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

What You Need to Know About Stool Test Accuracy

Key Points:

  • Stool tests may be useful to identify pathogens, or to screen for disease, such as colon cancer and inflammatory bowel disease.
  • However, not all stool test results are clinically useful or accurate and some brands of stool tests have not been fully validated by research.
  • In particular, gut health tests that map the specific microbes in your gut have little practical use for individuals.
  • Testing companies may suggest treatment recommendations on the back of their microbiota mapping tests that are not validated by science.
  • Any stool test should be interpreted carefully with the help of a professional. A good clinician will treat the person and their symptoms rather than be hyper-focused on a lab result.

Stool tests are widely popular, especially in the functional medicine field. But do they give you accurate information that provides health benefits and helps you get better faster?

The short answer is that it depends on the test.

There are several types of stool tests that can supply interesting information, but they can be oversold, or their results misinterpreted or relied upon too heavily. Patients and practitioners alike 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 gastrointestinal symptoms, your functional healthcare provider may order a stool test to check for gut infections.

Sample collection usually involves collecting a small amount of feces (poop) in a clean container held over the toilet bowl. Sometimes a swab smear from your toilet paper is enough. Either way, you 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 may look for:

  • Parasites, such as Giardia lamblia or intestinal worms (tests may also identify the eggs of these parasites) [1]
  • Bacterial infections such as Salmonella, Clostridium difficile, or Campylobacter 
  • Fungal infections, like Candida
  • Viruses like rotavirus
  • The specific makeup of bacteria in your gut microbiome

A growing number of stool tests are microbiome tests that evaluate the relative abundance or absence of certain “good bacteria” or “bad bacteria” in your gut microbiota. Some of these gut biome or gut microbiome tests claim to map out the trillions of microbes in your gut’s ecosystem.

Stool samples are also used in gastroenterology practices to check for signs of digestive tract diseases like bile acid malabsorption and pancreatic insufficiency [2], as well as to look for markers of inflammatory bowel disease [3].

The fecal immunochemical test is another common stool test that’s used for colorectal cancer screening [4].

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 (ova) using a microscope. These stool tests are still widely used in doctor’s offices [5].

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 [6].

Common stool tests that use DNA-PCR methods to test for viruses, bacteria, parasites, yeast, etc., and are available in the United States include:

DNA-PCR tests have a reputation for being more accurate at detecting small quantities of pathogens and being better parasite tests. 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.

One study showed the BD MAX test for gut pathogens like Salmonella had a sensitivity of 89% and specificity of 99.8% (1). Another study showed the BioFire test’s sensitivity was higher, between 94.7% and 100%, with specificity between 98.6% and 100% (21). Although Verigene’s sensitivity had a broader range (71.4% to 95.4%), its specificity was between 99.1% and 100% (21). In general, these tests correctly identified who had a gut infection and who didn’t most of the time.

The popular GI-MAP and GI360 functional medicine stool tests also use DNA-PCR technology and should therefore be similarly accurate for identifying pathogens. However, these tests are still quite new to the market, and haven’t yet been widely studied. 

The manufacturer’s of GI-MAP lab wrote a white paper that showcases its accuracy, but the data have not been verified by a third party.

Microbiome Mapping Tests Are the Least Useful

Should You Use a Stool Test to Check Your Gut Health? - The%20Usefulness%20of%20Gut%20Biome%20Testing Landscape L

It’s much less clear what DNA-based tests mean when they’re used to map the whole of your microbiome and/or to report on dysbiosis (imbalances or overgrowth of some types of 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 [7].

Another new test, called the GA-map® test (not to be confused with the GI-MAP test) has also been scientifically validated as a test for determining dysbiosis in patients with IBS or IBD.

But it’s the applicability of these results that’s in question, as we don’t yet clearly know what various levels of beneficial bacteria mean for your symptoms or overall health.

Although some companies claim they can identify disease processes and prescribe treatments based on your microbial composition, the science doesn’t yet bear this out.

  • One 2021 systematic review and meta analysis processed the data from 10 human gut microbiome studies and a total of 1,733 human stool samples. The authors of the review concluded that the web of human host-microbiota-metabolite relationships in the human gut is so complex that much more research is needed in order to decipher and characterize it [8].
  • A 2018 literature review explains that while microbiome testing is increasingly available commercially, the state of knowledge relating to microbiome diagnostics is not yet advanced enough to provide much clinical value to doctors or their patients [9].

The takeaway from all of this is that when it comes to dysbiosis (and many other health conditions), it’s better to treat the person and their symptoms than to treat a lab value. Even if we had an accurate test to diagnose dysbiosis, that test wouldn’t tell us how to treat it. The tests might be interesting, but not clinically helpful.

Can Stool DNA Tests Predict What Dietary Changes You Should Make?

Some direct-to-consumer tests, like Viome and Ombre, claim certain levels of beneficial bacteria can predict what diet or supplements a person should consume. That’s an exciting possibility for patients and providers alike, but a little premature as there’s little peer-reviewed data validating these particular claims.

At worst, these tests can be unhelpful or even fraudulent. A case in point is the company uBiome, which began in 2012 to offer microbiome tests to consumers. In 2019, the FBI raided uBiome for defrauding investors, health insurers, doctors, and clients [10]. It was discovered that the company’s datasets may have been tainted with stool samples from human infants and pet dogs [11].

Good and reputable tests do exist — for example, studies have shown the GI360 test can accurately predict which people will respond well to a low FODMAP diet based on their bacterial community [12, 13]. But it’s important to remember that our knowledge of the clinical implications of specific bacteria in the gut microbiome is truly in its infancy [14].

If you have any sort of microbiome testing it’s always best to do it under the guidance of an experienced practitioner who has a lot of knowledge in interpreting these results. Companies work hard to convince both patients and clinicians of the benefits of their tests, and without wise interpretation and an understanding of the nuances, you can come away from testing with the wrong conclusions.

Scientifically Validated Stool Tests

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 tests are a highly accurate indicator of inflammation in the large intestine. When elevated in someone with digestive symptoms, calprotectin can suggest inflammatory bowel disease [3].
  • Fecal elastase-1 (an enzyme) [15] and fecal steatocrit (fecal fat) [16] tests are indicators of exocrine pancreatic insufficiency (EPI) or bile acid malabsorption when positive in patients with diarrhea.
  • A fecal immunochemical test, also known as a fecal occult blood test or guaiac fecal occult blood test (FOBT or gFOBT), is useful for screening for colorectal cancer, though colonoscopy is still the gold standard [17].
Should You Use a Stool Test to Check Your Gut Health? - Scientifically%20Validated%20Stool%20Tests Landscape L

Stool tests that can sometimes be helpful include:

  • A glucose-based breath test for detecting small intestinal bacterial overgrowth or SIBO (less likely to produce a false positive than a lactulose-based one) [18].
  • Vinculin/CdtB antibody testing, which can be helpful to determine if diarrhea is due to irritable bowel syndrome, or whether more testing is needed to look for celiac disease or inflammatory bowel disease, such as Crohn’s disease and colitis.
  • Gut biome tests that look for specific pathogens or parasites that could be causing illness (examples include amoebas, worms, Giardia, and Cryptosporidium).

Some of the above gut health markers are included in DNA-PCR stool tests, or they’re also available through your regular doctor’s office.

How to Interpret Stool Tests

Since many stool tests haven’t 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. A microbiome mapping test might be useful as part of a data-gathering exercise (to establish what is a healthy microbiome at a population level), but not as a personal gut-healing or dietary prescription.

Fortunately, you usually don’t need a lab test or high-tech mapping of your digestive system to start healing your gut. 

A more cost-effective approach to gut health that works for many people is to use probiotics [19, 20, 21] and a low FODMAP diet [22].

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

The Bottom Line

Stool tests are best used for those who haven’t seen the results they hoped for with more basic interventions (like removing foods you’re sensitive to and trying probiotic therapy).

Stool tests are best left to experienced practitioners to administer and interpret, and should be used sparingly. Ultimately, not all stool tests are created equal, and your results need to be read with caution.

If you would like more direct help and advice to resolve your gut symptoms, consider reaching out to the clinic at the Ruscio Institute for Functional Medicine.

The Ruscio Institute has developed a range of high-quality probiotic formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

➕ References
  1. Ova and Parasite Test: MedlinePlus Medical Test [Internet]. Available from:
  2. Stool Elastase: MedlinePlus Medical Test [Internet]. Available from:
  3. Ayling RM, Kok K. Fecal Calprotectin. Adv Clin Chem. 2018 Oct 1;87:161–90. DOI: 10.1016/bs.acc.2018.07.005. PMID: 30342711.
  4. Fecal immunochemical test (FIT): MedlinePlus Medical Encyclopedia [Internet]. Available from:
  5. Fecal culture: MedlinePlus Medical Encyclopedia [Internet]. Available from:
  6. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, et al. Microbiome 101: studying, analyzing, and interpreting gut microbiome data for clinicians. Clin Gastroenterol Hepatol. 2019 Jan;17(2):218–30. DOI: 10.1016/j.cgh.2018.09.017. PMID: 30240894. PMCID: PMC6391518.
  7. Casén C, Vebø HC, Sekelja M, Hegge FT, Karlsson MK, Ciemniejewska E, et al. 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. PMID: 25973666. PMCID: PMC5029765.
  8. Muller E, Algavi YM, Borenstein E. A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations. Microbiome. 2021 Oct 12;9(1):203. DOI: 10.1186/s40168-021-01149-z. PMID: 34641974. PMCID: PMC8507343.
  9. Staley C, Kaiser T, Khoruts A. Clinician guide to microbiome testing. Dig Dis Sci. 2018 Dec;63(12):3167–77. DOI: 10.1007/s10620-018-5299-6. PMID: 30267172.
  10. Health Test Company UBiome Has Filed For Bankruptcy [Internet]. Available from:
  11. Poop From Pets and Infants Created Flaws in Research at Startup UBiome [Internet]. Available from:
  12. 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):429–36. DOI: 10.1007/s10620-017-4893-3. PMID: 29302878.
  13. Bennet SMP, Böhn L, Störsrud S, Liljebo T, Collin L, Lindfors P, et al. Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs. Gut. 2018 May;67(5):872–81. DOI: 10.1136/gutjnl-2016-313128. PMID: 28416515.
  14. Weiss GA, Hennet T. Mechanisms and consequences of intestinal dysbiosis. Cell Mol Life Sci. 2017 Aug;74(16):2959–77. DOI: 10.1007/s00018-017-2509-x. PMID: 28352996.
  15. Domínguez-Muñoz JE, D Hardt P, Lerch MM, Löhr MJ. Potential for Screening for Pancreatic Exocrine Insufficiency Using the Fecal Elastase-1 Test. Dig Dis Sci. 2017 May;62(5):1119–30. DOI: 10.1007/s10620-017-4524-z. PMID: 28315028.
  16. Sugai E, Srur G, Vazquez H, Benito F, Mauriño E, Boerr LA, et al. 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.
  17. Li JN, Yuan SY. Fecal occult blood test in colorectal cancer screening. J Dig Dis. 2019 Feb;20(2):62–4. DOI: 10.1111/1751-2980.12712. PMID: 30714325.
  18. Rana SV, Sharma S, Kaur J, Sinha SK, Singh K. Comparison of lactulose and glucose breath test for diagnosis of small intestinal bacterial overgrowth in patients with irritable bowel syndrome. Digestion. 2012 Mar 30;85(3):243–7. DOI: 10.1159/000336174. PMID: 22472730.
  19. Wang F, Feng J, Chen P, Liu X, Ma M, Zhou R, et al. Probiotics in Helicobacter pylori eradication therapy: Systematic review and network meta-analysis. Clin Res Hepatol Gastroenterol. 2017 Sep;41(4):466–75. DOI: 10.1016/j.clinre.2017.04.004. PMID: 28552432.
  20. García-Collinot G, Madrigal-Santillán EO, Martínez-Bencomo MA, Carranza-Muleiro RA, Jara LJ, Vera-Lastra O, et al. Effectiveness of Saccharomyces boulardii and Metronidazole for Small Intestinal Bacterial Overgrowth in Systemic Sclerosis. Dig Dis Sci. 2020 Apr;65(4):1134–43. DOI: 10.1007/s10620-019-05830-0. PMID: 31549334.
  21. Greco A, Caviglia GP, Brignolo P, Ribaldone DG, Reggiani S, Sguazzini C, et al. Glucose breath test and Crohn’s disease: Diagnosis of small intestinal bacterial overgrowth and evaluation of therapeutic response. Scand J Gastroenterol. 2015 May 19;50(11):1376–81. DOI: 10.3109/00365521.2015.1050691. PMID: 25990116.
  22. Marsh A, Eslick EM, Eslick GD. Does a diet low in FODMAPs reduce symptoms associated with functional gastrointestinal disorders? A comprehensive systematic review and meta-analysis. Eur J Nutr. 2016 Apr;55(3):897–906. DOI: 10.1007/s00394-015-0922-1. PMID: 25982757.

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