Best Microbiome Testing Companies

Knowing if your gut microbiome is in good shape can be a great tool for building the healthiest body you can! Here, Hannah, one of our resident nutritional scientists, reviews the top 5 best microbiome testing companies that you can work with to learn the ins-and-outs of your unique gut bacteria!

The whole adage “you are what you eat” really steps up to a whole new level when you think about your gut microbiome!

This vast community of bacteria, viruses, and fungi living in your digestive tract feeds on what you eat and plays a role in hundreds, if not thousands, of bodily processes, including:

Basically, your gut microbiome is critical for keeping your body healthy!  So, knowing if your gut microbiome is, itself, in good shape, can be a great tool for building the healthiest body you can!

And this is where microbiome testing can come in handy!

(If you want to dig deeper into the importance of the gut microbiome then you’ll also like Gut Health: 7 Reasons Why It’s Important.)

What is Microbiome Testing?

Microbiome testing offers you a way to build a profile of your gut bacteria.  It allows you to see what bacteria are living in your digestive tract. 

This is usually done by collecting poo samples (yum!) and sending them to a laboratory for testing.

The laboratory sequences the DNA from the bacteria in your sample.  This lets them build a picture of the types and ratios of bacteria you have in your fecal matter.

Currently, there are two main ways that commercial companies can test your gut microbiome: 

1. 16S rRNA Technology  

Essentially, this method collects a small sample of fecal matter on a cotton swab and sequences the bacteria down to the genus-level.  (This is like figuring out if DNA belongs to a dog or a cat. It will not, for example, be able to tell you if a dog is a miniature schnauzer or great dane.  Although advancements in 16S are making it better at telling the differences between species, it still struggles to tell similar strains of bacteria apart.)

2. Metagenomic Sequencing  

This method can identify bacteria down to a species level — that is to say, it could tell the difference between a schnauzer and a great dane. 

How Accurately Does Microbiome Testing Reflect Your Gut Health? 

Man holding gut microbiome testing tubes

Here is what we know about the microbiome and what microbiome testing can really tell you about your gut health.

Cause and Effect Relationships?

We know that some bacteria can be harmful to your health.  We also know that a lack of diversity — that is the variety of bacterial species you have in your gut — can have negative health consequences, as well.

But we don’t yet know how all the different bacteria work together.  This means that it may not be as simple as “good” bacteria and “bad” bacteria.  Whether your gut helps keep you healthy or is making you sick might have more to do with the relationships between bacterial types. 

In addition, most studies have worked with correlation, not causation.  This means that studies have found that “people with x symptoms tend to have x gut bacteria.”  But that doesn’t necessarily mean that x gut bacteria caused symptom x. Those types of bacteria might simply grow better when you have condition x, for example. 

Combined, these issues make it difficult to know exactly what microbiome testing results actually mean for your gut health.

All the Bacteria in Your Microbiota?

There is also some question of how accurately current microbiome tests reflect the make-up of your gut microbiome.


For one, many of the current microbiome testing methods require samples to be cultured in the lab.  This process biases the results towards bacteria that grow faster on Petri dishes.  This means it may look like you have lots more of one type of bacteria in your gut than you really do. 

Finally, researchers are becoming ever more aware of the fact that the bacteria in your stool may not necessarily be representative of how your entire gut microbiome looks.  This is because each part of your digestive tract has different bacterial make-up.  You miss what the bacteria in your mouth, throat, stomach, and small intestine really look like when you just look at the bacteria in your stool. 

So, while gut microbiome testing can give you interesting information about the make-up of your gut microbiome, it can’t offer you complete answers about your gut health. 

Related Reading: The Lactulose Mannitol Test: The Pros and Cons of Leaky Gut Testing

Can Microbiome Testing Help Your Health?

Medical report chart

As a huge proponent of gut health, I wish I could suggest microbiome tests were a breakthrough in gut diagnoses and treatment. 

Unfortunately, current microbiome testing cannot provide medical diagnoses.  It cannot even necessarily tell you that having a specific type of bacteria in your intestine is definitely good or bad for you, as an individual.

And, at the moment, they can’t even help you choose a personalized gut-healthy diet. We simply don’t know enough yet about the relationships between diet, microbiome, and specific diseases.

All that being said, we do know that the diversity of your gut bacteria is important.  An abundance or overgrowth of any one particular bacteria is almost certainly bad for your gut health. 

Since these tests can tell you if you have a really high number of a particular type of bacteria, they can help tip you off if you are at high risk for poor gut health.  This may even be the case if you don’t have any worrisome digestive issues yet. 

And keep in mind that these tests are ever-evolving.  The more people get their microbiome tested, the stronger the data is linking certain bacteria to certain conditions.  As the research comes in, gut microbiome testing companies update their reports and what their results mean. 

This means that even if you do a microbiome test now and it doesn’t tell you anything useful, it may be updated with helpful information in the future.  (Though, your gut microbiome changes over time. So, a test you take now might not reflect how your gut microbiome looks in a few months or years.) 

How Do You Get Your Microbiome Tested?

Man using a microscope to examine gut microbes

Currently, most tests are available commercially through an online lab or stockist.  You can simply order them and have them delivered to your house.

There were tests available via medical professionals that were partially covered by insurance.  Unfortunately, these have been withdrawn pending an insurance fraud investigation.

5 Best Microbiome Testing Companies

If you think you’d like to have your gut microbiome tested, which test should you order?  

There are a variety of brands available but a few definitely stand out in terms of popularity.  Here are my reviews of the top five main players in the microbiome testing sphere. 

5. uBiome

uBiome microbiome testing company

uBiome is a San Francisco-based biotechnology company that sequences customers’ gut microbiomes.  

Originally, uBiome offered both commercial and medically-ordered microbiome test kits.  Recently, though, uBiome has come under investigation for possible insurance fraud around its prescription testing kits.  At the time of writing, uBiome’s clinical tests are not available.

What Products Does uBiome Offer and What Do They Test For?

As their two clinical tests are “out of service”, uBiome currently offers just two test kits: 

  • Gut Explorer Kit 
  • Gut Time Lapse Explorer Kit 

These tests analyze the DNA in your stool sample and extract the sequences known to be from bacteria.  From here, they can offer you insight into which bacteria are most prevalent in your gut.

The first kit, Gut Explorer, is a single test.  Your results are compared to the results of all the other samples the company has tested.

The second kit, Time Lapse, is multiple tests.  Rather than comparing your results to other people’s samples, this kit lets you compare multiple of your own samples taken over a longer period of time.  This gives you insight into how your microbiome is changing (in response to a change in diet, lifestyle, or new medical treatment, for example).  

How Do uBiome Products Work?

It is relatively easy to take the uBiome microbiome sample.  When you use the restroom, simply wipe as per usual. Then collect a sample off the toilet paper with the swab they give you.

You only need a small amount on the swab — just enough to turn the swab light brown in color.  Then you stir the swab in the enclosed tube with stabilizing fluid, replace the cap, and shake for 1 minute.  Done!

Then all you need to do is send the completed sample back to the company.  (Don’t forget to enter barcode onto their user site so it can be assigned to you.)

Whilst uBiome claims that its technology uses “patented precision sequencing™ methods and advanced computational techniques”  there is not much to describe what this actually means.

What Do uBiome Customer Reviews Say?

“This kit is amazingly cool!  It’s super easy to use and is giving me info I’ve always wanted to know about the bacteria that work with me to digest food in my gut.  It’s awesome to take control of my health in this new and innovative way. So, I highly recommend this product to anyone who cares about science or knowing more about their bodies.”

“I did the one-time test with Ubiome hoping for the promised ‘actionable insight to understand and improve my gut health’.  I got my results in about 3 weeks; however, these results are virtually impossible to understand and interpret without the help of a gastroenterologist. 

I contacted Ubiome to see if someone could walk me through the report, and they said results are only intended for ‘healthcare professionals to assist in their clinical treatment decisions.’ This is a very different frame than what’s presented in their marketing materials.”

How Much Do uBiome’s Testing Kits Cost?

Explorer Kit  $89

Time Lapse Kit  $199 

uBiome Pros and Cons


  • uBiome is one of the leaders in microbiome sequencing
  • fast turn-around time
  • informative recommendations


  • company may be promising a little more than is scientifically feasible 
  • questionable “trust” factor: company is not forthcoming with the technology they use and recommended foods change dramatically every few months

Final Thoughts on uBiome

With the looming FBI raid casting such a large shadow over this company, it is hard to give them a gleaming review.  They are somewhat reminiscent of another health tech company that made dubious promises and went bankrupt in 2016.

However, I cannot entirely point fingers at uBiome for trying to be a leader in its industry. Arguably with dreams of running slightly before they have learned to crawl, this company can see the future of gut health technology — a world where microbiome testing will be the standard of care.  And they aim to make it accessible for all.

In complete fairness, they also state that their results are meant for education and research purposes only and not for medical diagnosis.  But this information is not presented as clearly on their website as it could be. 

You May Also Like: Sodium Butyrate Benefits: 9 Amazing Ways This SCFA Boosts Health

4. Viome

Viome gut microbiome testing company

Viome was born at the prestigious Los Alamos National Lab and originated from technology initially designed for national security.  It is based on a complete sequencing of the gut microbiome from a very small stool sample.

What Products Does Viome Offer and What Do They Test For?

Viome offers two test kits:

  • Gut Intelligence Test 
  • Food Sensitivity Intelligence Test

The Gut Intelligence test looks at what bacteria is in your digestive system and what metabolites they’re producing.  From this, Viome provides you with a breakdown of the function these bacteria are playing in your health (i.e. helpful or harmful).

The Food Sensitivity kit examines your tolerance of 40 different foods and gives recommendations on foods to avoid.

How Do Viome Products Work?

Viome uses RNA sequencing to look at not only what bacteria are in your gut but what those bacteria are actually doing.) 

Similar to the other commercial kits on the market, you need to take a swab of your stool sample, mix it into a solution, and ship it back to the lab.

You will also need to fill out some online health and diet questionnaires.

What Do Viome Customer Reviews Say?

Many reviews are amazed at how well Viome converted their results into meaningful steps for improving their microbiome.  They love the personalized nutrition information about foods which will help or hinder their health goals.

Most negative reviews are regarding Viome’s customer service which at times seems to be sluggish and at others downright lacking. 

Health commentators who’ve compared Viome to other services have found significant differences in the results from the various laboratories.  Many reviews were amazed at how Viome’s artificial intelligence kept updating their recommended foods

On one hand, this could be seen as progressive and positive.  On the other, it could suggest that the technology just isn’t yet up to making accurate recommendations. 

Here are some Amazon customer reviews:

“The results I got from this were extremely vague and bland.  I honestly learned next to nothing and would have not spent $50 on this if I knew this was all I was getting.  Total joke for $250.”

“This is the second kit I’ve purchased from Viome within a 1-year time span.  I’ve been quite happy with the overall process and enjoyed the fact everything was summarized and easily available via their app.  I can tell the company continues to invest in it’s processes and overall product/service as the second time around things seemed to flow even better.  It’s easy to check which foods to focus on and which ones to avoid so you can build a ‘meal plan’ that best suits your microbiome. I’m excited to see my new results.”

How Much Do Viome’s Testing Kits Cost?

Viome Gut Intelligence Test $149

Food Sensitivity Intelligence Test $49

(Use code NUTRISHATIVES10 at checkout to get a $10 discount!)

Viome Pros and Cons


  • provides meaningful, actionable results


  • company may be making claims not fully supported by the current science
  • poor customer service


  • use of artificial intelligence software to analyze data; may be cutting-edge or flimsy and prone to user error

Final Thoughts on Viome

Research on the DNA versus RNA sequencing techniques suggest they are both similar in their sensitivities, though DNA tests are typically thought to be easier to use to identify bacterial diversity.  This does raise some questions as to whether Viome is really able to draw the conclusions and make the recommendations they do.

Whilst they did a lot of comparison on their website claiming to be superior to other technologies, there was no real discussion on how their particular sequencing technique worked or the science to back up their claims of superiority.

3. Biohm

Biohm gut microbiome testing company

Primarily a probiotic supplement company, Biohm was created by Dr. Ghannoum, who describes himself as the preeminent microbiome scientist in the United States.  He was a leader in discovering how the microbiome as a whole — fungi included– work together to impact wellness.

What Products Does Biohm Offer and What Do They Test For?

Biohm is predominantly a probiotic supplement business, specializing in complete probiotics for the total microbiome.  They offer their gut microbiome test alongside their probiotic products. Unsurprisingly, their test looks at the total microbiome, not just bacterial species.

Biohm only offers one test but they offer two ways to receive your results:

  • a written report
  • a written report plus a phone consultation with a nutritionist

How Do Biohm Products Work?

Much like the other commercial test kits, Biohm’s test has you swab a stool sample from your toilet paper, place it in a sample container, and ship it back to the lab. 

Unlike some of the other companies on this list, Biohm does specify that they use the 16S sequencing.  This means that the test does not really break down your microbiome to the species level.

What Do Biohm Customer Reviews Say?

“I ordered the BIOHM Gut Test and I did a consultation with a nutritionist.  It has been great to get a clear picture on what cultures are active in my gut and which ones are missing.  The nutritionist that I talked with was very knowledgeable and now I have an action plan to improve my gut health.  The test and consult are so worth it — I highly recommend!”

“I had a great experience with BIOHM health.  I was given an update while my sample was being processed and was given notice once it was complete.  And I appreciated having a nutritionist contact me to discuss my results and point me in the right direction.”

“Result took about 2 months to come back that everything is kinda ok but I can eat more vegetables and more fruits.  Rather expected and didn’t need to run the service to know that. They were very nice upon reviewing the results with me though and answered all questions.”

How Much Do Biohm’s Testing Kits Cost?

Written report $179.99 

Written report and phone consultation $219.99 

(Use code NUTRISHATIVES10 at checkout to get a 10% discount!)

Biohm Pros and Cons


  • strong customer service
  • option to speak to a nutritionist


  • report is highly generalized and tends to offer the standard “healthy gut microbiome” advice (exercise regularly, avoid red meat, avoid alcohol, eat plant-based protein, consume lots of fiber, take a probiotic)
  • compares your microbiome to their sample group which may or may not be useful for tracking your personal gut health
  • company sells probiotic supplements which is a potential conflict of interest

Final Thoughts on Biohm

Biohm has an interesting niche with their focus on the role of fungi in the health of your gut microbiome.  They will always be at the forefront of research given their founder is a leading scientist in the area.

It is important to note that, as with the other probiotic provider on our list, there is some concern about conflicts of interest.  On one hand, the company may be able to offer you probiotics which specifically match your gut needs. On the other hand, it is hard to be 100% sure you can trust the company to be objective about who actually needs probiotics.

Related Reading: Probiotics: Benefits, Dangers, and Best Sources

2. American Gut

American Gut microbiome study

An interesting one on the list, American Gut is technically a massive research study.  Whilst they do offer you an analysis of your gut microbiome, you are providing your sample in the name of science, not to help a company earn money.

What Products Does American Gut Offer and What Do They Test For?

American Gut provides a sample-retrieving kit and they complete a  DNA sequence of your microbiome. 

You get your results compared with everyone else who’s participated in the study, but they make no recommendations and provide no feedback on what the results mean.

How Do American Gut Products Work?

I’m not sure I would entirely class this as a product.  You do pay for the kit and you get a scientific analysis of your gut microbiome and updates on what the research is uncovering.  But you are provided with no personal recommendations.

Additionally, since this is a scientific study, you are required to fill out much longer and more detailed questionnaires, including a 7-day diet recall.  

So, it’s a lot more work and you get a lot less practical information.

What Do American Gut Customer Reviews Say?

It is hard to find reviews of  American Gut’s testing process.  This is because they are mainly research-based and not really about consumer testing. 

Among the reviews I could find, there were some complaints that it took a very long time — four or more months — to get the results of the test back.  And other reviewers complained about the lack of information around what their results meant. 

However, American Gut is very clear that they are for education and research purposes not for medical diagnosis or to give clinical recommendations.  So, the second critique may not be particularly fair. 

How Much Do American Gut’s Testing Kits Cost?

Sample-collecting kit $99.  

Note: If you live outside of the United States, you also need to pay return shipping (approximately $25, depending on where you live).

American Gut Pros and Cons


  • a scientific study with no financial motivations or conflicts of interest
  • highly-structured study with strict ethical rules that have to be followed 
  • allows you to contribute to scientific discoveries in the gut microbiome


  • you pay nearly as much as for a personalized microbiome test without receiving any of the personalized, practical information

Final Thoughts on American Gut

If you were hoping for an answer to your health issues, or specific recommendations on how you can avoid gut-related diseases, American Gut is probably not a good choice for you. 

If you’d simply like to know more about your gut microbiome (and you’d like to help scientific progress in the field), this study may be the perfect fit.

1. Thryve

Thryve gut microbiome testing company

Thryve is a health-tech start-up based in the San Francisco Bay Area. 

In exchange for a stool sample, Thryve provides you with reports outlining:

  • your microbe population make-up 
  • health and wellness indicators found in your test
  • dietary recommendations
  • supplement recommendations

What Products Does Thryve Offer and What Do They Test For?

Thryve Gut Health Program is the company’s main testing product.  They claim it helps identify ways to improve: 

The test does this by testing for different bacteria and then offers food suggestions and probiotic supplements based on the results.

How Do Thryve Products Work?

Much like the other kits on this list, Thryve’s test has you collect a small swab sample of stool from your used toilet paper.  You then stir the swab into the enclosed tube with stabilizing fluid and shake the sample for a minute before sending it off to the lab.

You’ll also have to enter your barcode and fill out the health and diet questionnaires on their online portal so the company can create an accurate report for you. 

Thryve has its own take on 16S sequencing,  promising species-level identification of bacteria.

What Do Thryve Customer Reviews Say?

“Overall, a really good product.  The instructions and ease of collecting the sample are really straightforward.  I got my results back in less than two weeks. The website contains a lot of helpful resources to help understand what bacteria is in your gut along with suggestions, especially regarding diet.  I would definitely recommend to those who are just curious about their own gut health, and I would especially recommend to those with nutritional, digestive, or other health issues. Although it isn’t the equivalent of a visit to the doctor, it can help with understanding some of whatever might be going on.”

“Wasn’t helpful for me, but may be for others.  My results came back telling me I was low on all healthy bacteria.  It did share some basic information on what foods to eat to increase my levels of each healthy bacteria.  It also shared probiotic supplement information that I could buy from them to increase my levels. I was hoping for something a little more, but it literally will just tell you your levels, share general healthy eating information, tell you to buy their probiotics.  I already take a very reputable probiotic every day and eat a moderate amount of all the green veggies they suggest, so I was a little surprised when my results came back with no variation in levels of my gut bacteria: low on everything and I should do more of what I’ve been doing. Might be helpful for others but wasn’t for me.”

How Much Do Thryve’s Testing Kits Cost?

Thryve Gut Health $99

Thryve Pros and Cons


  • quick turn-around time (1-2 weeks)


  • questionnaire answers may influence results more than stool sample results
  • company sells probiotics, creating a potential conflict of interest

Final Thoughts on Thryve

I like Thryve’s customer focus and honesty. 

As with Biohm, there is some concern about whether their probiotic supplements represent a possible conflict of interest or an opportunity to get truly personalized probiotic supplements. 

Take Home Message

Microbiome testing companies use DNA or RNA sequencing to tell you about the make-up of your gut microbiome.  Microbiome science is new and there is a lot that these tests can’t yet tell you, including official medical diagnoses.  Nevertheless, general information about overgrowth of any one type of bacteria may be able to help you take better care of your gut and your overall health.

There are currently five main microbiome testing companies (uBiome, Viome, Biohm, American Gut, Thryve) that offer slightly different tests, result options, and degrees of personalized recommendations from your results.  Depending on exactly what you’d like to learn about your gut health, any of these companies might be a good fit!

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