Do At-Home Microbiome Tests Actually Work? I Got One to Find Out.

I’ve dealt with chronic indigestion, painful burps, reflux, and bloating for the past 15 years. In 2010, I underwent a range of diagnostic tests—a colonoscopy, an endoscopy, a gastric emptying test, and some bloodwork—before I was diagnosed with Celiac disease. I subsequently cut out gluten. My symptoms improved for a few years, but despite eating a strict gluten-free diet, they reappeared a couple of years ago.

In 2023, I visited a new gastroenterologist to see if another health condition may be affecting my gut. Yet again, I underwent a series of costly, time-consuming tests that ultimately determined my gastrointestinal (GI) system was in good shape, even though my symptoms suggested otherwise.

Frustrated, I reached out to a nutritionist who suggested I do a GI-MAP test. This at-home stool test examines your microbiome, which is the community of bacteria, fungi, and viruses that naturally line your GI tract. These tests, often sold by private companies and can cost anywhere between $100 and $500, can tell you if there’s an overgrowth of specific organisms that could be triggering digestive problems and inflammation, she told me. Desperate for answers, I wired her $300, and she ordered me a test kit. Here’s what I learned about microbiome testing and how my gut impacts my overall health and performance.

How Do Microbiome Tests Work?

Growing evidence suggests the microbiome plays a role in the development of many chronic conditions—such as allergies and heart disease. “A balanced microbiome is linked to better mood, energy levels, and overall health, while an imbalanced one can contribute to inflammation, digestive issues, or even chronic disease,” says Arpana Church, a neurobiologist with expertise in digestive diseases.

Microbiome kits claim they can help identify the bugs in your gut that may be contributing to health conditions like IBS, autoimmune diseases, skin issues like acne and psoriasis, brain fog, and even mental health problems like depression and anxiety.

Athletes can turn to tests for insights on how to improve their microbiome to reduce inflammation and enhance recovery.

They’re also simple to use. My provider ordered the kit online. When it arrived, I filled a small tube with my poop, then mailed it off to a laboratory that examines the bacteria in my stool sample. My results, along with an interpretive guide, arrived within ten days.

What My Microbiome Test Results Told Me

According to the kit, I had Helicobacter pylori (H. pylori), a bacterium that infects your stomach lining and causes inflammation and ulcers. There was also an abnormal growth of Staphylococcus aureus (the bacterium that causes staph infections) and Streptococcus spp., one of the bacteria responsible for strep throat. Both of these bacteria trigger intestinal inflammation and loose stools. The test also detected Methanobacteriaceae—a family of bacteria that produces methane gas and is linked to constipation, bloating, and IBS.

My gastroenterologist’s (not the same person who ordered my kit) response to my test results? “I don’t make clinical decisions off of kits like these.” Furthermore, he had taken a biopsy of my intestines during a recent endoscopy and found no signs of H. pylori. He would rather go off that, a scientifically sound measure, than a relatively new test kit. Needless to say, I was disappointed and confused.

Doctors Aren’t Sure How Accurate Microbiome Tests Are

According to Church, there are a couple of reasons why clinicians don’t trust these kits quite yet.

Science Hasn’t Pinned Down What a “Healthy” Gut Looks Like

The first is that the science backing their usage is still in its infancy. The main reason for this is that there isn’t a universal definition for what a “healthy microbiome profile” even is, she says. “A microbe that looks ‘high’ on your report may be harmless—or even normal for you,” she says. Furthermore, our microbiomes are always changing—week to week and even day to day, according to Church. “What you ate, recent illness, travel, or antibiotics can shift results,” she says.

I was determined to gain some actionable insights from my results. I interviewed Maggie Stanislawski, a biomedical researcher at the University of Colorado Anschutz Medical Campus, to get her perspective. Did the overgrowth of methane-producing bacteria in my gut mean nothing? The answer is murky.

Apparently, there are a variety of Methanobacteriaceae species that can have different effects, so it’s unclear what, if anything, this general overgrowth means, according to Stanislawski. Also, “Methanobacteriaceae isn’t a ‘bad’ bug,” she says. In fact, the bacterium helps break down carbohydrates, indirectly contributing to the production of short-chain fatty acids (SCFAs), she says. SCFAs, for context, offer a range of health benefits. They’re anti-inflammatory and contain protective properties for our brain, heart, and immune systems.

Everyone’s Microbiome Is Different

But the H. pylori in my stool sample? Surely that’s a red flag, I thought. But again, no. Some of these kits can produce inaccurate results. One study found that when seven different microbiome tests were used to analyze the same stool sample, the results varied drastically.

Just because H. pylori is detected doesn’t mean it’s an issue—“it could be present and not cause problems and that might even be healthy, especially if you’ve had it since you were very young,” Stanislawski says. These may be giving me issues, she says, but these levels may be normal—for me.

So, Can Microbiome Test Kits Tell You Anything?

Yes. These kits do a solid job of identifying infectious diarrhea-causing pathogens—such as  C. diff or Campylobacter—that standard medical tests also catch—and can be treated with antibiotics. But when it comes to all the other microbes? There, unfortunately, isn’t a clear-cut solution, Church says. “Those kits rarely lead to proven, tailored treatments that outperform good clinical care and diet basics,” Church says.

While it may be too soon to gain specific takeaways and actionable steps from these kits, there may be a time in the near future when that changes. According to Church, we need more research that investigates how various treatment approaches, based on their results, impact people’s health outcomes.

The best thing to do if you order a microbiome test is to work with a professional, Church says. These kits often contain recommendations for various herbs and probiotic supplements you can take to heal your microbiome (the goal being to increase beneficial bacteria and decrease harmful ones).

If anything, Church hopes the kits help people focus on the steps known to improve gut health: eating a diet rich in fermented foods, such as sauerkraut, kimchi, and kefir, and low in ultra-processed foods. Then, incorporate a variety of fiber-rich and prebiotic foods—such as leeks, bananas, and oats—that microbes thrive on.

How Athletes Can Benefit From Gut Health Testing

For years, my GI pain has impacted my workouts. Acid reflux has sent sharp pains up my chest when I jog, often causing me to wrap up early. And, in certain instances, abdominal cramps and indigestion have prevented me from even being able to get out the door in the first place.

Athletes can turn to tests for insights on how to improve their microbiome to reduce inflammation and enhance recovery, says Church. She says research suggests a healthy microbiome can help you extract energy from food, reduce inflammation, and recover faster from intense exercise. That means less pain and better performance. A more diverse gut microbiota may also help optimize energy metabolism, ultimately providing you with more fuel to crush your fitness goals.

While the microbiome kit was unable to heal my gut, it did serve as a reminder to brush up on all of the little things that help my gut run smoothly.

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