Here’s What You Can Learn from A Gut Microbiome Test

Gretchen Lidicker
Medically Reviewed
March 30, 2020

If you’ve ever suffered from gut issues—whether it be bloating , constipation, acid reflux , or diarrhea—you know they can be a real day ruiner. We often take our digestive systems for granted until something goes wrong, and only then do we realize we realize just how much work they do for us.

If something’s gone awry with your gut health , you might be considering a gut microbiome test. But what can you really learn from one of these tests? Are they worth the money—and let’s be honest—the inconvenience? Find out what a doctor has to say about microbiome testing.

What is a gut microbiome test and how do they work?

Most gut microbiome tests look at the good and bad bacteria in your gut, signs of potential pathogens, immune and inflammatory markers, and indicators of how your digestive tract is working.

Unlike a simple blood or saliva test, microbiome tests are a little more involved. Typically, the test is a take-home kit that instructs you to collect stool samples for three consecutive days, explains Dr. Darcy McConnell , a board certified family medicine physician at Parsley Health New York. It’s important to test three days in a row because certain infections, like parasitic infections, are not detectable every single day.

If your first thought is ew, you’re not alone. “Nobody likes to do it. But we make everyone do it and we do it ourselves; plus, you get to do it in the privacy of your own home,” says Dr. McConnell.

Who should get a gut microbiome test?

At Parsley Health, we will run several types of gut tests if you have GI issues or your doctor suspects your symptoms may be related to gut health. According to Dr. McConnell, “I’ll ask most patients with digestive symptoms if they’re interested.” These tests can be helpful if you’re experiencing chronic bloating , diarrhea, gassiness, or constipation or you have a diagnosed GI disorder such as inflammatory bowel diseases like Crohn’s and ulcerative colitis, irritable bowel syndrome, and celiac disease.

According to Dr. McConnell, these tests can be especially helpful if you’ve had GI issues for a long period of time and they don’t appear to be linked to what you eat. In other words, if you have a healthy diet but you’re still suffering from GI symptoms, these gut bacteria tests can help your doctor understand what’s going on.

But it’s not just GI symptoms that warrant a gut health test, either. Dr. McConnell will also suggest a test like this if you’ve been diagnosed with an autoimmune disorder. “Most patients with these need to look at their gut. If you have a microbiome issue, it’s going to affect your immunity,” she explains. In addition, “I’ll also do stool testing in patients with skin diseases (such as eczema, dermatitis, psoriasis) because the digestive tract and the skin are contiguous and how we eat has a huge influence on how our skin performs,” she continues.

What can you learn from a gut microbiome test?

If you and your doctor decide that gut microbiome testing is right for you, get ready to learn a lot about your gut health. The digestive system is an extremely complex part of the body, so these tests don’t check one or two biomarkers. In fact, depending on the exact test used, they can test for a bunch of different things, including:

1. Parasites

Labs will look under the microscope for signs of a parasite and also diagnose them by the presence of their DNA, explains Dr. McConnell. It might surprise you but parasites are more common than you think ; common infections include Blastocystis hominis and Dientamoeba fragilis, which cause symptoms like nausea and stomach pain.

2. Yeast overgrowth

Too much yeast, like the common yeast called Candida albicans , can explain a wide range of GI symptoms as well as other symptoms like acne , weight gain, and brain fog .

3. Bacterial overgrowth

This includes both “potentially pathogenic” and pathogenic bacteria. A “potentially pathogenic” bacteria is a type of bacteria that only becomes pathogenic if it’s allowed to overgrow. In other words, a small number of these bacteria won’t cause symptoms but a large number might. In contrast, pathogenic bacteria like salmonella are harmful at pretty much any number.

4. Calprotectin

Calprotectin is an inflammatory marker associated with irritable bowel disease and tumors. If your levels are significantly elevated, you’d need to consult a GI specialist about next steps.

5. Immune markers

Testing for immune markers helps reveal whether the immune system is over- or under-active. Specific inflammatory markers, such as IgA, point to a food sensitivity or something else in the GI tract—like a fungus or bacteria—that’s triggering an immune response. Elevated levels of eosinophils indicate an allergy or a parasite.

6. Pancreatic elastase

Pancreatic elastase is an enzyme that you should have appropriate amounts of; if not, your pancreas might not be functioning well and as a result, you might not be breaking down your food effectively.

7. Fat and protein

By testing for the presence of protein and fat in the stool, your doctor can tell how well you’re digesting and absorbing your food.

8. Beneficial bacteria

Finally, these microbiome tests also look for the good stuff. According to Dr. McConnell, “this test looks for short-chain fatty acids (like butyrate) that should be in your colon and stool in high quantities if you have a vast, robust microbiome.” If you’re not eating enough fiber , these bacteria might be missing.

How do your gut microbiome results affect your treatment?

“Running these tests can give us a bounty of info and we can be more specific with treatment,” says Dr. McConnell. For example, if you are low in beneficial bacteria, “we need to load you up with probiotics and fiber.” You may also have too much bad bacteria, which according to Dr. McConnell, would mean you could benefit from pharmaceutical-grade antimicrobial supplements that kill bacteria in the colon. And finally, if your gut shows that there’s a lot of inflammation , your doctor may suggest an anti-inflammatory diet with additional anti-inflammatory supplements.

The results of microbiome testing can be extremely helpful, but it’s important to keep in mind that the science surrounding the microbiome is very new. “It’s always morphing and changing and a lot of the studies are still very small,” says Dr. McConnell. Basically, these tests don’t tell us everything, so we shouldn’t rely on them alone to inform treatment. For example, there are specific bacteria that have been linked to specific health conditions, but the science isn’t strong enough yet to make any conclusions. “Getting too bogged down in the minutia isn’t helpful. It’s a much more big picture,” says Dr. McConnell.

It’s also best to do gut microbiome testing under the guidance of a doctor who can actually help you interpret your results. Without that, you run the risk of self-diagnosing and inappropriately treating.

When to skip gut microbiome testing

“We do these tests on people whose primary ailment is digestive,” says Dr. McConnell. But according to her, one exception is when she suspects SIBO , which stands for small intestinal bacterial overgrowth . “If it’s limited to upper GI symptoms I may forego doing a stool test and instead do a SIBO breath test,” she continues. A SIBO breath tests for specific gases emitted by bacteria in the supper GI tract that can’t be measured in a stool test.

Other patients that should hit the pause button on this type of test are those with a poor diet. If you’re eating processed and inflammatory foods on a regular basis, “I won’t always offer this test as a first pass,” says Dr. McConnell. Instead, “I go for food first,” she continues. If there’s a lot of room for improvement in your diet, simple changes can often resolve the GI issues — without the need for advanced testing.

So, how often should you get a gut microbiome test? These tests aren’t cheap (typically falling between $200 and $400 dollars) and they’re not something you need to do over and over again. In fact, “we typically do the test once, treat, see improvement, and then there isn’t a need to do it again for quite some time,” says Dr. McConnell.

Gretchen Lidicker

Gretchen Lidicker is a writer, researcher, and author of the book CBD Oil Everyday Secrets: A Lifestyle Guide To Hemp-Derived Health & Wellness. She has a masters degree in physiology and complementary and alternative medicine from Georgetown University and is the former health editor at mindbodygreen. She's been featured in the New York Times, Marie Claire, Forbes, SELF, The Times, Huffington Post, and Travel + Leisure.

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