Should You Use a Stool Test to Check Your Gut Health?

What You Need To Know About Stool Test Accuracy

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.

stool test: White toilet bowl in a bathroom

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
  • Fever
  • Nausea
  • 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
stool test: 3D illustration of a hand holding viruses and bacterias

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: 

  • Sensitivity measures how accurately a test correctly diagnoses a problem and avoids false positives. 
  • Specificity measures 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% [1] 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.

Stool TestSensitivitySpecificityThird-Party Verified?
BioFire94.7% – 100%**98.6% – 100%**Yes
Verigene71.4% – 100%**99.3% – 100%**Yes
BD MAX89-100%***100%*Yes

* For tested organisms, and compared to culture [2 Trusted SourcePubMedGo to source].

** Sensitivity varied depending on tested organisms [2 Trusted SourcePubMedGo to source]

*** Sensitivity of PCR compared to culture for Salmonella [1]

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. 

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?

Woman with a fork in her mouth and holding a bowl of vegetables

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.

Studies have shown the GI360 test can accurately predict which people will respond well to a low FODMAP diet based on their bacterial community [9 Trusted SourcePubMedGo to source, 10 Trusted SourcePubMedGo to source]. It’s important to remember that our knowledge of the clinical implications of specific bacteria in the gut microbiome is truly in its infancy [11 Trusted SourcePubMedGo to source].

How Should You Use Stool Testing?

Since many stool tests have not been validated with peer-reviewed published studies, your test results must be interpreted with caution and the insight of an experienced clinician. 

For example, a GI-MAP or GI360 can provide useful information, but your clinician should take into account the possibility of false positives.

Fortunately, you don’t need a lab test to start healing your gut. Basic interventions for gut health can be very effective and don’t require high-tech mapping of your digestive system.

A step-by-step plan like the one I provide in my book, Healthy Gut, Healthy You, offers many powerful options supported by clear data. 

A more cost-effective approach to gut health means that not everyone requires stool testing. Probiotics [12 Trusted SourcePubMedGo to source, 13 Trusted SourcePubMedGo to source, 14 Trusted SourcePubMedGo to source] and the low FODMAP diet [15 Trusted SourcePubMedGo to source], for example, are proven therapies that have helped many patients. Stool tests are best used for those who haven’t seen the results they hoped for with these more basic interventions. 

The Bottom Line

Ultimately, not all stool tests are created equal, and your results need to be read with a grain of salt.

Stool tests are best left to clinicians to interpret and should be used with caution only after you have completed more basic gut repair strategies. If you need help resolving your gut symptoms, consider applying to become a patient at the clinic or reach out to our health coach.

➕ References
  1. Hapuarachchi1 C, Jeffery1 K, Bowler1 I. Stool PCR may not be a substitute for enrichment culture for the detection of salmonella. Journal of Medical Microbiology. 2019. Volume 68, Issue 3. https://doi.org/10.1099/jmm.0.000923
  2. Anderson NW, Buchan BW, Ledeboer NA. Comparison of the BD MAX enteric bacterial panel to routine culture methods for detection of Campylobacter, enterohemorrhagic Escherichia coli (O157), Salmonella, and Shigella isolates in preserved stool specimens. J Clin Microbiol. 2014 Apr;52(4):1222-4. doi: 10.1128/JCM.03099-13. Epub 2014 Jan 15. PMID: 24430460; PMCID: PMC3993502. Trusted SourcePubMedGo to source
  3. Huang RS, Johnson CL, Pritchard L, Hepler R, Ton TT, Dunn JJ. Performance of the Verigene® enteric pathogens test, Biofire FilmArray™ gastrointestinal panel and Luminex xTAG® gastrointestinal pathogen panel for detection of common enteric pathogens. Diagn Microbiol Infect Dis. 2016 Dec;86(4):336-339. doi: 10.1016/j.diagmicrobio.2016.09.013. Epub 2016 Sep 22. PMID: 27720206. Trusted SourcePubMedGo to source
  4. Casén C, Vebø HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, Dzankovic S, Frøyland C, Nestestog R, Engstrand L, Munkholm P, Nielsen OH, Rogler G, Simrén M, Öhman L, Vatn MH, Rudi K. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther. 2015 Jul;42(1):71-83. doi: 10.1111/apt.13236. Epub 2015 May 14. PMID: 25973666; PMCID: PMC5029765. Trusted SourcePubMedGo to source
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  7. Sugai E, Srur G, Vazquez H, Benito F, Mauriño E, Boerr LA, Bai JC. Steatocrit: a reliable semiquantitative method for detection of steatorrhea. J Clin Gastroenterol. 1994 Oct;19(3):206-9. doi: 10.1097/00004836-199410000-00007. PMID: 7806830. Trusted SourcePubMedGo to source
  8. Li JN, Yuan SY. Fecal occult blood test in colorectal cancer screening. J Dig Dis. 2019 Feb;20(2):62-64. doi: 10.1111/1751-2980.12712. Epub 2019 Mar 5. PMID: 30714325. Trusted SourcePubMedGo to source
  9. Valeur J, Småstuen MC, Knudsen T, Lied GA, Røseth AG. Exploring Gut Microbiota Composition as an Indicator of Clinical Response to Dietary FODMAP Restriction in Patients with Irritable Bowel Syndrome. Dig Dis Sci. 2018 Feb;63(2):429-436. doi: 10.1007/s10620-017-4893-3. Epub 2018 Jan 4. PMID: 29302878. Trusted SourcePubMedGo to source
  10. Bennet SMP, Böhn L, Störsrud S, Liljebo T, Collin L, Lindfors P, Törnblom H, Öhman L, Simrén M. Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs. Gut. 2018 May;67(5):872-881. doi: 10.1136/gutjnl-2016-313128. Epub 2017 Apr 17. PMID: 28416515. Trusted SourcePubMedGo to source
  11. Weiss GA, Hennet T. Mechanisms and consequences of intestinal dysbiosis. Cell Mol Life Sci. 2017 Aug;74(16):2959-2977. doi: 10.1007/s00018-017-2509-x. Epub 2017 Mar 28. PMID: 28352996. Trusted SourcePubMedGo to source
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