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 20, 2019

Microbiome Testing | Innerbody

It is fascinating, really. 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 is still far from fully understood, the microbiome has been shown to play vital roles 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 come a long way over the last couple years. From the convenience of your own home, you can now choose to purchase testing kits that will allow you to assess the makeup of your gut biome. Our research team has tried and evaluated most of the tests currently on the market and will tell you which ones we think are best.

If you are in a hurry and just want to know which of these three we would recommend, here is our top choice:

Our Top Choice

Wellnicity Food Sensitivity Tests

Choose among three different tests which measure IgG reactivity levels to 44, 90, or 180 different types of foods.

Wellnicity is an emerging leader in the direct-to-consumer home health testing market. The company is known for free follow-up consultations with certified nutritionists and actionable supplement recommendations.

Current Deals: Save 15% with coupon code: INNERBODY

Why you should trust us

A conceptual depiction of three generations of a family

Over the past two decades, Innerbody.com has helped tens of millions of readers make informed decisions involving staying healthy and living healthier lifestyles.

The primary author of this guide is an internationally recognized nutrition and diabetes expert and certified health and wellness coach. She is a Registered Dietician (RD) and has earned M.S. and B.S. degrees in Nutrition.

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. We strive to give you, our readers, an unbiased, marketing-jargon-free description of the tests reviewed based on scientific evidence.

Who should take a microbiome test?

Microbiome tests attempt to detect the presence of different species of microorganisms in a fecal sample. From the test results, you can then get information such as the richness of the gut microbiome, diversity of the gut microbiome, and how it compares to that of others.

These tests are ideal for people who want to learn more about their body and the health of their gastrointestinal tract. Possible effects of having microbiome imbalances include:

  • Constipation, diarrhea, & irritable bowel syndrome
  • Gas/bloating
  • Trouble digesting foods
  • Chronic fungal infections
  • Fatigue

It is very important to keep in mind that these tests absolutely should not replace the advice of a physician or other healthcare professional. In fact, if you have symptoms that concern you, you should talk to your doctor before taking such a test. Your doctor will be able to determine if any medical interventions are required, or further investigations needed.

How do microbiome tests work?

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

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 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 wax paper. The entire collection process is not as bad as it may seem.

A quick tip: if you are 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 in the sample in the (usually) pre-paid postage box.

Step 3: Sample analysis: Your sample usually 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 the microbiome. The method of sequencing and analysis used is dependent upon the company. This entire process can take up to a month, but is usually shorter, again 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 microbe, along with how this relates to health, diet, lifestyle, or disease. This is usually followed by recommendations for lifestyle adaptations, such as dietary changes, supplements to take, probiotics to take or things to watch out for.

There are many at-home microbiome tests currently on the market, with new ones popping up each month. Our research team testing evaluated and compared most of the well-known tests and came up with our favorites. Our top 3 picks include:

Wellnicity’s My Gut - Bacteria & Yeast Plus

Thryve Gut Health Program

BIOHM Gut Test

Our Top Choice

Wellnicity Food Sensitivity Tests

Choose among three different tests which measure IgG reactivity levels to 44, 90, or 180 different types of foods.

Wellnicity is an emerging leader in the direct-to-consumer home health testing market. The company is known for free follow-up consultations with certified nutritionists and actionable supplement recommendations.

Current Deals: Save 15% with coupon code: INNERBODY

Wellnicity’s My Gut - Bacteria & Yeast Plus Test came out on top of our ratings, earning our Editor’s Choice Award, and it is our top recommendation.

The My Gut - Bacteria & Yeast Plus test attempts to assess the presence of bad bacteria, yeast, and other key GI health markers in your microbiome. We like this test for a number of reasons, including:

  • Wellnicity’s laboratory employs state-of-the-art equipment capable of identifying over 4,000 specific microorganisms–many times more than standard laboratories can identify.

  • Wellnicity offers our readers a 15% discount on all orders (just use discount code: INNERBODY at check-out).

  • You have access to a nutritionist via chat for personalized advice before, during, and after the test-taking process (during normal business hours).

  • We appreciate how Wellnicity focuses only on tests and getting you the most accurate results. The company does not try to sell you any probiotics or other products after giving you your results.

It is worth noting that Wellnicity does offer another, more comprehensive microbiome test called My Gut - Health. While more expensive, this test covers all of the biomarkers covered in the Bacteria & Yeast test but adds additional parasites and inflammatory GI markers, as well as gluten antibodies. If you are experiencing GI symptoms or just want no stone left unturned, then this may be the best test for you.

Also Great

Thryve Gut Health Program

Thryve’s Gut Health Program goes simply giving you rest results by including personalized probiotics recommendations to repair your gut.

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

Another solid choice is the Thryve Gut Health Program . The test assesses your microbiome wellness and diversity by analyzing the presence of microbes in your gut. Test takers are then given dietary suggestions and a personalized probiotic blend.

We really like how 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.

The Thryve test is best for those who not only want to take a microbiome test but also want easy access to personalized probiotics (that’s why they call it a “program” rather than simply a test). After you receive your results and probiotic recommendations, you will have the option to purchase the actually recommended probiotics customized for you based on your test results.

Thryve’s results reports are clear and detailed, and the company offers one of the less expensive tests currently on the market.

Last but not least, our third recommendation is the BIOHM Gut Test.

Also Great

BIOHM Gut Test

BIOHM’s Gut Test is among the best tests at recognizing not just bacteria but fungi as well. The test’s probiotic recommendations are also excellent.

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.

The BIOHM Gut Test is very similar to the Thryve test in that it aims to not only give you results and recommendations, but also the option to purchase recommended supplements in its online store.

BIOHM’s test distinguishes itself from other testing kits by having a strong focus on the role of fungi in the microbiome. In fact, the founder, Dr. Mahmoud Ghannoum, is a world-leading expert on microbiome fungi.

Once you receive your results from BIOHM, they will come with 3 sections:

  • Overall Gut Score - you receive a grade of “microbiome diversity” on a scale of 1-10.
  • Comparison - analysis of specific strains of bacteria and fungi, along with comparison to others in the population.
  • Actionable Recommendations - based on your results, you receive recommendations about your diet and lifestyle, and suggest supplements you could take that might improve your gut health.

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. One way to think of them is as another measure of your body that you have never had access to before. 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 you are concerned about, you should absolutely consult your physician, and not rely on these tests to detect any health issues.

It is impossible to directly link certain microbiome features with symptoms. What these tests do is identify patterns in microbiome composition with symptoms and with what is known in the scientific literature.

This means there is no guarantee that by making changes you will feel better, as correlation does not imply causation. Currently, the tests might leave you with more questions than answers. However, as we gather more information, the tests will potentially become more accurate and informative. A recent guide on microbiome tests for clinicians also cautions health care professionals against taking the results of these tests seriously, due to the limited research on their effectiveness.