” more tests may be needed (or the stool culture repeated) to find the cause of the symptoms.

A Word From Verywell

A stool culture might be a little embarrassing but it's not difficult and is fairly straightforward. The results from the test should be available in a few days and that helps either confirm a bacterial infection or rule one out. There is likely to be follow-up from the test with either a positive or a negative result because treatment is needed for a positive result and more testing might be needed in the case of a negative result.

2 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Michigan Medicine, University of Michigan. Stool culture.

  2. Lab Tests Online. Calprotectin.

By Amber J. Tresca
Amber J. Tresca is a freelance writer and speaker who covers digestive conditions, including IBD. She was diagnosed with ulcerative colitis at age 16.