Stool tests are widely popular, especially in the functional medicine field, but do they give you accurate information that can help you get better faster?
The short answer is maybe. Though stool tests can give you a lot of interesting information, there are a lot of caveats, including:
Stool tests vary widely in their accuracy and may tend to give false-positive results.
Some brands of stool tests have not been fully validated by research.
Stool test companies may provide treatment recommendations that are not validated by science.
Not all stool test results are clinically useful.
What does this mean for you? You need to understand exactly what stool tests can and can’t tell you and how to use them appropriately.
In this article, we’ll explain what a stool test is, which tests are on the market, and what the data says about their accuracy. We’ll also discuss what to do with your stool test results.
What Is a Stool Test?
If you have persistent or distressing digestive system symptoms, your functional healthcare provider may order a stool test to check for gut infections.
After you take the test kit home, you collect a stool sample in a clean container held over the toilet bowl (while wearing latex gloves) and return the sample to a lab or your doctor’s office for analysis.
What Are Stool Tests Used For?
Stool tests can be a valuable diagnostic tool to assess your digestive tract if you have signs and symptoms of gut infections, such as:
Severe abdominal pain and bloating
Frequent bowel movements, diarrhea, bloody diarrhea, or mucous in your stool
Other unexplained digestive and non-digestive symptoms
What Do Stool Tests Look For?
Stool tests look for:
Ova (eggs) and parasites, such as Giardia lamblia or intestinal worms
Bacterial infections such as Salmonella, Clostridium difficile, or Campylobacter
Fungal infections, like Candida
Viruses like Rotavirus
Some stool tests also evaluate the abundance or absence of beneficial bacteria species, such as Lactobacillus and Bifidobacteria.
Stool samples are also used in gastroenterology practices to check for signs of digestive tract diseases like Inflammatory Bowel Disease (ulcerative colitis and Crohn’s disease), bile acid malabsorption, pancreatic insufficiency, and indicators of colon cancer.
Next Generation Stool Tests: DNA-PCR
Stool tests traditionally looked for pathogens by doing a stool culture to grow bacteria or yeasts or by looking for parasites and their eggs using a microscope. These stool tests are still widely used in doctor’s offices.
But in the last decade, several companies have developed stool tests that use a newer technology called DNA-PCR. DNA-PCR testing looks for fragments of microorganism DNA.
Common stool tests that use DNA-PCR methods and are available in the United States include:
DNA-PCR tests have a reputation for being more accurate at detecting small quantities of pathogens. Companies suggest that this increased detection ability leads to better clinical outcomes for patients.
However, it’s worth taking a critical look at these claims.
How Accurate Are the New Stool Tests?
The data for these next-generation stool tests are still early, so we want to be careful how we use them.
Lab test accuracy normally refers to two measurements:
Sensitivitymeasures how accurately a test correctly diagnoses a problem and avoids false positives.
Specificitymeasures how accurately a test correctly finds that you don’t have the problem and avoids false negatives.
The sensitivity of the BD MAX test for gut pathogens like Salmonella was shown in a study to be between 89%  and 100% [2 Trusted SourcePubMedGo to source]. The BioFire, Verigene, and BD MAX tests’ specificity were shown in another study to be between 98.6% and 100% [3 Trusted SourcePubMedGo to source]. This means the tests correctly identified who had a gut infection and who didn’t most of the time.
*** Sensitivity of PCR compared to culture for Salmonella 
Popular functional medicine stool tests, like the GI MAP and the GI360 use these methods to test stool samples, so should have similar accuracy. However, these tests are relatively new to the market, and haven’t yet been widely studied.
Though these stool tests appear to have good sensitivity and specificity for gut pathogens, it’s less clear what their results mean when they report imbalances of normal bacteria. A study did confirm that the PCR-DNA portion of the GI360 test could correctly identify a pattern of dysbiosis in IBS and IBD patients [4 Trusted SourcePubMedGo to source]. But we don’t yet clearly know what various levels of beneficial bacteria mean for your symptoms or overall health, so it’s best to leave interpretation of your stool test to trained practitioners.
Scientifically Validated Stool Test Markers
There are some individual stool test markers that have been scientifically validated and can give you useful information about the health of your digestive system.
Fecal calprotectin testsare a highly accurate indicator of inflammation in the large intestine. When elevated in someone with digestive symptoms, calprotectin can suggest Inflammatory Bowel Disease [5 Trusted SourcePubMedGo to source].
Some of these gut health markers are included in DNA-PCR stool tests, or they are also available through your regular doctor’s office.
Can Stool Tests Predict What Diet You Should Eat?
Some direct-to-consumer tests, like Thryve or Viome, claim certain levels of beneficial bacteria can predict targeted diets and supplements. That’s an exciting possibility for patients and providers alike.
However, there is little peer-reviewed data validating these particular claims.
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