Stool and Microbiome Tests Sold in Integrative Practice: What They Show and Do Not Show
What stool and gut microbiome tests sold in naturopathic and integrative settings measure, what expert panels and a national standards lab found, and which stool tests have proven medical uses.
Content last updated . This page has not been medically reviewed.
Start here
This page is information only and does not replace medical care. Stool tests are ordinary medical tools for some problems. MedlinePlus lists symptoms such as blood or mucus in the stool, weight loss and fever among the reasons a provider may order a stool test for parasites. [1] Symptoms like these, or symptoms that are severe or getting worse, are a reason to see a doctor first rather than to start with a mail-in kit. If you are sick right now, see a clinician or call your local emergency number (911 in the United States).What the tests are
Some naturopaths, functional medicine clinicians, medical doctors and other practitioners offer stool or "gut microbiome" tests, and some companies sell them straight to consumers. The tests describe which microbes (bacteria and sometimes fungi) are found in a stool sample and often add scores or "balance" ratings. The FDA notes that some direct-to-consumer tests measure "levels and types of bacterial flora" (the microbiome), and that these tests have varying levels of evidence behind their claims. [2] Different kinds of practitioners may offer or order them, including licensed naturopathic doctors (ND), medical doctors, nurse practitioners, dietitians and unlicensed naturopaths; training, regulation and legal scope differ by state and country, and this page does not rank them. See credentials, titles and scope of practice.What reviewers found
| Question | What the source found | Strength of evidence |
|---|---|---|
| Is a microbiome test useful for diagnosing or guiding care? | An international expert panel (2025) said evidence supporting clinical usefulness "is scarce" and that direct-to-consumer tests exist without consensus on regulation or any proven value in clinical practice. [3] | Expert consensus, no proven clinical value for routine use |
| Do different companies give the same result? | A national standards laboratory (NIST) sent one standardized stool material to seven direct-to-consumer services; variability between providers was on the same scale as biological variability between different donors. [4] | One analytical study; points to unreliable measurement |
| Are they regulated like medical tests? | The FDA says direct-to-consumer tests for general wellness or low-risk purposes are generally not reviewed before they are offered. [2] | Regulator statement (United States) |
The NIST authors also wrote that analytical performance is a prerequisite for making sound clinical recommendations. [4] This page does not name or rank any company.
What a stool test can legitimately do
Stool tests with a clear purpose exist. An ova and parasite test looks for intestinal parasites and their eggs by checking a stool sample under a microscope, and it is used to see whether parasites are causing symptoms that look like an intestinal infection. [1] That is a different question from asking for a general picture of your microbiome, which is the marketed use this page checks. Proper evidence not found, in the sources we read, that a general microbiome report should change diet or supplement choices for people without a diagnosed condition. We searched PubMed, FDA and MedlinePlus pages and a general web search for this and found the expert consensus and standards study above rather than trials of test-guided treatment.Limits to keep in mind
- The NIST study shows the same standardized material can come back with different results from different services. [4]
- A "low" or "imbalanced" score does not by itself diagnose a disease. The consensus panel's aim was to set minimum requirements and limit inappropriate tests. [3]
- Extra tests can lead to more tests and worry. See over-testing and false positives.
Questions to ask before any test
- What medical decision will this result change, and who will interpret it?
- Is the test cleared or reviewed by a regulator, and for what use? The FDA says if it does not regulate a home test, the U.S. government has not determined it is reasonably safe or effective. [5]
- What does it cost, does the person ordering it also sell supplements, and what happens to my data?
- Will my own doctor review the result and my medicines?
Where to read more
The Biohacking section covers microbiome tests in more depth. The wider overview of tests in this setting is tests sold in integrative practice. To weigh a claim, use how to evaluate a therapy claim and choosing a qualified practitioner.Frequently asked questions
Can a microbiome test diagnose a disease?
An international expert panel said evidence supporting the clinical usefulness of microbiome diagnostics is scarce. [3]
Do different microbiome test companies agree?
In a NIST study of seven services using one standardized stool material, differences between providers were as large as differences between different donors. [4]
Are stool tests ever medically useful?
Yes, for specific questions. An ova and parasite test checks stool for parasites and their eggs when symptoms suggest an intestinal infection. [1]
Does the FDA review every direct-to-consumer test?
No. The FDA says tests for general wellness or low-risk purposes are generally not reviewed before they are offered. [2]
Should I skip my doctor and use a mail-in kit?
No. Blood in stool, weight loss, fever or worsening symptoms are reasons to see a clinician, and a kit does not replace that visit. [1]
References
- MedlinePlus (U.S. National Library of Medicine). Ova and Parasite Test. Read 2026-10-22.
- U.S. Food and Drug Administration. Direct-to-Consumer Tests. Read 2026-10-22.
- Porcari S, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol 2025;10(2):154-167. Read 2026-10-22.
- Servetas SL, et al. Evaluating the analytical performance of direct-to-consumer gut microbiome testing services. Commun Biol 2026;9:269. Read 2026-10-22.
- U.S. Food and Drug Administration. How You Can Get the Best Results With Home Use Tests. Content current as of 2017-12-28. Read 2026-10-22.
Education, not medical advice. This page is for general information. It does not diagnose or treat any condition and is not a substitute for care from a qualified health professional. Natural does not automatically mean safe. Ask a clinician or pharmacist before changing your care, especially if you take medication, are pregnant or breastfeeding, or have a health condition.