Best Way to Test Your Microbiome AKA Best Stool Test

A stool test is a critical part of a comprehensive gut evaluation. However, not all stool tests are created equal. And unfortunately, your doctor may not know that. Many health practitioners understand that treating the gut is important for many health conditions, but most of them don’t know the best way to evaluate the gut. Many of my patients come to see me after working with another health practitioner and I rarely see a practitioner utilizing the right stool test. So let’s review stool testing so you don’t waste money on the wrong one.

There are two main types of stool testing: culture and DNA.

Culture Test

A culture test attempts to grow bacteria from your stool sample. It can only grow bacteria that can metabolize oxygen. This is a problem because MANY of the bacteria in your gut can’t metabolize oxygen. So this test will not be able to provide information on a large part of your microbiome.

The second major issue is that it can’t accurately tell you how much of what bacteria is present in your gut. Generally, the lab quantifies bacteria as no growth up to 4+ based on how many colonies of that bacteria grew in culture. But this is not necessarily reflective of how well the bacteria grow in your gut.

Most of these tests also include analysis of yeast and parasites. Most tests will try to culture yeast and use a microscope to look for yeast in the stool sample. They also use the microscope to look for parasites. For a variety of reasons, it is easy to miss yeast and parasites with these methods.

So the bottom line is culture stool test is VERY limited in accuracy and specificity.

The majority of stool tests on the market offered by doctors are culture stool tests. Lab companies include Great Plains Lab, Doctor’s Data, BioHealth, Genova (CDSA tests), and many others.

DNA Test

A DNA test extracts bacterial DNA from your stool sample and then uses that DNA to identify and quantify bacteria. With this technology, we can identify hundreds of different bacteria. We can also get a much more accurate idea of how much of each bacteria is present in your gut.

While this test is far superior to culture tests, it is not perfect. The technology has to be looking for a specific bacteria in order to detect it, so it is possible that we may be missing some bacteria. This technology can also struggle to accurately identify bacteria down to the species level. It is pretty solid at the genus level, but it can have a hard time differentiating between species because the DNA may be very similar.

This type of testing also uses DNA to identify yeast and parasites, which again, is much more accurate. I have seen this test pick up yeast and parasites that the culture tests failed to identify.

There are not as many options when it comes to DNA testing. My preferred test is the GI-MAP by Diagnostic Solutions Laboratory. The Genova GI-Effects also utilizes this methodology but in my opinion, the GI-MAP is the superior test because it reports more bacteria and does a DNA based assessment for yeast instead of a culture. Pricing ranges from about $300-$500 for these tests depending on your provider and insurance. Both tests are only available through doctors.

Commercial Tests

If you don’t have access to a doctor who will order the GI-MAP, you may want to consider a commercial DNA stool test.


  • Typically cheaper than prescribed tests (usually about $100)

  • Often assess for more bacterial species than the GI-MAP


  • Most don’t assess for yeast

  • Most don’t assess for parasites

  • You need to know how to interpret the raw data

The biggest issue with the commercial tests is the lack of clinically relevant information. Since these companies are not doctors, they cannot diagnosis and treat disease, so they don’t provide a clinically relevant interpretation of your test results. They do provide you with a lot of information in an attempt to seem relevant, but almost NONE of it is helpful. And a lot of it is completely inaccurate. So for these tests to be worthwhile, you need to be working with a doctor who knows how to interpret the raw data. Unfortunately, it is rare to find a doctor who can do that.

Companies for commercial tests include uBiome, Thryve, DayTwo, and Viome. There is also a research group doing these tests called the American Gut Project.

Best Way to Test Your Microbiome

To get the most comprehensive assessment of your gut, I recommend testing with GI-MAP AND a commercial test at the same time. At this time, I am not endorsing any specific commercial test as I need more information.

If funds are limited, then a commercial test may be sufficient but I highly recommend that you work with a doctor who can interpret the raw data because the information the lab companies provide is worthless in my opinion.

Now, just because the GI-MAP is a superior test doesn’t mean that the culture tests have no value. They still can provide clinically relevant information, they simply can’t provide the whole picture.

Getting the right test done is important, but it is more important that you are working with a doctor who knows what to do with the information. All too often, I see other practitioners failing to correctly interpret the test results or appropriately treat based on the testing. How do you know if the practitioner has adequate training in this area? Ask them if they know how much Proteobacteria in the gut are considered healthy. If they don’t immediately respond with less than 4% and the lower the better, they do not have sufficient training in the microbiome.


While I utilize labs from several of the companies mentioned in this article, I do not profit from contracting with these companies and I have not received compensation for this article. My opinions presented in this article are based on my clinical judgement and not money.

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I'm Dr. Carly and my mission is to create a health revolution. I believe that another prescription is not the answer. I believe in using natural therapies that go beyond the symptoms. And I believe that doctors should spend way more than 7 minutes with a patient.