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Microbiome Testing: Finding the Best Test

Our experts tell you everything you need to know about gut biome testing + current discount codes.

Last Updated: Nov 18, 2021
microbiome testing

According to the National Institute of Health, within the average human live hundreds of trillions of microorganisms, including bacteria, fungi, and archaea. Collectively, these microorganisms are often referred to as our “microbiome.” Though these organisms live throughout the body, this entire guide focuses on testing the microbiome located specifically in your gut or gastrointestinal tract.

The importance of the human microbiome is becoming increasingly clear. While the contributions of individual microbes in human health are still far from fully understood, the microbiome has been shown to play a vital role in synthesizing vitamins and amino acids, generating important metabolites, protecting against pathogens, utilizing non-human biochemical pathways, contributing to the immune system, and much more.

Microbiome testing (also referred to as “gut flora testing”) is a relatively recent phenomenon that has advanced considerably over the last several years. From the convenience of your own home, you can now purchase testing kits that will assess the makeup of your gut microbiome. Our research team has tested, analyzed, and compared all of the major tests on the market. In this guide, we’ll explain our findings and recommendations about which microbiome tests are best for you in 2021.

If you are in a hurry and just want to know our recommendations, here is a quick summary without further ado.

What is the best gut microbiome test?

Summary of our recommendations for best microbiome test

  • Best overall: Viome
  • Best for bacterial support: Viome
  • Best for fungal support: Viome
  • Best budget option: Thryve
  • Best for privacy: Viome
  • Best whole-health insight: Viome
Our Top Choice

Viome Gut Intelligence Test

Viome’s Gut Intelligence Test can tell you more about your gut microbiome than the competitors.

With Viome, you can learn about your gut bacteria, fungi, bacteriophages, archaea, viruses, and parasites. This provides a more comprehensive set of results, which you can use to improve your health. You can save $20 using purchase code INNERBODY20.

Why you should trust us

Innerbody Research recently celebrated its 20-year anniversary online. Over the past two decades, we have helped tens of millions of readers make informed decisions involving staying healthy and living healthier lifestyles. Our testing team has purchased and compared over 500 health-related tests to date, and we are constantly updating our reviews based on the latest test advances.

This guide, like all health-related content on Innerbody Research, is thoroughly vetted by one or more members of our Medical Review Board for accuracy. Additionally, we extensively analyze each health testing service we review. We evaluate the entire experience from ordering to receiving results and then offer unbiased, marketing-jargon-free analysis based on the latest scientific evidence and medical standards.

Who should take a microbiome test?

In our opinion, the short answer is: everyone who can afford to do so. Advancements in microbiome testing and the scientific understanding of our gut microbiome have reached the point at which everyone can potentially benefit from taking a test and then discussing the results and ensuing actions with trusted healthcare professionals. (If you want to know more about why we believe this, skim the surface with our 10 interesting microbiome facts below.)

Microbiome tests attempt to detect the presence of different species of microorganisms in a fecal sample. From the best test results, you can then gain a wealth of information about:

  • The richness of the gut microbiome and diversity of its microorganisms
  • How your gut microbiome compares to that of others
  • What this might say about your overall health and aging process
  • What those microorganisms are actually doing for you
  • How you can improve your health through specific dietary modifications

Imbalances in your gut microbiome could make you more susceptible to opportunistic or harmful bacteria and viruses, leading to a multitude of possible symptoms such as:

  • Subpar immune response
  • Constipation, diarrhea, and/or irritable bowel syndrome
  • Gas and bloating
  • Poor absorption of nutrients
  • Brain fog and reduced cognitive function
  • Unhealthy skin
  • Faster aging
  • Stress management issues
  • Mood fluctuations

It is very important to keep in mind that these tests shouldn’t replace the advice of a physician or other healthcare professional. If you have symptoms that concern you, you should talk to your doctor, who will be able to determine if any medical interventions are required or further investigations needed.

There are many at-home microbiome tests on the market, with new ones becoming available seemingly every month. Our research team has tested, evaluated, and compared all of the well-known tests – including tests from Viome, Wellnicity, BIOHM, Psomagen, Thryve, Sun Genomics (Floré), and more – in order to arrive at our recommended favorites. Our top 3 picks include:

Here is a quick chart with details of the three tests – read on for more in-depth information.

  Viome BIOHM Thryve
Current price $149 $130 $99
Approx wait time after shipping back 2-3 weeks 4-6 weeks 2-4 weeks
Tests for bacteria
Tests for fungi
Tests for archaea
Tests for parasites
Tests for phages
Tests for viruses
Supplement service after testing?

10 interesting facts about your gut microbiome

If you are still wondering whether you should test your gut microbiome, here are ten interesting facts about it. These may convince you of the importance of microbiome testing, bearing in mind that the sophisticated technology and science behind the testing and takeaways will continue to develop.

  1. Your gut microbiome alone encompasses roughly 100 trillion microorganisms. The full microbiome (throughout the entire human body) is populated with trillions more, which kind of makes you think of your body differently, doesn’t it?

  2. Your gut microbiome is considered by many scientists to be an additional organ in your body – that’s how big a role it plays in your overall health. Encompassing all of the microorganisms in your gut, this organ generally weighs about 4 pounds (2 kilograms). We test other organs in order to safeguard our health – why would we not test our microbiome?

  3. Microbiome testing wasn’t even possible 15 years ago. Thanks to next-generation sequencing and the rise of metagenomics, it is now possible.

  4. Evidence suggests that our microbiome begins developing before we are even born.

  5. Evidence also suggests that how we are delivered into the world (vaginal vs. C-section) affects our microbiome.

  6. The average gut microbiome actually includes some pathogenic bacteria such as E. coli.

  7. Diet and distancing from natural bacterial exposure in our environment (through dirt, animals, etc.) can rob the American gut of beneficial diversity in our microbiomes.

  8. You may have heard something about fecal transplantation – the process of putting a small, microbe-healthy fecal sample from a healthy person into the gut of an unhealthy person in order to help recolonize the gut. While this sounds like an extreme or unusual idea to many people, the treatment is actually over a thousand years old and used in Chinese medicine.

  9. While still in its early stages, the studies and science surrounding the gut microbiome indicate profound health impacts from these microorganisms. For instance, studies indicate that patients with atherosclerosis or type 2 diabetes show particular patterns in their gut microbiomes. For type 2 diabetics, the pattern is more predictive of the disease than body mass index values.

  10. Our gut microbiome helps us metabolize and extract vitamins from the food we eat, but did you know these microorganisms also help us produce serotonin? Serotonin plays a significant role in our sense of happiness. Insufficient serotonin can make people more susceptible to depression and anxiety.

Viome Gut Intelligence test

Editors' Choice for best overall microbiome test

Viome Microbiome Test

Viome offers two very sophisticated tests and several reasons why it belongs at the top of our list as the best overall test for your gut microbiome, as well as the best company for whole-health insights.

Viome’s Gut Intelligence test, the most affordable of the company’s two tests ($149), analyzes the trillions of microorganisms in your gut more thoroughly than any other test in our guide. Included here are:

  • Bacteria
  • Fungi
  • Bacteriophages (also simply called phages)
  • Viruses
  • Parasites
  • Archaea

Viome sequences the RNA of these microorganisms in order to tell you what is present in your gut – and in what quantities. Other companies like Thryve and BIOHM provide valuable insights focused on bacteria and/or fungi. However, their analysis of DNA means that the microorganisms they analyze may not be active and alive in your gut.

Put simply: we want you to benefit from the best scientific approach and have concluded that Viome’s approach is more comprehensive and more useful from a scientific standpoint. Studies indicate that a focus on RNA rather than DNA can allow Viome to focus specifically on the active microorganisms and what they’re doing. In this way, the whole picture of your gut microbiome becomes clearer.

Note: You can get an additional $20 off of the price by using our code INNERBODY20 upon purchase.

Editors' Choice for best whole-health insights

If you want to go beyond your gut microbiome (though that isn’t the primary focus of this guide), Viome offers a pricier Health Intelligence service that combines the gut microbiome insights with an examination of your blood in order to give you insight into your cell metabolism, biological aging process and more. To read more about this, check out our full Viome review.

Viome is also best for those with privacy concerns

Viome’s Gut Intelligence test does not examine your DNA; instead, it analyzes the RNA of the microorganisms living inside of your gut. We shouldn’t say “only”, because there are tens of trillions of microorganisms in there! But the point here is that this data, while very valuable to you, is not sensitive or identifiable information in the same way as your DNA. There isn’t something intrinsically “yours” about it, or anything personally identifying.

It’s also worth noting that Viome protects your data rigorously. The other companies in this guide take the necessary steps to respect and protect your privacy as well. Thryve, for instance, easily lets you opt out of having your anonymized data being used in scientific studies of any kind. But if you are somebody who is more comfortable with fewer companies holding your sensitive data such as DNA information, for instance, you can breathe a sigh of relief with Viome’s Gut Intelligence test.

Best for putting testing insights to use: Viome

In past years, we recommended BIOHM and Thryve for post-testing fungal and bacterial support, respectively, since they (not Viome) offered convenient, quality supplements that would address your gut microbiome’s specific needs after testing was complete. But one of Viome’s most recently introduced services is an optional prebiotic and probiotic subscription program after analysis of your test results. Because Viome tests most comprehensively and focuses on the more useful data from your fecal sample (the RNA), the company now claims our top spot in this area. Viome’s monthly supplements are formulated specifically for you based on the needs identified during your testing.

Depending on which tier of service you choose, Viome will even include periodic re-testing so that your monthly supplies of prebiotics and probiotics remain as useful to you as possible. Why is this important? It’s because our bodies are an evolving ecosystem, with life events that can disrupt our healthy gut microbiome as well as natural aging processes that alter our biological needs over time. Probiotics and prebiotics shouldn’t remain rigidly fixed over time because our bodies don’t do that, either.

BIOHM Gut Test

A solid runner-up

Biohm Microbiome Test

BIOHM’s test historically has focused strongly focus on the role of fungi in the gut microbiome. In fact, the founder, Dr. Mahmoud Ghannoum, is a world-leading expert on microbiome fungi.

At this time in 2021, we conclude that BIOHM is a high-quality runner-up choice for microbiome testing. While BIOHM’s Gut Test is not as comprehensive as Viome, it does test for both fungi and bacteria and does so at a slightly lower cost to you. But unlike Viome, BIOHM only reports about fungi and bacteria (which is more limited in scope) and relies on DNA analysis, which could end up producing some results based on microorganisms that were not alive and active within your gut.

Your savings with BIOHM are $20, compared to Viome’s most affordable test option. Based on the limitations described above, this isn’t sufficient savings to recommend BIOHM as more than a very solid runner-up to Viome. Plus, when you consider the $10 discount that we can help you get at Viome, your savings reduce to just $10.

Best Budget Choice

BIOHM Gut Test

BIOHM’s Gut Test is among the best tests at recognizing not just bacteria but fungi as well. But we believe it's not the best. The test’s probiotic recommendations are also quite good.

BIOHM was founded by Dr. Mahmoud Ghannoum, one of the world’s leading microbiome researchers. He has published over 400 papers and his research has been cited over 20,000 times by other scientists.

As with our other two top recommendations, the BIOHM Gut Test aims to give you not only results and recommendations but also the option to purchase recommended supplements directly from BIOHM, based on your gut microbiome test results.

When you receive your results from BIOHM, they will be presented to you in 4 sections:

  • Overall Gut Score – you receive a grade of “microbiome diversity” on a scale of 1-10.
  • Comparison – comparing the levels of major bacterial and fungal groups in your microbiome to average or normal levels in the broader population.
  • Strain-Level Analysis – diving into the nitty-gritty, analyzing your bacterial and fungal microbiome composition at the strain level.
  • Actionable Recommendations – based on your results, you will receive recommendations about your diet and lifestyle, along with suggestions for supplements to improve your gut health.
three sections of Biohm test results

BIOHM’s supplements, which they’ll recommend based on your test results, make the company a convenient, one-stop shop for people whose gut fungi and bacteria are out of balance and in need of help. BIOHM’s goal following your testing is the same as yours – to get your gut microbiome composition into a healthy, “normal” range of diversity with beneficial microbiota galore.

For an additional fee, you can also include an in-person consultation with a BIOHM nutritionist to discuss your test results and what the recommendations mean. We found their written report to be very clear, thorough, and understandable, but it is a nice, customer-friendly feature to be able to schedule an in-person consultation if desired.

Thryve Gut Health Program

Another very solid choice in our top three microbiome tests is the Thryve Gut Health Program. Right now, Thryve’s test isn’t the most comprehensive test available (that distinction goes to Viome); this test focuses on gut bacteria, a narrower scope than BIOHM and significantly narrower than Viome’s test. Thryve intends to offer more comprehensive gut microbiome testing in the future.

Best budget option

Thryve’s focus may be what allows the company to sell their gut microbiome test at a significantly lower price than the other two companies that comprise our top three testing options. The fact that you can save $50 or $30 compared to Viome and Thryve, respectively, makes Thryve’s test our top choice for those with a very tight budget. You can save considerable money and still learn valuable information by testing with Thryve. Just keep in mind that there is a more comprehensive test available that we recommend more highly at this time if you can afford it.

Thryve’s test assesses your gut microbiome’s wellness and diversity by analyzing the presence of bacteria in your gut. After testing, you’re then given dietary suggestions and the opportunity to subscribe for a personalized probiotic blend, crafted specifically for you based on your test results.

Best Bacterial Support

Thryve Gut Health Program

Thryve’s Gut Health Program focuses on improving the bacteria in your gut microbiome by including personalized probiotics recommendations to repair your gut.

Thryve focuses exclusively on promoting gut bacterial health and the company is good at it. Thryve also prides itself on providing transparency as to what the tests can tell you and what they cannot.

Of course, you could opt to save a little more money with one of the company’s pre-formulated probiotics. But Thryve doesn’t stop at providing a small set of formulas. Based on scientific research, however, we recommend that you forgo those added savings and opt for the personalized formula because no mass-produced formula has the potential to benefit you as much as a formula created to address your specific needs. In reality, some bacteria that are beneficial for one person can be harmful to another person.

We really like that Thryve’s marketing and reports are transparent and honest about the science the company uses to interpret your microbiome and to make personalized recommendations. All recommendations come with a grading scale based on scientific study type and whether or not scientific literature agrees. To learn more, visit our full Thryve review.

Thryve’s results reports are clear and detailed, and the company offers one of the less expensive tests currently on the market. We recommend them for their adherence to sound science, their transparency, and their ability to customize a beneficial probiotic blend specifically to help your own gut microbiome, which is unique.

How do microbiome tests work?

Flore Microbiome Test

The whole microbiome test-taking process is fairly straightforward. Individual tests vary, but here are the basic steps that most of the tests commonly share.

Step 1: Test purchase: Hopefully this guide is providing you with the information you need to determine which microbiome test, if any, would be best for you. After choosing, you simply go to the test company’s website and place your order. You should receive your test kit within 5-10 business days.

Step 2: Sample collection: Microbiome testing requires extraction of nucleic acids (either DNA or RNA, depending on the test) from fecal material. So yes, you will need to collect a stool sample by following the directions inside the kit. For most tests, this will be done using a paper and a tiny scoop. Don’t worry – the entire collection process is not as bad as it may sound. You can fit the paper onto your toilet and will only need to collect a very small amount of stool.

A quick tip: if you’re having trouble producing a sample, we recommend eating some foods with high fiber content, such as a green salad. Also, if you have recently taken any antibiotics, your microbiome could be significantly disrupted. We recommended refraining from antibiotics for at least 3 months before taking microbiome tests.

Send your sample in the pre-paid postage box.

Step 3: Sample analysis: Your sample goes directly to a lab facility. You do not have to do anything at this step. The nucleic acids extracted from your submitted sample are sequenced and compared to references, allowing analysis of your microbiome. The method of sequencing and analysis used for testing is dependent upon the company. This entire process can take up to a month, but is usually shorter, depending on the specific testing company chosen.

Step 4: Receive results: Usually within 2 to 4 weeks, you will receive your test results.

Although the results reports from each testing company vary and focus on different areas, they all essentially offer some detailed information about different classes or species of microbes in your gut microbiome, along with how this relates to health, diet, lifestyle, or disease. This information is usually followed by recommendations for lifestyle adaptations, such as dietary changes, supplements to take, and probiotics to add to your regimen. All of our top recommendations in this guide can continue to serve you and improve your gut health by providing unique probiotic formulae to suit your needs.

How do we choose our test recommendations?

We customize our evaluation criteria depending on the type and nature of the test. For most health-related tests, we have five areas that we use for our evaluations, including:

Accuracy: Do the testing companies use the latest and most accurate testing technologies available? How accurate are the tests compared to alternatives?

Value: Are you getting your money’s worth? Are there any hidden costs or charges? Does the test provider offer discounts to our readers?

Customer Support: How well does the testing company help you choose the best test? How clearly are the results presented? How well does the testing company help you understand results and get treatment if necessary?

Privacy: Are all test kits sent in discreet packaging? Will your data be stored securely? Could your data ever be shared without your permission?

Test Results Speed: How fast will you receive your test results from the moment you click “buy?” Are the waiting times stated by the testing companies accurate and consistent?

Caveats but not dealbreakers

Microbiome tests are not FDA-approved and should not be used as a diagnostic tool. Instead, they are another measure of your body, providing insights that you have never before been able to access. These insights could prove useful for you if you are ready to make some health or lifestyle overhauls and want a new way to look at your gut health.

However, if you have any persistent symptoms that are troubling you, you should consult your physician, rather than only relying on tests to detect any health issues.

It is impossible to directly link certain microbiome features with symptoms. High-quality microbiome tests analyze your microbiome and then rely on the latest and best scientific understanding along with identifiable patterns between microbiome composition and symptoms in order to offer suggestions for how you could improve your gut health and overall wellness.

There is no guarantee that, by making changes, you will feel better; correlation does not imply causation. Currently, the tests might leave you with more questions than answers. A recent guide on microbiome tests for clinicians also cautions health care professionals against taking the results of these tests too seriously, due to the limited research on their effectiveness. However, as our understanding of the microbiome continues to grow more sophisticated and a larger number of people test themselves, the tests become more accurate and informative.

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