by Jill Neimark & Dr. Bill Rawls
Posted 4/6/18

One of the great discoveries of modern medicine is that humans are inhabited by trillions of bacteria, viruses, parasites, and fungi. And not just in the gut, as once believed, but in tissues throughout the body. You are not one, but many—and in an optimal state of health, you coexist in harmony with your microbes.

Scientists are now engaged in the enormous endeavor of cataloging the microbial map of our mouth, skin, lungs, urogenital tract, blood, eyes, and of course, our gut. The initiative is called the Human Microbiome Project, and it relies on extraordinarily advanced sequencing tools. The great challenge: To discover what constitutes the normal microbiome of every tissue and organ, and better yet, to learn how to restore proper balance when those microbial communities are disrupted.

The largest and most complex microbiome is that of our GI tract, which is estimated to contain as many as 1,000 microbial cells in every gram of stool. Though we are in the early days of truly understanding the gut microbiome and its impact on health and illness, there are already numerous tests available to analyze your gut flora, as well as to look for markers of inflammation or poor digestion.

Many of these tests are widely used by doctors who practice integrative or functional medicine, and a few can be ordered without a doctor’s prescription. In either case, taking the test is as simple as collecting a fecal swab and sending the results to a lab for analysis. But given how little scientists know about what a healthy microbial mix should look like in the gut, just how useful are these microbiome tests?

We took a look at the options, and spoke with Dr. Bill Rawls, author of the bestselling book Unlocking Lyme, to get a sense of whether they’re worth your time and investment.

What Typical Microbiome Tests Promise

If your medical doctor orders a stool test, there’s a number of things he or she might be looking for in the results. This can include overgrowth of parasites, bacteria, and fungi; evidence of leaky gut and inflammation; and evidence of incomplete digestion of fats, starches, or proteins. Doctor-ordered tests can also measure stool pH, molecules associated with a healthy immune response, and short-chain fatty acids associated with gut health.

Many specialty laboratories offer these stool tests, including Genova Diagnostics, DiagnosTechs, Doctor’s Data, Great Plains Laboratory, and more. The tests usually rely on one of two approaches.

The first cultures the stool for organisms using a sophisticated mass spectrometry technique, which, in very simple terms, measures the masses of chemical species in the sample to determine what they are. The second method uses sequencing and something called PCR technology to identify the DNA of organisms. These tests can cost many hundreds of dollars, and they may or may not be covered by your insurance.

If you’d rather skip the doctor’s office and pay for a test out of pocket, there are now a handful of companies offering direct-to-consumer tests, and given their popularity, likely more are on the way. Here’s how six of the most well-known consumer tests compare:


What it does: This crowd funded research project sequences 16S rRNA — an RNA subunit that’s purportedly helpful for identifying bacteria and archaea (single-cell microorganisms). Results are shared anonymously in open repositories to help further microbiome research around the world.

Price: $99

Where to find it:

What you get: A report on which bacteria and archaea are present, and how your microbiome compares to the 10,000-plus others in the project database. You’ll also receive information on how your diet and lifestyle might contribute to your microbiome makeup.

Notes: It takes four to six weeks to receive your testing kit, and up to three months to get results — by which point your microbiome may have changed significantly, depending on any changes in your diet or lifestyle.


What it does: Sequences the genes of both the bacteria and fungi in your gut at a genus and species level. A candida specific test is also available.

Price: $135

Where to find it:

What you get: A profile of your gut makeup, and comparison to normal levels of bacterial strains from the NIH Human Microbiome Project and/or fungal strains from Case Western Reserve University School of Medicine.

Notes: For an additional fee, you can receive diet and lifestyle recommendations from a registered nutritionist. Biohm also sells their own line of probiotics.


What it does: Geared toward people with diabetes and prediabetes, DayTwo uses a stool test to sequence the DNA of your microbiome, and a blood test to measure HbA1C, which provides an idea of blood sugar levels on average.

Price: $349

Where to find it:

What you get: A profile of your microbiome composition and diversity, and a Personalized Nutrition App dedicated to helping you manage your blood sugar levels via customized advice on foods to avoid and meal and snack recommendations.

Notes: The tests and personalized plans are based on a five-year clinical research project licensed from Weizmann Institute of Science.


What it does: Like American Gut, it uses 16S rRNA sequencing to sequence your microbiome down to a species level.

Price: $105

Where to find it:

What you get: A rundown of which healthy bacteria are low and which pathogens are high, and a “wellness score” based on how your results compare to data from the American Gut Project. You’ll also get personalized daily dietary and supplement recommendations.

Notes: Thryve sells probiotics ($42/bottle) for gut health, general health, weight management, and immune support, which they deliver on ice in the summer.


What it does: Sequences the DNA of your gut microbes to identify pathogens associated with conditions like Irritable Bowel Syndrome (IBS) and Crohn’s Disease.

Price: $89-$399

Where to find it:

What you get: You’ll get a breakdown of the pathogens and commensal bacteria in your microbiome, how your biome compares to the company’s database of 150,000+ samples, and an overview of how well it’s functioning.

Notes: uBiome also offers SmartGut, a physician-ordered test that might be covered by insurance. Your doctor will receive a microbiome report and possible links to specific infections and gut conditions. Editor’s note: uBiome is currently under FBI investigation for financial misconduct.


What it does: Uses metatranscriptomic analysis to sequence all the RNA in your stool and identify all living gut microorganisms (bacteria, viruses, bacteriophages, archaea, fungi, yeast, parasites, etc.) at a species and strain level.

Price: $399

Where to find it:

What you get: A gut score (health of your microbiome), metabolic score (fitness and nutrition level), and body score (overall shape and lifestyle choices) based on your results and findings from peer-reviewed articles.

Notes: Viome also measures the metabolites your microbes produce after you’ve eaten, then offers personalized food and nutrition plans for minimizing production of harmful metabolites and maximizing production of beneficial ones.

But Do They Deliver on Their Promise?

Rob Knight, a professor at the University of California, San Diego, and cofounder of the American Gut project, put it this way: “The enthusiasm of the manufacturers simply goes well beyond where the science is right now,” he told MIT Technology Review last March.

Dr. Rawls agrees. He also understands the desire to get tested. “It may show that you carry certain pathogens, and make you feel that your symptoms are justified. There can be some solace in that,” he says. “And the potential for harm in getting these tests is negligible. But that doesn’t change the fact that these tests are not a diagnostic tool.”

Instead, one of the best ways to detect a microbiome imbalance is to listen to your body: “If you’ve got symptoms, you’ve got a skewed microbiome—given,” says Dr. Rawls. “And the solution is the same whether you have a positive test or not, which is that you need to reverse the things that caused the imbalance to begin with.”

Poor diet is one of the biggest factors. “The modern diet is loaded with processed grains and carbohydrates, and carbs feed the bad bacteria,” explains Dr. Rawls. “You’ve got to minimize those and eat more vegetables than anything else. The fiber in vegetables feeds a better spectrum of microflora than the fiber in grains.”

Stress is another player. “But lowering stress is easy to say, hard to do,” says Dr. Rawls. “So I tell people to focus on slowing down around food. Be more mindful when you’re eating, chew your food – it aids the digestive processes – and take more time in general at the table.”

Finally, Dr. Rawls points to herbs as the most cost effective and efficacious way to resolve the problem. “Taking the right herbs provides phytochemicals that go a long way in balancing the microbiome and restoring immune function,” he says. “These chemicals are plants’ built-in defenses against pathogens, and they’re transferred to us.” A few he highly recommends include berberine, andrographis, cat’s claw, and sarsaparilla.

Gut ecology is vast and complex. One day, we may truly unpack the ways in which the human genome and the intestinal genome are linked together into a “metagenome.” We may walk into our doctor’s office for a microbiome analysis, whole genome sequencing, and a unique personalized health report with tailored guidelines and solutions.

But you don’t have to wait. Eating a plant-centric diet, limiting stress, making sure to get enough exercise, and turning to time-tested herbal medicines will often help bring your gut and overall health into balance — without the expense and stress of testing.

Dr. Rawls is a physician who overcame Lyme disease through natural herbal therapy. You can learn more about Lyme disease in Dr. Rawls’ new best selling book, Unlocking Lyme.

You can also learn about Dr. Rawls’ personal journey in overcoming Lyme disease and fibromyalgia in his popular blog post, My Chronic Lyme Journey.