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 microbiome. 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 a genetic analysis (DNA or RNA).

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, Genova (CDSA tests), and many others.

Genetic Analysis

PCR

The first type of genetic analysis assesses DNA using a technique called PCR. Bacterial DNA is extracted from your stool and then analyzed. Depending on the exact PCR methodology, the test may only report presence of absence of the microbe or it may quantify the amount of the microbe (qPCR).

While this test is far superior to culture tests, it is not perfect. The technology has to be looking for a specific microbe in order to detect it, so they generally only report on a minimal percentage of the microbiome. However, PCR testing can identify any type of microbe: bacteria, yeast, or parasite. For the most part, PCR is quite accurate IF the lab is using are using the correct primers. Primers are short DNA sequences designed to target the microbes being tested. If the primers are poorly designed, they may miss microbes or falsely report other microbes as the target microbe.

Options for PCR testing include GI-MAP by Diagnostic Solutions Laboratory, Genova GI-Effects, and Doctor’s Data GI 360. Quest and Labcorp also run PCR testing for pathogenic microbes only. Pricing ranges from about $300-$500 for these tests depending on your provider and insurance. These tests all require a doctor’s order. There are pros and cons for each test and differences in what microbes and markers they assess.

Please note that I no longer recommend using the GI-MAP. After extensively testing alongside more advanced stool testing, I found it to be completely inaccurate. The reference ranges are not accurate and it may falsely report the presence of pathogenic bacteria and H. pylori. Other doctors have reported getting completely different results when sending in stool samples from the same patient and the same stool sample.

Next generation sequencing

There are a variety of other ways to analyze the genetic material of microbes that can provide a complete and comprehensive profile of the microbiome. These are methods that have primarily been used in research and not clinical practice. But advancements in technology have made these technologies commercially available for reasonable prices.

The most widely used method is called 16S rRNA sequencing. It can provide a comprehensive profile of all the bacteria in your large intestine. While 16S testing is only for bacteria, it doesn’t need to know what it is looking for to provide information about that bacteria. It is also reasonably inexpensive, only about $100 and you do not need a doctor’s order to get it. However, 16S testing is not accurate down to the species level. So if you are looking to see if you have specific species in your gut, this test is not the best. 16S tests also do not report on yeast or parasites.

The available 16S tests are Biomesight, Ombre, Kean Health (Gut, not Gut+), and the American Gut Project. I have used all tests except American Gut Project with my patients and I prefer Biomesight—it provides the most clinically relevant report. Use the coupon code BIOADAPT to save ~$75 off your stool test. Ombre provides a lot of clinically irrelevant information or even false information and simply pushes their supplements. Kean has some significant issues in their pipeline, generating inaccurate raw data.

A newer type of next generation sequencing involves assessing the entire genome, called metagenomic sequencing. This can also be referred to as shotgun sequencing or whole genome sequencing. Like 16S testing, metagenomic sequencing does not need to know what it is looking for to report on it. But unlike 16S sequencing, it can also report on other microbes like parasites and yeast. And since it is sequencing more of the genome than 16S sequencing, it can accurately report on species. Lastly, it can also more accurately report on function of the microbes. For example, it can report on genes that are involved in butyrate production, which may provide a more accurate assessment of butyrate production in the gut. However, just because a bacteria has a gene does not mean the gene is actively being expressed, so it is not a definitive analysis. Metagenomic sequencing is more expensive than 16S sequencing. It is also subject to pipeline issues like 16S sequencing. The other downside is that reports from metagenomic sequencing do not provide access to all the data, so you don’t get all the data about all the bacteria in your microbiome. As more research is conducted and whole genome sequence libraries are refined and the technology becomes less expensive, this may be the go-to stool test.

Available tests include BiomeFx by Microbiome Labs (requires a practitioner), Kean Health Gut+, Microba, Flore, Genova Microbiomix, and Thorne Gut. I have tested out BiomeFx and Kean Health Gut+. Kean Health Gut+ produced very similar results to a 16S stool test from the same fecal sample, whereas BiomeFx had some big differences. After using BiomeFx with a number of patients, I noticed a few trends. Bacteroidetes may be reported as higher, whereas Proteobacteria, Lactobacillus, and Faecalibacterium may be reported as lower. At one point, all samples returned no Lactobacillus in the microbiome and this was for all patients after a certain point in time. This made me wonder if there are issues in their pipeline, the software systems used to interpret the raw sequencing data.

It is important to note that with commercial stool testing, there are a few issues. One is how they report the information. These companies are not doctors, so they are not able to really link your microbiome to your health or symptoms. In my experience, most of the “interpretation” provided by these labs is nonsense based on single research studies. The second issue is that any “recommendations” they provide are 100% biased and most of these companies are simply using the test to sell you products. As a doctor, I only use these tests for the raw data to see the relative abundance of specific bacteria in the patient. I then consult the research about the bacteria in relation to the patient’s symptoms and diseases, as well as therapeutic tools to modulate bacterial levels.

What about Viome? Viome is doing their own thing. They use “proprietary” mRNA sequencing technology (different type of genetic analysis). As a doctor, I prefer full transparency and steer aware from proprietary products, whether that is a test or a supplement. I have seen many Viome reports from patients and all I can say is their recommendations are utter nonsense—apparently, no one can eat red peppers due to a virus that is not proven to cause any symptoms or disease (WAY more research is needed to make any sort of health claims). So I don’t use Viome in clinical practice.

Cons of Stool testing

Your microbiome is not static. It can change throughout the day depending on your last meal, when you last exercised, what supplements and medications you took that day, and more. A lot of individuals believe that the dynamic nature of the microbiome means that stool testing is completely useless. This is not true. The presence or absence of certain microbes are significant to your health. Even transient elevations of certain microbes are significant to your health.

Best Way to Test Your Microbiome

As you can see, there are a wide variety of ways to test your microbiome. Most often, I start with a 16S test (typically Biomesight), as it is the most cost effective. If I am concerned about other microbes, I may layer on PCR testing.

It is also important to collect your samples correctly. Most commercial kits have you collect a small sample from your toilet paper. But this is a very poor collection methodology. Not only will it be contaminated by your skin microbiome, it will also not be accurate. Your stool is not homogenous with your gut bacteria. There can be clumps or clusters of gut bacteria in your stool. I advise patients to collect as much stool as they can in a container and insert the swab into 10-15 different locations of the stool at various depths.

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.