What is a stool culture?

A stool culture can help your doctor understand and treat problems with your digestive tract, or gastrointestinal tract. There are many reasons why you might experience uncomfortable digestive symptoms. In some cases, bacterial infections are the cause. Your doctor can order a stool culture to check a sample of your stool, or feces, for harmful bacteria.

A stool culture is different from an ova and parasite analysis of the stool. Sometimes it is necessary for the laboratory staff to analyze someone’s stool under a microscope to see if any ova (eggs) and parasites can be seen.

In a stool culture, laboratory staff will grow, or “culture,” bacteria living in your stool. This can help them learn if any disease-causing bacteria are present. They will smear a sample of your stool on special plates. Those plates will contain a gel that acts as a growth media and will support the growth of bacteria. Then laboratory staff will try to identify the bacteria they find, using dye staining, microscope analysis, and other testing.

For example, laboratory staff may look for the following bacteria in your stool:

  • Campylobacter species
  • Salmonella species
  • Shigella species

If you’ve recently travelled outside of the United States or have other risk factors, they may also check for:

  • Vibrio species
  • Escherichia coli 0157:H7 (a type of E. coli)
  • Yersinia entercolitica
  • Pleisomonas
  • Aeromonas

They may also perform other tests, including a test for the Clostridium difficile (C. difficile) toxin or an ova and parasite exam to look for parasites.

Infections of your digestive tract can cause uncomfortable symptoms. In some cases, they can even be life threatening. Many different infections cause similar symptoms, such as:

  • fever
  • nausea and vomiting
  • abdominal pain and cramping
  • severe diarrhea that has you going to the bathroom every 30 minutes
  • blood in your stool

Testing your stool for harmful organisms can help your doctor identify the cause of your symptoms. A stool culture can help them learn if harmful bacteria are present. It may also help them learn which treatments may kill those bacteria.

To conduct a stool culture, your doctor will need to collect a sample of your stool. They will likely give you a sample container to collect it. This is usually a clean, dry, wide-mouth container with an airtight lid. Some labs even include a special kind of toilet paper that can be used to collect your sample. Alternately, you may be asked to provide your own sample container.

You can use a bedpan or other large container to collect your stool sample. You can also collect a stool sample by loosely placing plastic wrap over your toilet seat before defecating. Then you can use the plastic wrap to transfer the sample into your collection container. Try to avoid mixing urine or regular toilet paper into the sample.

The stool collection process can be more difficult with infants in diapers or people with active diarrhea. If you’re collecting a stool sample from your baby, your doctor may advise you to use a cotton swab to collect a sample from their rectum. They may also advise you to place plastic wrap in their diaper to collect a sample. It can be tricky to collect a sample that’s free of urine. Ask your doctor for tips.

Your sample must be sent to a laboratory for culturing as soon as possible. At the lab, technicians will smear a sample of your stool onto plates containing gels that encourage bacterial growth. They will examine the bacteria that grow under a microscope. They may stain them with special dyes to help them identify the types of bacteria that grow. They may also expose the bacteria to drugs that could potentially kill them. This can help them learn what treatments may be effective.

The laboratory will send the results of your stool culture to your doctor.

Your doctor can help you understand the results of your stool culture. They can also recommend appropriate follow-up steps, which may include treatment or further testing.

If harmful bacteria are found in your stool, your doctor may prescribe antibiotics or other treatments. If no dangerous bacteria are found, your symptoms may be due to other causes. Your doctor may order more follow-up tests or examinations. For example, they may look for signs of irritable bowel syndrome, parasitic infection, or other problems.

When you’re healthy, a variety of “good” bacteria and other organisms live inside your intestines. This normal flora is sometimes called your microbiome. It helps to maintain your health. When you become infected with disease-causing organisms, they can kill off good bacteria in your intestines and make you sick.

Taking broad-spectrum antibiotics can also leave you vulnerable to disease-causing organisms. These antibiotics kill off bacteria in your intestines, including your normal flora or good bacteria. In some cases, your normal flora may not reestablish themselves after a course of antibiotics. This can leave you open to opportunistic infections.

Potentially harmful bacteria that are antibiotic-resistant can survive and take over your digestive tract. For example, C. difficile is one of those harmful bacteria. C. difficile infections can be very difficult to treat. They can cause pseudomembranous colitis. This condition is an uncomfortable and potentially life-threatening inflammation of your colon.

A new and exciting treatment for C. difficile is fecal bacteriotherapy. This is also called a stool substitute transplant. In this procedure, a stool sample from a healthy person is implanted into your colon. In a similar procedure, a purified bacterial culture may be implanted in the same way. The good bacteria from donor stool or a purified culture can recolonize your colon. This can help you recover from a persistent C. difficile infection.