Dozens of at-home testing companies claim that they can analyze the bacteria, fungi and other microbes in your stool to create a snapshot of your gut microbiome — the community of trillions of microorganisms living in your digestive tract — and then advise you on things like which diet you should follow and what supplements you should take to optimize your health.
But a new study in the journal Communications Biology suggests that consumers should be cautious. The research found that when identical stool samples were sent to seven companies for gut microbiome analyses, each provided very different results.
“It’s like having your blood drawn, sending it to different labs and getting different results from each lab,” said Diane Hoffmann, an author of the study and the director of the law and health care program at the University of Maryland Carey School of Law. “That would be very concerning and troubling to our whole medical system. We assume we should get the same results from each lab.”
Experts said the findings highlight an underlying problem with direct-to-consumer microbiome testing. Different companies use different collection methods, quality-control protocols and procedures to analyze their customers’ gut microbiomes. This lack of standardization means that consumers cannot be sure that they are getting reliable test results, and they have to be careful about acting on the health recommendations that companies provide, Hoffmann said.
“It’s buyer beware,” she added.
The new research is important because it demonstrates that the industry needs clear standards and validated methods so that people can receive accurate results, said Karen Corbin, a microbiome expert and associate investigator at the AdventHealth Translational Research Institute for Metabolism and Diabetes in Orlando.
She said that consumers who want these tests “should proceed with caution.”
The rise of at-home microbiome testing
The burgeoning industry of consumer microbiome tests has been fueled by a growing number of studies showing that the gut microbiome plays an intricate role in our health. Researchers have found that our gut microbes transform the foods that we eat into thousands of enzymes, hormones, vitamins and other metabolites that influence our immune systems, metabolisms and appetites.
Some studies suggest that the composition of your gut microbiome and changes to it can affect your risk of developing obesity, Type 2 diabetes, inflammatory bowel disease and other chronic diseases. Scientists have found that having certain microbes in your gut — along with a wide variety or diversity of microorganisms — is associated with better health, and that lifestyle behaviors such as diet and exercise can influence the makeup of your microbiome.
But cause and effect are murky: It’s not entirely clear whether changes in the gut microbiome are an underlying cause of some diseases or simply a consequence of them. And because the makeup of each person’s gut microbiome is both unique and fluctuates on a daily basis, researchers say that there is no clear definition of what constitutes an optimal or “healthy” gut microbiome.
Many companies nonetheless claim that they can assess your microbiome and use the results to give you personalized health recommendations. These tests, typically costing between $100 and $600, require customers to send in a stool sample, which companies analyze using a variety of methods.
Customers then receive a report detailing things such as the different types of microbes in their guts, their level of microbial diversity, and dietary and lifestyle changes that they can make to improve their gut health and address conditions like eczema, food allergies and constipation. Some testing companies also recommend and sell expensive probiotic supplements to their customers.
Same microbiome, different results
One reportin 2024 identified more than 30 companies that offered microbiome-testing services.
Hoffmann and her co-authors wanted to study and compare some of these services. So they selected seven companies, ordered their testing kits and sent them identical stool samples from an individual donor. For each company, the researchers ordered three testing kits and sent in three identical stool samples under different names at different times.
When the reports came back, the researchers discovered striking differences between each company’s results. The companies reported a varying abundance of major species of gut bacteria that play important roles in a person’s health. One example that stood out was C. difficile, a potentially serious pathogen that can cause severe diarrhea and inflammation of the colon (colitis). Three of the companies reported that it was present, while four reported that it was not.
The researchers also found that one company reported the donor as having a “healthy” gut microbiome on two occasions and an “unhealthy” gut microbiome on a third occasion — even though all three samples it tested were identical.
The lack of consistent results between companies is not entirely surprising because each company uses different procedures, said Scott A. Jackson, a co-author of the study and founder of the Nest, a biotechnology consulting firm.
The different companies ask customers to collect stool samples in different ways and with different tools, such as brushes, swabs or pads. The samples are then sent through the mail, exposing them to ambient temperatures that can affect bacterial concentrations. There are also dozens of methods that companies can use to extract and sequence DNA from the microbes, which can lead to very different outcomes, Jackson said.
Focus on fiber and whole foods
Corbin said that people who want to have their microbiomes analyzed should talk to their doctor or health care provider, especially if they plan on following any health recommendations made by a testing company.
“Curiosity about personal health is a positive thing,” she added. “But if someone decides to pursue testing, I recommend that they avoid making any changes that are outside of what their health care team might recommend.”
She said that there are some simple steps you can follow to feed your gut microbes in a way that will benefit your health — no testing required. You should eat more fiber and resistant starch, which you can find in plant foods such as fresh fruits, vegetables, whole grains, beans, peas and lentils. These foods nourish the microbes in your gut, which in turn produce short-chain fatty acids and other beneficial compounds that promote good health.
You should also avoid ultra-processed foods and focus on eating minimally processed whole foods. Ultra-processed foods such as white bread, bagels, sweetened breakfast cereals, soft drinks and sugary, salty packaged foods — which typically contain very little fiber and resistant starch — are quickly broken down and absorbed in your small intestine. Their less-processed counterparts contain those important nutrients that go undigested until reaching the large intestine, where the majority of gut microbes live and can metabolize and ferment them.
“The gut microbiome is connected to far more than digestion,” Corbin said. “It plays a role in immune function, metabolism, inflammation and even communicates with the brain. When we support gut health through simple, sustainable habits, we’re influencing interconnected systems throughout the body, which is why we see it as part of whole-person health.”
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