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How to Find Out if You Have a Healthy Microbiome

Do You Have a Healthy Microbiome? Here’s How to Find Out!

Yvette La-Garde

Well Blog Editor, VitaMedica

Are you having a hard time losing weight? Do you suffer from bloating, indigestion or gas? Is your mood more sullen than sunny? If so, your gut microbiome – the collection of microbes that line your digestive tract – may be at fault.

You may be surprised to learn that your gut microbes, which are comprised primarily of bacteria, play an important role not only in digestion and immune system function but metabolism, cravings and even mood!

As studies have shown, individuals with a healthy gut microbiome - as measured by a diverse and balanced internal ecosystem - are more likely to be lean and less likely to suffer from digestive disorders, allergies, asthma, anxiety, and depression.

But, how does your gut microbiome become unbalanced?

While our mix of bacterial species stays remarkably the same over time, environmental conditions including stress, drugs, gastrointestinal surgery, infections and toxic agents, can alter our microbial balance.

The most common cause of dysbiosis, or imbalance of bacteria in the gut microbiome, is antibiotics (in humans and in our food supply). But, a diet high in refined carbohydrates, sugars and saturated fats and low in fiber is also a major contributor.

Getting Your Microbiome Tested

Even if you don’t exhibit any of the health issues listed above, how do you know if your gut microbiome balanced? The best way to find out is by getting your microbiome tested.

Just like labs are drawn to determine your metabolic health (i.e., cholesterol, triglycerides, blood sugar) fecal samples can now be collected to determine your gut microbiome health. What’s the difference? Instead of providing the lab with a urine or blood sample, you’ll need to provide a stool sample.

Currently there are research organizations that offer microbial testing kits, such as the American Gut Project and uBiome. In these instances, you buy a kit, send in your sample, receive your microbiome data, and then compare yourself to other people who have had their microbiomes tested. From a commercial standpoint, the only lab in the U.S. that offers a gut microbiome test is Genova Diagnostics (MetaMetrix). Below, I provide more information along with the pros and cons of using each of these lab tests.

American Gut Project

The American Gut Project, initiated in 2012, gives everyone an opportunity to participate and compare the microbes living in and on their body to thousands of other people in the U.S. and around the world.

The American Gut Project is built on open-source, open-access principles. To date, scientists have sequenced microbiota samples from more than 3,500 American adults and children. To see what they have learned so far, click here.

You (or your pet!) can participate in the American Gut Project by providing a donation (the price varies depending on how many sites you survey). You’ll need to fill out an online questionnaire with some basics about yourself, diet and lifestyle. Note, if you live in the UK or anywhere else in Europe, you can join the British Gut research project.

In January 2014, I participated in the American Gut Project by submitting samples from four body parts. As it turns out, the major players in my gut microbiome are Bacteroidetes and Firmicutes. My forehead is teaming with Corynebacterium but has significantly fewer Propionibacterium – the group which includes Propionibacterium acnes or P. acnes - the species linked to the skin condition acne. To be expected, more than 97% of the bacterial genus found in my “lady parts” was Lactobacillus. But, my mouth seems to have more diversity with 7 different major bacterial families fighting it out for survival. You can see my results here.


You’ll not only find out more about your microbiome but you’ll be contributing to the greater good of science. For a reasonable price (you make a donation of $99.00 per test site), you can get your microbiome tested for various sites on your body (oral, skin, vagina, gut). The gut collection process is pretty easy, just requiring a few swabs from your stool. Plus, online videos walk you through the process to ensure that the microbes aren't compromised. You can even send in a swab from Fido and learn more about his microbiome!


You’ll need to track your diet for 7 days and wait another 6 to 9 months to get your results. The test results are pretty limited in terms of the information provided.


A new company called uBiome lets you see the species of bacteria in your microbiome and how it compares to others in the study.

To participate, you’ll need to complete a short online survey. Then your kit will be sent straight to you. You’ll collect your samples with a quick swab of the site (mouth, ears, nose, gut, or genitals) and mail it back to uBiome.

In September 2014, I submitted a sample of my gut microbiome to uBiome. By logging into my online account, I can review and compare my results to others’ in the study (i.e., vegetarians, recent antibiotic use). Online tools like their taxonomy tree, give a visual representation of your gut bacteria. It was difficult to compare my results to those from American Gut because in the interim I had been on a course of antibiotics for a root canal gone bad. Notably, the amount of Firmicutes in my gut was at almost 70% - a pretty big difference than the 59% that American Gut found nine months earlier.


You can order a kit to sample your microbiome for around $89 and obtain the results in about six weeks. You can sample your gut plus another site for $159 and five sites for $399. The study results are more visual than from American Gut and can be viewed online by logging into your account.


While it’s great to know more about the microbial workings of your body, what you do with the information is a challenge. However, it can be a useful tool to see how your gut microbiome changes with modifications made to your diet and lifestyle.

Genova Diagnostics (MetaMetrix)

If you’re working with a doctor, he/she may opt to assess your gut health using Genova Diagnostics’ GI Effects Stool Profile lab test. This comprehensive test gives you and your doctor a very complete picture of your gut health. To find a doctor in your area that offers this test, you'll need to fill-in an online form.

Earlier this week, I submitted my stool samples to be analyzed by Genova Labs. I should receive the results by early August 2015 and will share them once they arrive. Of note, Dr. David Rahm, VitaMedica's chief medical officer, is running a clinical trial to determine how diet, lifestyle and a probiotic-based supplement program (LeanBiotics) helps overweight adults lose weight and modify their gut microbiome. All participants will have their gut microbiome tested using the GI Effects test kit prior to and at the conclusion of the 8-week study. Stay tuned for clinical study results!


In less than 3 weeks, you'll receive a visual report of your results which are easy to read. Of course, your doctor who ordered the test will also explain the findings and develop a dietary and lifestyle plan tailored to your unique needs. Genova's Stool Effects provides the most complete picture of your gut microbiome health - including information on digestion, inflammation and immunology, microbial inhabitants (insufficiency, imbalance, diversity and relative abundance) and infection.

This test is useful to determine if you have celiac, IBS or an inflammatory bowel disease such as ulcerative colitis or Crohn’s disease. But, it is also can tell a story if you’re overweight or obese. Armed with this information, your doctor can develop a treatment plan (including diet & lifestyle changes) then re-test your gut microbiome for changes in "lean" versus "obese" bacteria.


GI Effects requires some handling of your stool, which can be a turn off if you’re squeamish about all things fecal. While you'll need to place stool in three different test tubes, mix thoroughly and shake, this more involved process helps to secure the "data". This test is quite expensive, costing upwards of $600 however some insurance companies may cover the test. Unlike uBiome or American Gut, you can't order this kit on your own; you'll need to go to a doctor that offers this lab test. But, unlike with the other lab tests, you'll have a medical professional who can interpret the data.

An Evolving Technology

Advances in computer technology have allowed scientists to develop more reliable techniques to measure the microbes that inhabit the human microbiome. As a result, the human microbiome has the potential to become one of the most important new tools for personalized health and medicine.

However, moving from a basic research environment to the clinic requires some of the kinks to be worked out. How the DNA extraction is done (the technique which identifies the various microbes) can make a big difference in the results. In addition, how stool samples are handled can also influence the data (some bacteria grow while in the mail, skewing the results). So samples taken from the same stool and processed by two different labs, can yield different results.

The Microbiome Quality Project, which is tasked with standardizing and developing quality controls in the technologies and computational methods used to measure the microbiome, was established to bring consistency to the field.

In the meantime, getting your microbiome tested is a very cool way to learn more about the microbes that inhabit your body!

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