Gut microbiome tests are everywhere. Should you get one?
[November 04, 2025]
By DEVI SHASTRI
At-home gut microbiome tests are trending, selling insights to the
curious, empowerment to the chronically ill and a claimed path to
longevity to the wellness-conscious.
Private companies are offering tests, costing $100 to $500 or more, that
promise a bacterial inventory of your intestines.
But can microbiome tests actually provide actionable health information?
As more patients arrive at doctors appointments with results in hand,
frustrated gastroenterologists want people to know the tests have
limits.
There's a world in your gut and we still don't know a lot about it
Inside our intestines, entire ecosystems of bacteria help us digest our
food, absorb key vitamins, combat inflammation and much more. Research
shows a healthy gut microbiome may play a role in preventing things like
liver disease and diabetes and could even influence mental health.
The gut microbiome is incredibly complex and our understanding of it "is
in its infancy,” said Dr. Mark Benson, a gastroenterologist for the
University of Wisconsin-Madison's health system.
“But there's growing evidence that there are changes in the gut
microbiome that are associated with different diseases, including
diabetes, liver disease, obesity and inflammatory bowel disease,” he
said.
There's a key catch, though: In many cases, it's unclear if the gut
microbiome change is the cause — or an effect — of the disease.
On top of that, each person's gut microbiome is unique, like a
fingerprint. It can even vary within one person's gut.
”Most of the variability between people, we don’t understand," said Dr.
Eamonn Quigley, the chief of gastroenterology and hepatology at Houston
Methodist Hospital, who has spent 30 years researching the gut
microbiome and disorders of gut-brain interactions, like irritable bowel
syndrome.
How do gut microbiome tests work?
In most cases, a microbiome test involves taking a stool sample, usually
using a swab or a wipe for collection. The samples are mailed to a lab
for analysis.
The companies then provide a report of how the person’s mix of gut
microbes compares with a supposed ideal, or outlines where things are
imbalanced.
These direct-to-consumer tests are not meant for clinical use and are
not federally regulated, so it’s nearly impossible to say how reliable
they are. Different companies can set different standards and methods
for their tests.
That raises many questions for doctors: Is the sample collection
consistent and reliable? What is the science behind the benchmarks they
are comparing results to? Is the stool the best place from which to take
a sample, or should it come from higher up in the gut?
What can doctors do with the test results?
Physicians sometimes order stool tests, but they typically are looking
for specific problems: infections, inflammation from foodborne illnesses
or antibiotic use, or cancer.
When patients come in with their own results from an over-the-counter
test, there is little advice to give.
“If you talk to patients, these tests are appealing. They’re cool.
They’re all this data,” said Dr. Sean Spencer, a physician scientist at
Stanford University. The frustration for doctors, he said, is with the
lack the tools to change the microbiome.
Spencer, Quigley and Benson have all had patients bring them the results
of microbiome tests. But antibiotics and diet are really the only proven
tools doctors have to change the gut microbiome, Spencer said.
Occasionally, the tests show a measure of inflammation in the gut or
pancreatic function that can be useful to doctors, Quigley said. But
beyond that, “for most people, they’re actually wasting their money,” he
said.
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This photo provided by Tiny Health in October 2025 shows the
company's swab for their gut health test. (Tiny Health via AP)
 The list of gut bugs and purported
imbalances don’t align with any medically backed treatments, the
doctors said.
“The technology is jumping ahead of the clinical application,” said
Quigley. “Just because you can measure something doesn’t mean to say
it’s worthwhile.”
Some test results come with a pitch
The companies offering tests say they are not treating any specific
conditions. But many of them — some 45%, according to a March 2024
article in Science Policy Forum — also sell supplements that they
recommend to customers alongside their results.
One of those is Thorne, a wellness company that sells gut microbiome
tests and includes recommendations for their supplements with their
test results, alongside recommended lifestyle changes.
Chief Scientific Officer Nathan Price said he doesn’t see that as a
conflict of interest. Customers are “not mandated” to buy anything,
he said, but many are looking for solutions. Thorne's test can then
track if probiotics are changing their results over time.
Probiotics and other supplements are not regulated as drugs by the
Food and Drug Administration, leaving many questions about which
ones work and if they even contain what they claim. Research on the
potential for probiotics to treat several chronic health conditions,
like atopic dermatitis, high cholesterol and irritable bowl
syndrome, have yielded mixed results or limited impact.
Another company, Tiny Health, recommends supplement brands based on
its own testing, but it does not sell them or get money from
affiliate marketing. That was an important line for Dr. Elisa Song,
the company's chief medical officer and an integrative pediatrician.
“I was very clear that Tiny Health should not be selling probiotics,
because there should not be that conflict of interest there,” Song
said. “You have to keep the science clean.”
You don't need a test to improve your gut health
The gastroenterologists who spoke to The Associated Press agreed
that there is no harm in taking one of these tests if you're curious
about your gut or want to contribute to a company's research.
But you can improve your gut health without the tests, the doctors
said.
“I would not significantly change therapy or take a bunch of
expensive supplements based on these results,” Benson said.
Instead, eat lots of plant-based fiber and protein. Improve your
sleep. Move your body. See a doctor for serious gut symptoms, such
as bloody stool, ongoing constipation and diarrhea or severe pain.
Spencer, who is the medical director of the Microbiome Diagnostics
and Therapeutics at Stanford Medicine, looks forward to the day
doctors treat the microbiome by tailoring treatments to address
imbalances.
He and the other gastroenterologists said they understand the
frustrations of people with complex, hard-to-treat digestive
conditions. The testing companies say they are trying to drive that
technology forward.
“I think there has to be more research. We need the evidence," Song
said. “We need to have the evidence to make this the standard of
care.”
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