Same Sample, Different Results

Interest in gut health has exploded in recent years. We now know that the trillions of bacteria living in our digestive system play an important role in digestion, immunity, and even mental health. That excitement has helped fuel a growing market of at-home gut microbiome tests that promise to analyze your stool and tell you how “healthy” your gut is.

But new research suggests those tests may not be as reliable as many people assume.

Scientists at the National Institute of Standards and Technology (NIST) recently ran an unusual experiment. They created a carefully prepared, well-mixed stool sample and sent identical portions of it to seven different at-home gut testing companies. The companies did not know they were part of a study. The results were published in Communications Biology.

When the reports came back, they did not agree.

Some companies reported hundreds of bacterial species, while others reported fewer than a hundred. Some described the sample as diverse and balanced. At least one company could not clearly decide whether the very same sample represented a healthy microbiome or not. In fact, the differences between companies were sometimes as large as the natural differences you would expect between completely different people.

That is a red flag.

Testing the gut microbiome is complicated. A lot can change between the moment a sample leaves your body and the moment it is analyzed in a lab. If a sample sits at room temperature for days during shipping, the balance of bacteria can shift. Different companies use different collection tools, different storage liquids, different DNA extraction methods, different sequencing machines, and different computer programs to interpret the data. Each step can change the final result.

There is also a deeper issue: scientists still do not fully agree on what a “healthy” microbiome looks like. There may not be one perfect mix of bacteria. Many different combinations might support good health. That makes it difficult for any company to confidently label a microbiome as good or bad.

Right now, there are no FDA-approved clinical gut microbiome diagnostic tests in the United States. Many mail-in tests are sold as “wellness” products rather than medical tools, which means they do not go through the same level of oversight as medical tests ordered by a doctor. Some companies are careful about their claims, but others suggest their results can guide diet changes or supplements that will “fix” your gut.

The NIST study does not mean gut bacteria are unimportant. The science linking the microbiome to health is real and growing fast. But it does suggest that the commercial testing industry is moving ahead of the science.

If you are considering one of these tests, it is best to think of it as informational and experimental, not as a medical diagnosis. A low “gut health score” does not necessarily mean something is wrong. A high score does not guarantee everything is right.

Yet, repeated testing within the same lab could produce useful trend data - especially in research settings with many samples and standardized methods. But for individual consumers, interpretation remains limited because we still lack clear definitions of what counts as “healthy” and what actions reliably improve outcomes.

Microbiome research is still young. As scientists develop better standards and more consistent methods, these tests may become more useful. For now, however, the safest approach is healthy skepticism.

REFERENCES

Servetas, S.L., Gierz, K.S., Hoffmann, D. et al. Evaluating the analytical performance of direct-to-consumer gut microbiome testing services. Commun Biol 9, 269 (2026). https://doi.org/10.1038/s42003-025-09301-3

Same Poop, Different Results: At-Home Gut Health Tests Are Wildly Inconsistent, Study Finds