Microbiome Testing Explained + Best Microbiome Testing Companies

Microbiome Testing: Wild Goose Chase or Modern Miracle?

By now, most people have heard of the best consumer DNA testing services, such as 23andMe or AncestryDNA. These services test the DNA in your cells to help you discover your ancestry and genetic variants which may affect your health.

But, this is only a tiny part of the overall picture of health. In fact, scientists are beginning to understand that while your DNA plays a role, your environment plays a much larger role. And, as scientists are learning, the bacteria and small organisms which live inside you and on your skin heavily influence how your body experiences the environment. 

Microbiome testing (gut microbiome tests and skin microbiome tests alike) is essentially DNA testing for the small creatures which inhabit your body. Scientists have found that the ecosystem they form may be more important for overall health than the DNA in your cells.

In this article, we analyze the origins of, findings of, as well as the best microbiome companies providing test kits. Is microbiome testing a scientific wild goose chase, or is it a miracle of modern science?

Keep reading to find out!

The Origin of Microbiome Testing

While it sometimes feels like the world of science moves at a slow, but steady pace, this couldn’t be farther from the truth. In reality, it stagnates for years then expands rapidly. For example, science has known about DNA molecules since 1869. Then, it took nearly 100 years for Crick and Watson to discover the structure of DNA in 1951.

Finally, in 1990, the Human Genome Project was initiated. By 2003, it was complete. Not only did the project result in a better understanding of human genetics, but it led to much better DNA processing technology. By 2006, companies like 23andMe were using this technology to analyze consumer DNA at a rate thousands of times faster than methods available in 1990. 

But, researchers didn’t stop with human DNA. Some researchers decided to use DNA technology to take a look at the organisms which live inside of us. This was the Human Microbiome Project, started in 2009 and continuing today. What they found was nothing short of shocking:

Each and every one of us has thousands of species of bacteria, archaea, viruses, and macrophages in and on our body. Don’t believe me? Check out this graphic of all the different groups of bacteria scientists have found on our skin alone!

What Can We Learn From Our Microbiome?

Each of the groups of bacteria found on the human body may contain hundreds of species. This means there is an entire ecosystem of bacteria and other microorganisms living on your body! But, can we actually learn anything about our health through a microbiome test kit?

The entire theory that the microbiome may be just-as or more important than your own DNA originated in the 1880s with a scientist named Elie Metchnikoff. Elie, a Ukranian zoologist, received the Nobel Peace Prize for his work on immunity cells and their functions. But, the more Elie researched, the more he felt the microbiome was incredibly important. He even started the “probiotics” movement, eating yogurt and dairy products daily to bolster his own microbiome. Unfortunately, he died at 71 of heart failure, possibly from eating so many dairy products over his lifetime. 

However, modern microbiome testing companies are continuing Elie’s train of thought. They advertise many health-related benefits of getting your microbiome tested, such as weight loss or relief of stomach pain. Some doctors are even starting to perform fecal transplants, a process which is supposed to change your gut microbiome by depositing a new microbiome in your gut. This process has been found to work on some gut infections with great success. Other scientists have found strong correlations between certain diseases and various microbiomes.


Is Microbiome Testing Proven to Work?

The answer to this question is yes, and no. While microbiome testing can help determine whether or not you have certain conditions, there is still much research to be done. For instance, in the early 2000s a study was published suggesting that obese individuals had a specific microbiome. Reanalysis of the data from that study show that this correlation was not nearly as strong as was suggested by researchers.

Further, more recent research has shown that the microbiome is much too dynamic to be measured accurately in a single testing session. For example, an article published in Nature suggested that the microbiomes associated with Irritable Bowel Disease can range dramatically depending on the day. One moment they can clearly be a disrupted microbiome, other times they are no different than the microbiome of a healthy person.

Other scientists had this to say of microbiome test kit companies:

“We caution patients and providers that the current microbiome tests, given the state of knowledge and technology, do not provide much value in clinical decisions. Considerable research remains to be carried out to make this objective a reality.”

That being said, you may still be interested in microbiome testing, just out of curiosity.


How Does At-Home Microbiome Testing Work?

Just like DNA testing, when you buy a microbiome test for your skin or gut microbiome, the microbiome testing company will send you a sampling kit. Most of them call their basic test “Smartgut”. Instead of sampling your cheek cells or filling a tube with saliva, microbiome testing requires a sample of your microbiome. And that only comes from one place.

Most microbiome tests have you take a rice-sized sample of your feces when you go to the bathroom. Considering that your intestines are around 25 feet long, a rice size sample is curiously small. It’s essentially the equivalent of taking a cup of water from a lake and trying to determine all the species in the lake. This, along with the fact that most microbiomes fluctuate regularly, suggests that microbiome testing is not as rigorous as it should be to accurately determine the organisms living inside you. 



What are the Top Microbiome Testing Companies?

Though there are only a handful of microbiome testing companies, we have compiled the best microbiome testing companies here:

ViomeThis company tells you what foods your body can process well, and which you should avoid, based on your microbiome. Supposedly, their recommendations will allow you to obtain the best nutrition for the bacteria in your system, leading to better health. They offer tests for weight loss, sleep, mental clarity, digestive issues, skin health, and more. But, the company’s website does not provide the actual studies where this information was obtained. Supposedly, the company is actively completing its own studies, but it is unclear whether this information is published in scientific journals. One article was found, but it was on a preprint server and had not yet been peer-reviewed.

In other words, the company is posting their science, but is not waiting for confirmation from other scientists before moving forward with their marketing campaign.

We are currently working on a comprehensive VIOME review discussing costs, background, offering, quality of results, data protection and collective user opinions in the same fashion we do when we compare DNA kits.

uBiomeOne of the only sites to actually post the scientific publications they are basing their tests on, which is very promising. This company claims to offer many of the gut-health benefits, such as weight loss, offered by other companies. One great opportunity the company provides is the ability to measure your microbiome three times: before, during, and after a lifecycle change. This allows you to more fully understand how diet and exercise can affect you.

However, you should also know that uBiome was raided by the FBI for repeatedly billing customers for tests without their consent. While this issue has since been resolved, it sheds a poor light on the company’s culture.

We have finished working on a comprehensive uBiome review discussing costs, background, offering, quality of results, data protection and collective user opinions in the same fashion we do when we compare DNA kits.


smartDNAYour doctor can order this microbiome test, which will help them determine if any negative species in your gut could be causing a health problem. However, it does not appear that this test is available to patients without a doctor’s order. This is actually a great service to their customers because microbiome testing is on the leading edge of science. In fact, it is likely that even your doctor will struggle to understand the full implications of your test results. The company also has some unique offerings, such as their test for potential cardiac events based on the biochemical markers in your blood. .


This company will not only test you microbiome, but will suggest specific probiotics to help any conditions you may have. User be warned: Probiotics are essentially the vitamins of the microbiome industry. Science has had very mixed results with the use of probiotics. So, Thryve is essentially combining two unproven techniques – probiotics and microbiome testing – into a product which they claim will change your gut’s ability to process food. Interestingly, the CEO of Thryve completed an “Ask Me Anything” post on Reddit. When a Reddit user commented that one of the scientific papers used by Thryve actually discredited the microbiome testing industry, the CEO simply said that 23andMe had similar criticisms that they overcame.

Yes, My Heritage DNA isn’t a microbiome company. It is rather a DNA test kit (which we believe is the best DNA test kit for most uses). Where science and the implementation of science is currently at, we simply think this is more of a valid test than any of the top microbiome testing kits currently on the market. For $79 (or less when there’s a special offer), it’s a worthwhile test to try!

Where is Microbiome Testing Headed?

Though the current science behind microbiome testing is confusing, the potential of microbiome testing is enormous. Though studies disagree on the effects and composition of different microbiomes, many studies agree that microbiomes matter. Many of the companies listed above are actually at the forefront of research into the microbiome. In twenty years, microbiome testing may be a standard medical practice that every doctor integrates into diagnosing and treating disease.

What to do instead of a Microbiome Test?

If you are curious about microbiome testing, but are dissuaded by the price or the uncertainty of the science, you should know that changing your microbiome is as easy as eating different foods. Since different microorganisms survive on different food sources, you can help or hurt them depending on the type of diet you eat. In general, a meat-heavy diet with low fiber selects for microbiomes which may negatively impact your gut microbiome. Greens, vegetables, fruits, and nuts are generally related with good health and a healthy microbiome. If you think your microbiome is messed up, try switching to a whole-foods, plant-based diet. This diet has been shown to alleviate many conditions, from obesity to heart disease. 

Final words about Microbiome Testing and Test Kits

If you want to “GutSmart” test yourself through a microbiome test then you need to verify you understand the science behind it at least to a basic extent and take all the information you get today with a grain of salt. Don’t rush into changing your lifestyle or panic about certain prospects, but rather repeat the test a few times knowing that your microbiome portfolio changes heavily and rapidly throughout the day and in between different days.  Among the best microbiome companies like uBiome and VIOME you can find a variety of tests for reasonable costs.