How to use (or not use) stool DNA tests

Why I use stool DNA tests with caution, if at all, in my practice

If you've ever sent a stool sample to one of those mail-in microbiome companies to learn about your gut health, here's something important you should know: the results depend heavily on which company you used — not just what's actually living in your gut.
A new study put this to the test in a pretty clever way.

​What researchers didScientists at a top government lab (NIST) took stool from a single healthy person and carefully divided it into identical samples. They then sent the exact same material to seven different consumer microbiome testing companies — the kind that promise to tell you about your gut bacteria and what it means for your health.
The idea was simple: if these tests are reliable, the same sample should produce roughly the same results everywhere.

What they foundIt didn't.
The companies came back with wildly different answers — different bacteria detected, different amounts reported, and different "health scores." In fact, the differences between companies were about as large as the differences you'd expect between two completely different people.
A few companies at least got consistent results when testing the same sample multiple times. Others couldn't even agree with themselves.
Perhaps most concerning: the same sample sometimes landed in different health risk categories depending on who analyzed it. "Normal" with one company could mean "at risk" with another — using the exact same stool.

Why does this happen?Each company uses its own process from start to finish — how they handle the sample, how they extract DNA, how they sequence it, and especially how their software interprets the data. There are no universal standards, and the "healthy" vs. "unhealthy" cutoffs companies use are largely made up in-house, with little scientific backing.

What this means for you

• Don't treat these results like a medical test. They are not held to the same standards as clinical diagnostics.
• Don't compare results across companies. Switching services and noticing a change likely reflects the companies' differences, not changes in your gut.
• Be skeptical of health scores and risk labels. The thresholds behind them are not standardized or clinically proven.
• Use them as a curiosity, not a guide. If something in a report concerns you, talk to your doctor and rely on conventional testing and clinical judgment.

The bottom lineConsumer microbiome testing is a fascinating window into an emerging science — but the technology isn't ready to reliably guide health decisions. Researchers are calling for standardized testing practices, more transparency from companies, and proper regulation before these tests should be used clinically.
This puts functional medicine physicians in a quandary because the article doesn't say which companies were at least consistent with themselves. If a company can reliably come up with the same answer, it might be believable that they can tell us when a person's stool is changing over time. Many clinicans may argue that "they know" because they have seen it in their practice. BUT don't get me started on the research showing how biased clinician's impressions typically are.

For now, I absolutely would use these tests with enormous caution.