Microbiome Testing: Finding the Best Test

According to the National Institutes of Health, the average human body is host to hundreds of trillions of microorganisms, including bacteria, fungi, and archaea.1 Collectively, these microorganisms make up our microbiome.2 Though “microbiome” refers to the community of microorganisms throughout the body, this guide focuses specifically on testing the microbiome in your gut or gastrointestinal tract.

Microbiome testing (also called “gut flora testing”) is a relatively recent phenomenon that has advanced considerably over several years. From the convenience of your own home, you can purchase testing kits that will assess the makeup of your gut microbiome. Some companies even use the data they extract from your sample to offer you probiotic blends tailored to your results.

Our research team has tested, analyzed, and compared all of the major tests on the market. This guide explains our findings and recommendations about which microbiome tests are best for you in 2024.

If you’re in a hurry and want to know our recommendations, here’s a quick summary.

Summary of our recommendations for the best microbiome test

• Best overall: Viome [2024 Editors’ Choice]
• Best probiotic options: Viome
• Best budget option: Ombre [formerly Thryve]
• Best whole-health insight: Viome
• Best for pregnant people and their babies: Tiny Health
• Best option for using health insurance: Floré
• Best for privacy: Viome

At Innerbody Research, we extensively test each health service we review, including all of these at-home microbiome tests. All told, our team has spent over 540 hours testing and researching services and digesting hundreds of scientific papers regarding the microbiome and metagenomic sequencing. We’ve even visited company labs and spoken with on-staff scientists to help evaluate sequencing methods. With companies that offer post-testing supplements based on test results, our team tested the supplement services for several months.

Additionally, like all health-related content on this website, this review was thoroughly vetted by one or more members of our Medical Review Board for accuracy. We’ll continue to monitor the microbiome testing landscape to discover new companies and keep this guide up-to-date.

Over the past two decades, Innerbody Research has helped tens of millions of readers make more informed decisions to live healthier lifestyles.

We can’t always get the full experience a testing company offers when those tests have simple positive or negative results. If members of our team don’t test positive for an illness or deficiency through a particular test, we can’t avail ourselves of the company’s solutions. But with microbiome testing, we had the opportunity to evaluate the testing process and what comes afterward.

Investigating genomic sequencing methods allowed us to focus first on accuracy, which is a critical requirement for taking the right course of action after testing. As such, it most heavily affected how we regarded each company’s products. Since this kind of testing isn’t particularly cheap — and since you may also want retesting throughout treatment — cost became our second most important criterion.

We also took close looks at how these companies presented results, as well as their privacy policies to ensure personally identifying DNA material would be safe. These are crucial points on nearly equal footing with cost and accuracy.

Typically, the last part of the process is some kind of treatment, which comes either as recommendations in your results package or as probiotics and other supplements you can get from the testing company directly. In other words, given that the test results are hopefully actionable, how well does the company help you take meaningful next steps?

Let’s look at each criterion to see which companies fared the best.

Accuracy

Winner: Viome

Viome’s sequencing methods are both fast and accurate, and the company is constantly working to improve the machinery it uses for sample handling and sequencing. This not only helps control costs and save money for the consumer, but it delivers increases in speed and accuracy with each new development.

What has set Viome apart in the past several years is the company’s advanced AI, which leverages a massive database of microbiome data from thousands of scientific papers and the entire collection of reports generated for customers. That system allows Viome to be accurate in terms of species identification and the functional health of various microbes and vital pathways in the gut and elsewhere.

Despite being newer to the game than many others, Tiny Health should be considered a runner-up in this category. The company’s downside is that it uses DNA sequencing rather than the RNA that Viome does; using DNA can identify present but inactive strains, which isn’t as useful for you. Tiny Health’s specific methodology (shotgun metagenomics, which we’ll discuss later) also has a few more shortcomings than Viome’s metatranscriptomics and isn’t bolstered by Viome’s advanced AI.3

Cost

Winner: Ombre

Comparing costs among microbiome tests gets a little complicated once subscriptions and tailored probiotics enter the equation. For example, Viome’s model is essentially a subscription for probiotic and supplement shipments that occur every month. The program comes with your first test free, and Viome retests you for free every 12 months. Tiny Health also has a membership program, but since the company doesn’t have its own probiotics, you’re just paying to get discounts on its tests.

If budget is your primary concern, then your best bet is Ombre, which offers a microbiome test for $120. And if you plan on retesting, a subscription can get you the tests for as low as $90. Value derives, as well, from comprehensive dietary recommendations and a complete comparison of your microbiome health against the larger population. However, one thing that keeps costs down is that the company’s sequencing method doesn’t provide as much resolution at the species level, meaning it may not distinguish one bacterial species from another with the same accuracy as a competitor like Viome, which uses a much more refined (and more expensive) technology.2

Ombre’s operational side is a little slower than its competitors, too, with mid-range processing times and long shipping times, and it doesn’t offer things like custom-tailored probiotics (it still sells probiotics, but they’re pre-formulated). These sacrifices save you money, so if you can’t afford Viome but are looking for a test that can give you dietary guidance or a starting point for a microbiome-related conversation with your doctor, Ombre is the least expensive place to start.

Below is a quick look at the base test prices of our top-rated companies with Innerbody reader coupon codes applied where available. There are additional factors to consider even at the base price level, like what a given test can detect and whether you have to pay extra to speak with a staff doctor at a particular company. But this chart should give you an idea of the pricing you can expect from each brand:

It’s worth noting here that Floré offers some of its products by prescription, which may make them eligible for coverage through insurance. You’ll have to check with your insurer first, but choosing Floré may get you microbiome testing at a reduced cost.

Results

Winner: Viome

Viome and BIOHM offer extremely comprehensive results, but Viome takes the upper hand for its ability to sequence more than just bacteria and fungi. And when you add Viome’s various other tests to the picture, your results go even further. Of course, it’s one thing to provide a customer with comprehensive information, and it’s another thing to give it to them in a format that they can understand. Some testing companies bombard you with information that can be difficult to digest, but we found that Viome provides context and comparison points that make potentially complex data easy to interpret.

The degree to which your results offer actionable insights is critical. Obviously, having tailored probiotics, prebiotics, and nutritional supplements helps you take charge of your microbial health, but there are other complementary treatments you may want to explore. These can include certain dietary adjustments or even treatment for disorders you didn’t know you had. The degrees of actionability vary from company to company, but Viome’s reports contain the most in-depth advice and information about your health and ways to improve it.

Privacy

Winner: Viome

Ultimately, Viome takes this category for its transparency. A fair amount of digging allowed us to get most of the information we needed to understand our top companies’ policies and practices, but Viome lays out these measures in its privacy policy with a high level of clarity.

Nowadays, it would be unusual for a company not to offer things like SSL encryption for sensitive personal information. Each company we evaluated does a trustworthy job protecting basic personal information like credit card numbers and addresses.

So, ultimately, privacy in the microbiome space comes down to what happens to your sample during and after use. Because Viome relies on mRNA for its sequencing, it removes personally identifiable (DNA) information from the equation. It also allows you to opt out of additional studies that might include your sample or results to improve the company’s technology and techniques. Some companies destroy your sample after testing, but Viome stores it using de-identified alphanumeric coding for potential use in research. However, the company must explicitly obtain your permission to use sample data and other information from your test for its research and AI improvement purposes.

Of note, all of these companies are currently obligated to turn over certain information to law enforcement in the course of an investigation, especially if they receive a subpoena.

Customer support

Winner: Viome

Several things go into our consideration for customer support, and Viome comes out ahead in nearly every aspect:

• An intuitive website
• Fast and friendly email communication
• Transparent testing process
• A valuable and comprehensive blog
• Quick, reliable service
• An outstanding mobile app

Many other companies have some of these features, but not all, and certainly not to the level of detail and care we see from Viome.

One of the most important aspects of customer support occurs after you get your results, and that’s guidance about what to do next. Most companies offer some kind of consultation, though some, like BIOHM and Tiny Health, charge extra for it. In a rare knock on the company, Viome does not offer one-on-one consultations.

We also love seeing subscription services offered in the microbiome testing space, as any attempt to improve your microbiome will need retesting for verification. When a company like Viome or Floré can provide you with custom-made probiotics, retesting is that much more important to make any necessary adjustments to your formula. Given its massive well of potential ingredients for use in probiotics, prebiotics, and nutritional supplements, Viome’s personalized products are our preferred option, and the company will retest you for free each year to adjust your formula as needed.

In our opinion, everyone who can afford to take a test should do so. Advancements in microbiome testing and the scientific understanding of the gut microbiome have reached the point that everyone can benefit from not only taking a test but also discussing the results and ensuing actions with trusted healthcare professionals. (If you want to know more about why we believe this, you can skim the surface with our ten microbiome facts below.)

Most microbiome tests attempt to detect the presence of different species of microorganisms in a fecal sample.2 From the best test results, you can then gain a wealth of information about:

• The richness of your gut microbiome and the diversity of its microorganisms
• How your gut microbiome compares to those of others
• What the microorganisms in your gut are doing for you
• What this might say about your overall health, metabolism, and aging process
• 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:4

• Weakened immune response
• Constipation, diarrhea, 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 disorders
• Chronic inflammation

Some other microbiome tests look at areas other than your gut, like the vaginal tests available from Tiny Health and Ombre, or the oral microbiome tests available from Viome.

To be clear, there’s no “correct” microbiome makeup. You can’t ace a microbiome test. Studies show that one very healthy person’s microbiome can be wildly different from another very healthy person’s microbiome. And yet another very healthy person’s microbiome might be nearly identical to that of a person on their deathbed at 22. This is likely because the gene-level activity of these microorganisms is going to perform differently for the varying genetic makeups of individuals.2

Just as a genealogy test uses a massive database of sequenced genomes and their associated regions to determine the likeliest origins of your ancestors, microbiome tests compare your specific microbial balance with enormous databases of other test results to learn what your most probable health conditions may be. Ultimately, the results depend heavily on the quality of those databases, which is why Viome’s AI-driven system continues to be our preferred resource.

It’s important to remember that these tests shouldn’t replace the advice of a physician or other healthcare professional. They are not diagnostic tools, per se. If you have symptoms that concern you, you should talk to your doctor to determine if any medical interventions or further investigations are needed.

There are many at-home microbiome tests on the market, with new ones coming out frequently. Our research team has tested, evaluated, and compared the most well-known tests — including Viome, Wellnicity, BIOHM, Psomagen, Ombre (formerly Thryve), Sun Genomics (Floré), and more — to arrive at our recommendations.

If you have the budget for it, Viome’s most comprehensive test (Full Body Intelligence Test — $289) is the one that we believe can provide you with the most valuable, actionable insights (more about this test in the “Viome” section later in this guide.) For great value at lower initial prices, consider our top three entry-level picks:

• Viome Gut Intelligence Test (top recommendation)
• Tiny Health
• Ombre Gut Health Test

Here is a quick chart with details of the three tests:

It’s a testament to Viome’s in-house hardware and software development that it can produce such a fast turnaround while using a sequencing method that’s too costly and time-consuming for other companies to use.

More people are becoming familiar with the microbiome every day. As Jordan Stachel, registered dietitian nutritionist and member of our Medical Review Board, puts it, “I think that the public’s understanding of the microbiome has evolved significantly over the last five years or so, with more discussion and awareness in general surrounding this topic. This is promising, as the health of the microbiome directly correlates with one’s overall health and systemic wellbeing.”

If you’re still wondering whether you should test your gut microbiome, here are ten interesting facts that may convince you to give it a try. Read on past the list for a deeper dive into microbiomes.5

1. Your gut microbiome alone includes roughly 100 trillion microorganisms. The microbiome that exists throughout the entire human body contains trillions more.
2. Many scientists consider the gut microbiome to be an additional organ. Together, all of the microorganisms in your gut generally weigh about four pounds (2kg). We test other organs in order to safeguard our health — why not test the microbiome?
3. Microbiome testing wasn’t even possible 20 years ago. Thanks to next-generation sequencing and the rise of metagenomics, now it’s not only possible but also highly accurate.
4. Evidence suggests that a person’s microbiome begins developing before they’re born.6
5. How a person comes into the world (vaginal birth vs. C-section) affects their microbiome.
6. The average gut microbiome 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 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 to help recolonize the gut.7 While this sounds like an extreme or unusual idea to many people, the treatment is over 1,000 years old.
9. The microorganisms in your gut microbiome can have profound impacts on your health. For instance, studies indicate that patients with atherosclerosis or type 2 diabetes show particular patterns in their gut microbiomes.8 For type 2 diabetics, the pattern is more predictive of the disease than body mass index values.
10. Your gut microbiome helps you metabolize and extract vitamins from the food you eat. It also helps you produce serotonin, which plays a significant role in your sense of happiness. Insufficient serotonin can make people more susceptible to depression and anxiety.9

The term microbiome is typically used to refer to the symbiotic microorganisms that live on and in your body, where they help with everything from digestion to immune function. While the contributions of individual microbes in human health are still far from fully understood, the microbiome appears to play a key role in many vital functions, including:4

• Synthesizing vitamins and amino acids
• Generating important metabolites
• Protecting against pathogens
• Utilizing non-human biochemical pathways
• Contributing to the immune system

Microbiome vs. microbiota

Technically, the everyday use of the term “microbiome” to mean the microorganisms in your body isn’t quite accurate. That’s because your microbiome is the collection of genomes from microorganisms and not the microorganisms themselves. The term for the physical entities that make up what we often mistakenly call the microbiome is “microbiota.”

The tests on our list all use genetic sequencing to identify the genomes present in your microbiota, and thus they catalog your microbiome.

It’s possible that the continued rise of probiotics and microbiome testing will evolve the way we talk about the microbiome and microbiota. We’ll either all start using “microbiota” as the terminology becomes clearer, or “microbiota” will eventually be phased out in favor of “microbiome.” For now, we’ll continue to use the term “microbiome” as it’s used by most people, describing a collection of microorganisms.

How does the gut microbiome affect your health?

Your gut microbiome has profound effects on your health, some of which may be more obvious than others. For example, microorganisms in your intestines play a crucial role in breaking down the foods you eat and allowing your body to absorb nutrients more efficiently, which can have a lifelong impact on your health.10 That process makes sense, given that these microorganisms live within your digestive tract. What might be less apparent is how they function as part of your immune system and overall mental health.

Your gut is home to both beneficial and harmful microorganisms. Suppose the balance between them sways too far in the wrong direction. In that case, your immune system may weaken, or you may experience a bout of inflammation in the form of a migraine, arthritis, or other painful condition.

When we get sick, we often reach for antibiotics, hoping to kill off whatever bacterial infection plagues us. But antibiotics destroy nearly all of the bacteria in their path — good and bad. That’s why you should use antibiotics only when your doctor believes them to be the necessary course of action. And if your doctor does prescribe you an antibiotic, ask them what the most appropriate probiotic would be to take alongside it.11

A healthy microbiome has an ideal balance of microorganisms working alongside one another to maintain homeostasis so you can maximize nutrient absorption, fight off illness, and sustain a hormonal balance. However, microbiome tests almost always reveal a picture of a gut that isn’t quite balanced. You can address these imbalances by eating more of certain foods and less of others, but sometimes that’s not enough. That’s where probiotics and their supporting players come in.

We asked Stachel about the common complaints that led to a probiotic or prebiotic recommendation in her experience as a nutritionist. “In general, some conditions that may warrant supplementation include diarrhea, constipation, and IBS,” she said. But she emphasized, “Common GI complaints that lead to supplementation with a probiotic or prebiotic can vary, as this also tends to be more multifaceted or bio-individual.”

Probiotics

Probiotics are like living supplements that enter your gut and slowly colonize it. There are far more probiotic strains out there than we could reasonably list, but you don’t need to take all of them. That’s because most of us have enough of certain strains that only need to be there in small quantities. Imbalances concerning the more critical and abundant strains can make a greater difference.

Most probiotic supplements contain one strain, while others offer a handful of strains. You’ll rarely see a probiotic supplement with more than five or six strains, mainly because the strains compete for food in your gut. When you take a probiotic supplement, you essentially overwhelm the numbers of harmful bacteria, allowing them access to less food and rebalancing your system as they die off. Introduce too many strains at once, and they’ll end up competing with each other and less effectively outnumbering the bad guys.

With most off-the-shelf probiotic supplements, you’d be performing an inexact science. You might reach for something incredibly common like Lactobacillus acidophilus or Bifidobacterium longum, but without knowing the current makeup of your microbiome, you’d merely be hoping for a positive result.

Some of the companies in this guide will provide you with a detailed recommendation of specific probiotics that you can buy from them or elsewhere. Some will formulate a custom probiotic for you to balance your unique microbiome. They’ll all also make dietary suggestions that can help influence your microbiome.

Even before taking a test, you can access a litany of helpful probiotics by consuming fermented foods or drinks such as:

• Yogurt
• Kimchi
• Tempeh
• Sauerkraut
• Kefir
• Kombucha
• Some pickled foods like cucumber, beets, etc.
• Certain kinds of vinegar
• Miso

Prebiotics

Prebiotics are food for probiotics. They tend to contain one or more types of fiber that most users, even those with digestive issues, would tolerate well. Manufacturers select these fiber sources to act as pure fuel for probiotic colonization, providing the bacteria with all they need to multiply and thrive.

That said, certain prebiotic fibers contain FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols). People on low-FODMAP diets for specific gastrointestinal issues should speak with their gastroenterologist before selecting a probiotic or prebiotic.

Because companies often design prebiotic formulas specifically with their probiotics in mind, it’s usually a good idea to get your prebiotics and probiotics from the same maker. That way, you’ll know that the food you send to your gut is exactly what your probiotics will best utilize.

As with probiotics, you can find a good amount of prebiotic fiber in foods. The following are some of the more common items you can eat to increase your prebiotic fiber intake:

This list is far from exhaustive, and the results of your microbiome test should include a more specific outline of foods that will offer prebiotic fiber to your specific microbiome.

Supplements

Gut health is interwoven with so many other bodily systems that treating the gut alone might only provide partial relief. That’s especially true if your microbiome imbalance results — at least in part — from another disorder or deficiency. Supplements like vitamins, minerals, and amino acids can help correct deficiencies where they exist and provide additional benefits. That’s why Viome offers its Full Body Intelligence Test with an option for tailored supplements designed to address any issues it finds in your results. You may see some benefit just by taking random vitamins, but a tailored approach would target your health goals more exactly.

Best overall, best for privacy, best whole-health insights, and best probiotics option

In addition to five sophisticated microbiome tests, Viome provides several reasons why it’s our 2024 Editors’ Choice for the best overall testing company for your gut microbiome, as well as the best for whole-health insights.

The testing process is about the same on the user end as it is with most other tests, but what happens to your sample when it reaches the lab is very different. That’s because Viome utilizes AI-driven metatranscriptomics to evaluate its samples. Up until the late 2010s, metatranscriptomics was considered to have some of the greatest potential among sequencing methods, but it required a degree of sample stabilization that wouldn’t suit a test-by-mail system.

Viome has been on the cutting edge of this technology, developing tools, machinery, software, and even its own reagents to maximize the readability of days-old specimens. And since one of the shortcomings of metatranscriptomics is the need to compare results to an unfathomably large amount of data, Viome developed its own AI system for this specific purpose.

Given the broad scope and granular specificity of the metatranscriptomic approach and the inference capabilities offered by its AI, Viome’s results pages are incredibly thorough. They offer deep and valuable insights that you can address on your own or — more preferably — with your doctor. That’s especially true with the Full Body Intelligence Test, which may reveal syndromes or disorders you never knew you had and provide you with guidance on how you can address them.

Among the ways you might address microbial imbalances are custom probiotics, prebiotics, and nutritional supplements. Viome is one of the few companies in the space to tailor such products to fit its users’ results. And with more than 200 potential ingredients at the company’s disposal, it’s the only one to do so with such a high level of accuracy and comprehensiveness.

Viome also recently added a screening test for oral and throat cancers that received Breakthrough Device approval from the FDA. The test offers incredible accuracy from nothing more than a saliva sample, and it makes Viome the only company in the microbiome space that offers cancer screening.12

Here’s a quick look at what Viome’s gut microbiome testing services cost when you apply the coupon code INNERBODY:

And here’s a quick look at the company’s various subscription plans for testing and supplements, with 15% off the first six months when you use coupon code INNERBODY15:

It’s important to note that the subscription plans listed in this chart have associated fees if you cancel within the first three months of your purchase. The fee is equivalent to one extra month of service. For example, if you’re on the Precision Probiotics + Prebiotics plan, which costs $68/month, your cancellation fee will be $68.

Now let’s look at each test in a little more depth.

Gut Intelligence Test

Viome’s Gut Intelligence test, the most affordable of the company’s tests at $169, sequences RNA to identify the types, quantities, and metabolic activities of the trillions of microorganisms in your gut — more thorough than any other test in our guide. Included in the analysis are:

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

Other companies like Ombre and BIOHM offer valuable insights focused on bacteria or fungi, but these results provide a less specific picture than what you get from Viome. Tiny Health is the only other company in our guide that also extends analysis to phages, viruses, parasites, and archaea, but it does so with a slightly inferior sequencing method that doesn’t offer the activity-level information that Viome achieves.

Viome’s use of RNA sets it apart from companies like Floré and BIOHM, both of which focus on DNA. Studies indicate that concentrating on RNA rather than DNA allows Viome to focus on the active microorganisms and what they’re doing, providing a clearer picture of your whole gut microbiome.13 That makes sense if you recall that your microbiome is the genomic makeup of the microorganisms in your gut, and dead microorganisms leave DNA behind that can muddy the picture.

You can subscribe to Viome’s Precision Prebiotics + Probiotics plan ($68/month) — which delivers tailored prebiotics and probiotics to your door — as part of your Gut Intelligence Test purchase. With this subscription, you’ll also receive a free test kit every 12 months to retest, allowing Viome to make changes to your personal formula as needed. Viome gives our readers a discount on subscription plans — using code INNERBODY15, you can save 15%, effectively saving $10 per month.

Note: You can take $110 off the normal price of any Intelligence test by using our code INNERBODY at purchase.

Health Intelligence Test

Viome offers a pricier Health Intelligence Test for those who want to go beyond the gut microbiome (though that isn’t the primary focus of this guide). This test combines gut microbiome data with an examination of your blood to give you insights into your cell metabolism, biological aging process, and more. It does so by looking for biomarkers of stress and inflammation at the cellular level and examining pathways for cellular activities like oxalate metabolism.

The Health Intelligence Test costs $229. There’s no prefabricated subscription plan built around the Health Intelligence Test, but you can sign up for Precision Prebiotics + Probiotics within six months of taking any microbiome test from Viome. The only downside here is that there are no extra savings on the initial test. You’ll still have paid full price for it before changing over to the subscription model. For that reason, if you have the budget and desire to undergo microbiome testing in a broader context and gain even more actionable insights, we recommend you invest the extra cost in the Full Body Intelligence Test.

Full Body Intelligence Test

Viome’s most comprehensive test is its Full Body Intelligence Test, which takes all the insights you’d gain from the company’s other tests and adds oral, cognitive, and cardiometabolic health to the picture. It does so with a simple saliva sample added to the stool and blood required by the other kits. If you can afford this test, we highly recommend it.

At first glance, it might seem odd that your spit could tell you that much about your brain or your heart, but studies back it up. One study, for instance, looks closely at a specific pathway known as the oral microbiome brain axis (OMBA).14 The OMBA modulates things like cranial inflammation and other physical aspects of your brain that can positively or negatively affect cognition. Another study defines a link between the balance of microbes in your mouth and your likelihood of cardiovascular disease.15

These insights help Viome tailor supplements to go along with your prebiotics and probiotics if you subscribe to them.

Like the Gut Intelligence Test, the Full Body Intelligence Test is available both on its own and as part of a subscription plan. Viome’s Precision Supplements & Probiotics + Prebiotics plan includes yearly testing with the Full Body Intelligence Test, custom-tailored prebiotics and probiotics, and custom supplements for $199 per month (or $169 using code INNERBODY15).

That may sound like a lot of money, but if a high-quality, off-the-shelf probiotic costs $50 for a one-month supply and a prebiotic costs about the same, then you’re already more than halfway to the cost of Viome’s plan. And that’s before accounting for the supplements, the free retesting, or the fact that the products shipped to you will be formulated for your individual needs (rather than pre-formulated for the general population).

The Health and Full Body Intelligence Tests are rare in the industry, as most microbiome testing companies focus on the gut and occasionally span out into other microbial areas of interest. One such area where Viome is currently lacking is vaginal health, for which both Tiny Health and Ombre offer tests (and for which Ombre offers specific probiotic formulations).

Fortunately, Viome is constantly funding microbiome-related research studies through its research wing, Viome Life Sciences. At the time of this writing, the company is recruiting for a longitudinal study of the vaginal microbiome, which will likely lead to the development of a test and the integration of vaginal health into Viome’s probiotic design.

Oral Health Intelligence Test

In addition to the microbial information you’d glean from Viome’s Full Body Intelligence Test, the Oral Health Intelligence Test provides insights concerning:

• Oral pathogen activity
• Gum health
• Breath odor
• Inflammatory pathways
• Cavity-promoting microbes

As with Viome’s other foundational tests, the Oral Health Intelligence Test is available on its own for $149 or as part of a subscription for $59/month that includes Viome’s VRx My·Biotics Oral Lozenges, which are custom-tailored probiotics delivered directly to their target (your mouth). You get free yearly retesting, as well.

To read more about our top pick, check out our full Viome review.

Best budget option

Another solid choice is the Gut Health Test offered by Ombre, formerly known as Thryve. It isn’t the most comprehensive test on the market at this time (that distinction goes to Viome), but its $89.99-$119.99 price tag makes it the most budget-friendly option, and the company intends to offer more comprehensive gut microbiome testing in the future.

The generalized nature of Ombre’s test is ultimately what makes it less expensive. It focuses on gut bacteria — a narrower scope than BIOHM and significantly more limited than Viome or Tiny Health. Its sequencing provides you with information at the genus and species levels, but Viome and others can offer greater details about species and even strains. When you account for the sometimes significant differences in health benefits among different species and strains of the same genus, such in-depth information can be critical. Still, at the genus level, you’ll still be able to make strong inferences about your microbiome and what probiotics might help balance it out.

You can purchase a single Gut Health Test from Ombre or set up a subscription for regular testing. There’s also a Gut Health Program that offers savings to those who know they intend to use one of Ombre’s pre-formulated probiotics.

Here’s a quick look at how pricing works out for Ombre’s Gut Health Test:

Ombre is just one of just two companies in our guide to offer a test for vaginal health (as well as a pair of probiotics that target vaginal health, which we discuss below). Requiring a simple vaginal swab, it assesses the vaginal microbiome using the same sequencing method used for gut testing. A single test costs $119.99 and discounted tests are available with a subscription, but subscription savings on the Vaginal Microbiome Test are lower compared to the Gut Health Test, and there’s no vaginal health program at this time.

Ombre probiotics

Ombre’s probiotic formulas have evolved over the years. The company has expanded its catalog from three formulas to eight. Previous formulas also used to contain small quantities of vitamins and minerals, but those have since been removed, and specific probiotic strains included in some formulas have been replaced with similar strains from within the same genus and species.

Unlike Viome, Ombre lets you purchase its supplementary products without taking its Gut Health Test. If you like what Ombre has to offer, have already tested elsewhere, and know enough about probiotics to know what you want, you can buy the products on their own.

We like that Ombre’s marketing and reports are transparent about the science that goes into interpreting your microbiome and making personalized recommendations. However, if you want more comprehensive results, you’ll have to purchase your way through the company’s $10 paywall. Fortunately, you can upgrade to this premium tier at any time, so unless you’re urgently concerned with something like food intolerance or cardiovascular health, Ombre’s essential platform is a great starting point.

Shipping from Ombre is free, but when we tested the service, it took an unreasonably long time for us to receive our kit (well over a month). The company was upfront about this, sending an email that notified us of the delay. To learn more, visit our full Ombre review.

Best for pregnant people and their babies

While Tiny Health offers a gut microbiome test for adults, the company’s principal mission is addressing the microbiomes of babies and carrying microbial wellness efforts from childhood to adulthood. Other companies may offer probiotics for young children, but Tiny Health is the only one we recommend for testing a baby’s microbiome. All of the company’s tests employ shotgun metagenomics, which we regard as second only to Viome’s AI-driven metatranscriptomics in terms of accuracy and detail.

Ideally, you would start with the company’s Pregnancy Gut Health Test before giving birth. It provides useful information from the time you’re trying to become pregnant to the weeks and months after delivery. During that period, Tiny Health’s Vaginal Health Test can help you maintain the microbial environment through which your child will be delivered — the first significant building block in their own microbiome.

As your child grows, Tiny Health’s tests for babies and children can help you design a diet and probiotic regimen for optimizing their microbiome and decreasing their risks for certain diseases or developmental issues.

Given the roadmap that Tiny Health lays out for parents, the costs can add up quickly. Each test costs $249 (or $229 with the INNERBODY20 coupon code), and consultations with Tiny Health’s in-house doctors and microbiologists cost $100 each. At least shipping is always free.

The best thing you can do to save money on Tiny Health’s products is to enroll in the company’s membership plans. They cost $400/year but include two Gut Health Tests, two gut health reports, a free coaching call, unlimited text and email support, and $30 off any additional testing kits you might want.

Ultimately, a membership only saves you about $100 compared to the costs of individual components, but the unlimited text and email support may come in handy if questions arise when implementing aspects of a new health plan. Tiny Health also has the most impressive range of tests and services geared toward pregnant people and their babies.

BIOHM’s Gut Test costs $129.99, with no opportunities for subscription discounts or bundles to lower the price. Fortunately, shipping is free, and you can pay with an FSA or HSA card.

The test has historically had a strong focus on the role of fungi in the gut microbiome. (The founder, Dr. Mahmoud Ghannoum, is a world-leading expert on microbiome fungi.)

While BIOHM’s Gut Test is not as comprehensive as Viome’s, it does test for both fungi and bacteria and does so at a slightly lower cost. It just doesn’t offer insights into other microbial life-forms in your gut, like viruses. It also relies on DNA analysis, which could produce results based on microorganisms that aren’t alive and active in your gut.

For the information offered, the company does provide reports that are comprehensive and easy to understand. BIOHM presents your results across four sections:

• Overall Gut Score: A microbiome diversity grade 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: Analyzing your bacterial and fungal microbiome composition at the strain level.
• Actionable Recommendations: Recommendations about your diet and lifestyle, along with suggestions for supplements to improve your gut health, based on your results

Following testing, BIOHM’s goal is the same as yours — to get your gut microbiome composition into a healthy, “normal” range of diversity with beneficial microbiota. To that end, BIOHM, like many microbiome testing companies, has a line of probiotics and other nutritional supplements you can use to address any gut issues discovered in analysis. There are even a handful of bundles you can select to save money if you’re interested in multiple products.

Below is a snapshot of BIOHM’s probiotic catalog. We use the company’s term “superfoods” despite its relative meaninglessness.

• Total Gut Probiotic, $44.99: A combination of well-researched bacterial strains, a helpful fungus, and a digestive enzyme
• Immunity Probiotic, $21.99: A smaller dose of the same probiotic mix found in Total Gut, with high doses of vitamin C, vitamin D3, and zinc
• Women’s Probiotic, $44.99: BIOHM’s most complex probiotic mixture accompanied by a prebiotic blend and pomegranate extract
• Kids’ Probiotic, $29.99: A one-sixth dose of the blend used in Total Gut
• Microbiome Multi, $24.99: A comprehensive multivitamin mixed with a one-third dose of the Total Gut formula
• Super Greens, $44.99: A combination of one-half the dose of the Total Gut probiotic formula combined with blends of superfoods, greens, and fiber
• Super Greens Clean Energy, $44.99: Identical to regular Super Greens, but with the smallest Total Gut Blend in the lineup and the addition of green coffee extract, yerba mate, and a blend of digestive enzymes
• Digestive Reds, $31.99: A blend of red-colored antioxidant superfoods and the same small probiotic dose found in Super Greens Clean Energy
• Super Kids, $32.99: A small dose of the Total Gut blend combined with flaxseed oil powder, digestive enzymes, and an antioxidant blend similar to the one in Super Reds

You can bring the cost of any probiotic or bundle down by 20% if you subscribe to automatic billing and shipping. For an additional $60, you can also include an in-person consultation with a BIOHM nutritionist to discuss your test results and what the recommendations mean. We found the company’s written report to be clear, thorough, and understandable enough on its own, but an in-person consultation is a nice, customer-friendly feature to have.

Best option for using health insurance

Floré’s test kits are thoughtfully and thoroughly assembled, though the basic gut test costs $299, which is more than most. The company also offers a custom-tailored probiotic blend based on your results for just $79/month. Unlike many other testing companies whose prices have gone up in recent years, this is actually a reduction from Floré’s previous $99 monthly cost for custom probiotics. However, that’s still $10 more than Viome’s custom probiotic prescription, and Floré’s testing is DNA-based and less accurate than Viome’s. Perhaps the difference in cost is partly due to the fact that Floré offers retesting every four months as opposed to every 12, giving you two more yearly tests for free than you get from Viome.

That $79 price point is the same whether you get probiotics for an adult, a child, a toddler, or a baby. But keep in mind that probiotics for children are going to contain far fewer colony-forming units than those designed for adults, meaning those products have a much higher profit margin for Floré. Some of that cost difference could have been passed on to the customer as savings, but it wasn’t.

When we tested Floré, we found the results themselves to be somewhat underwhelming. They do a good job painting a picture of the various bacteria in your gut and give you a simple sense of how you compare to the rest of the population, but they’re missing some critical information. For example, the other companies on our list provide comprehensive insights about food and lifestyle changes you can make to improve the health of your microbiome. Floré’s dietary recommendations are seriously limited by comparison. Indeed, the dietary portion of our results was so short that we can present it here in its entirety:

“…your diet appears to contain high protein and high saturated fat with average fibrous vegetables. Provided there is no known allergy, we recommend maintaining Faecalibacterium through the consumption of cruciferous vegetables such as broccoli, cauliflower, and Brussels sprouts. We also recommend increasing the abundance of beneficial Bacteroides through the consumption of unsaturated fat-containing food such as avocados, walnuts, olive oil, and omega 3, 6, 9 containing food.”

So, the extent of the company’s recommendations is to eat more healthy fats, broccoli, cauliflower, and Brussels sprouts.

At $299, Floré’s Gut Health Test (without a probiotic subscription) is more expensive than its top three competitors, and it offers inferior value in its results. And that price has gone up significantly since we started covering the company ($169 at the time of our last review). If Floré can do more to control costs and make its results useful for its customers beyond pushing them toward the company’s probiotics, it would undoubtedly rise in our estimation.

Microbiome testing is extraordinarily complicated, and there are multiple ways that companies attempt to identify the microbes in your sample. Here, we’ll provide a little background and a basic sense of what these companies do to glean critical health information from what we typically consider waste.

The technology

The Human Genome Project launched in 1990 and was completed in 2003. Its intended goal was to account only for a little over 92% of the genome. We didn’t reach 100% until May of 2021, and there are still unverifiable aspects in about 0.3% of the data.

At the project’s outset in 1990, sequencing was a long, arduous process that required massive and expensive machinery. The computing power scientists have to work with today is vastly superior. Much of the process — from nucleic acid extraction to analysis — is now automated, and the technology continues to get smaller and more accurate.

But the technology is still relatively young, so some of the companies we’ve reviewed have decided to develop their own technologies for sequencing, as well as AI algorithms to compare sample results to massive amounts of data from the American Microbiome Project and beyond.

For example, Ombre utilizes a well-established sequencing method that uses 16S rRNA expressions in two of nine potential hypervariable regions to focus on bacterial presence.29 One of the two regions sequenced is the same one that the Earth Microbiome Project prefers (region V4), which gives Ombre access to a wealth of data against which it can compare your results. But 16S rRNA sequencing begins to lose accuracy beyond the genus of a bacterium. Better forms of testing can accurately tell you the species and sometimes the strains of the bacteria present.

Viome is on the cutting edge of development for sequencing technologies and techniques. It relies on polymerase chain reaction preparations and metatranscriptomics to calculate mRNA expression.30 It also creates its own reagents specifically for its analysis method. What’s more, the company has begun to design and build smaller, more accurate machines for processing and sequencing, so it can keep everything in-house and not rely on anyone else for its needs.

What the process is like for you

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