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 the bacteria that live in your GIT (or gastrointestinal tract).  This profile will give you a detailed breakdown of what kind of bacteria live throughout your tract as well as what ratios these bacteria can be found in.

This kind of testing can help us pinpoint if we have something called dysbiosis (which is when there are more pathogenic (or bad bacteria) than beneficial ones. 

Microbiome testing usually involves using a home testing kit to collect a fecal sample (aka your poo) and then send this sample off to a laboratory for testing.

The lab then sequences the DNA (or genetic material) from the bacteria that are found in your sample. This sequencing helps the technicians to build your unique microbiome profile (think of it as your GITs report card, it’s going to tell you if you are passing with flying colours, or need to do a little more homework). 

Before we go into the two most commonly used microbiome sequencing methods, let’s understand some terminology associated with naming and classification of the different groups of bacteria that live inside of you (also known as taxonomy).

The different levels include:

  • Domain
  • Kingdom
  • Phylum
  • Class
  • Order
  • Family
  • Genus
  • Species

This classifies all living organisms from broad (domain) to very specific (species) levels. Let’s look at example of a domesticated dog:

  • Domain – Eukarya (multicellular)
  • Kingdom – Animalia
  • Phylum – Chordata (presence of a nerve cord along the back)
  • Class – Mammalia (presence of hair and milk glands)
  • Order – Carnivora (meat eaters)
  • Family – Canidae (dog family)
  • Genus – Canis
  • Species – Familiaris

Interestingly, all domesticated dogs fall into this same species, but other members of this family (but which are a different species) include the fox (Canis lupus) and the coyote (Canis latrans). 

Scientists have applied this same principle to all the bacteria that live in your GIT and then have gone a step further than species to give us different strains (as it seems to be that these bacteria have strain specific health benefits).  Imagine that is like telling the difference between a great dane and a chihuahua. 

At the moment, there are two reliable methods to sequencing your microbiome: 

    • 16S rRNA technology  

This method sequences the bacteria down to the genus level.  This would be like figuring out that the DNA in these bacteria belong to a member of the dog family but does not tell us if it is a domestic dog, a fox or a coyote (and I am sure you will agree that these are all very different animals). 

    • Metagenomic sequencing  

This method sequences the bacteria down to the species level.  It would be like telling us that the DNA is from a domesticated dog, but it cannot go further than that (i.e. it cannot tell us the breed of the dog). 

The two phyla Firmicutes and Bacteroidetes make up approximately 90% of the human microbiome, but even though they make up the majority, the other players (Actinobacteria, Fusobacteria and Proteobacteria) seems to also be important to our health.

In fact, one of the most commonly studied and consumed probiotics (Bifidobacteria) comes from the Actinobacteria family and we know that having a good dose of these is important for great gut health (despite it being in the minority).


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.) 

Who Should Get a Gut Microbiome Test?

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 Most Popular 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. Wellnicity

Wellnicity was founded in Austin Texas in 2016 and its main selling point is that their tests are all backed by science offering proven results.

There are a number of tests and products available on the Wellnicity website, including a variety of food sensitivity tests: 

  • My Gut – Health

One of their key slogans is that ‘We don’t tell you what you need. Your body tells us’.  They highlight the fact that symptoms are the body’s way of trying to communicate that there is a problem and that their tests help to decode this message.  People with the following symptoms are encouraged to take the test:

  • Chronic yeast/ fungal infections
  • Constipation, diarrhea and IBS
  • Fatigue
  • Gas/ bloating and trouble digesting food

How Do Wellnicity Products Work?

As with most of these microbiome testing companies, Wellnicity requires a stool samples, but where they differ is that they require some saliva samples as well.  The laboratory that they use boasts the ability to identify over 4000 specific microorganisms (which is 100 x more than standard laboratories are able to do). 

What Do Wellnicity Customer Reviews Say?

“My body is jumping for joy after I took the at home My Gut Health test with @wellnicity. I am going on my third month working with Wellnicity and talking to my clinician and let me tell you I have learned so much about my body. Getting education on my body has helped me make much more informed choices.”

“So far I have been unable to register this test and therefore have been unable to use it. I have sent an email to the asking for assistance. It will take 24 hours to contact me. I hope they can assist as 300 dollars is excessive for a product that doesnt work.”

How Much Do Wellnicity’s Testing Kits Cost?

My Hut – Health $329

Wellnicity Pros and Cons


  • quick turnaround time 5-9 days
  • results are evaluated and explained by a clinician in a one on one consultation
  • supplements recommended are professional grade
  • Test is all inclusive of test kit, shipping, laboratory fees, clinical consultation, Wellness Report and Wellness Plan


  • cost
  • not available in New York
  • possible issues with registration

Final Thoughts on Wellnicity

It is promising that Wellnicity offers an all inclusive service but at this price, it is definitely expected! Having a clinician walk you through your results is very helpful for people who do not have a background in health and wellness.

If their customer service is on par and helps to resolve the registration issues, this may be a great option for those of you trying to learn more about your gut health.  Unfortunately by also offering you supplements, this causes us to worry about conflict of interest.

It becomes difficult to tell if the supplements recommended are really needed and backed by science or if the company purely wants to increase revenue. 

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 

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 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. 

What happened to uBiome?

uBiome was a San Francisco-based biotechnology company that sequences customers’ gut microbiomes. Originally, uBiome offered both commercial and medically-ordered microbiome test kits.

However, they were placed under investigation byt the FBI for insurance fraud around their prescription testing kits. In late 2019, the company filed for bankruptcy and shut down, and so their tests are no longer available to purchase.

Best Microbiome Testing Companies Summary




American Gut







Test & report – $179.99

Test, report & consultation – $219.99

$149 (Use code NUTRISHATIVES10 at checkout to get a $10 discount!)

Explorer Kit- $329

Turn-Around Time

1-2 weeks

Up to 4 months (or more)

Up to 2 months

Not indicated

5-9 days







Food Suggestions






Supplement Suggestions

Yes (but from own range)


Yes (but from own range)


Yes (but from own range)


Most Budget-Friendly: Thryve (American Gut costs the same, but with far fewer benefits)

Ease of Use: Biohm and Wellnicity (if you take the option for the consultation), having someone walk you through the report is a valuable investment. 

Our Top Choice for Microbiome Testing: Biohm (it ticks all the blocks, but you wait a little longer for your results) or Wellnicity (if you are happy to pay more, but want your results quicker).

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 (Wellnicity, 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!

Read Next: Top 5 Best Butyrate Supplements for Leaky Gut Cure  


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