Gut microbiome testing isn’t currently recommended for routine clinical care by major gastroenterology societies (AGA, NIH, NHS, IDSA).

The 2025 International Consensus Statement (69 experts, The Lancet Gastroenterology & Hepatology) found there isn’t enough evidence yet to recommend routine use, and these tests don’t have proven value in clinical practice right now.

They identify bacteria only at the genus level (so they tell you “who’s there” but not “what they do”), there are no reference values to figure out what’s normal versus abnormal, there aren’t any evidence-based treatments you can do with the results, and different companies can give you different results from the same stool sample.

The bottom line: for now, testing remains mainly a research tool, and results can’t diagnose disease or guide treatment. If you’ve been tested through a naturopath, sharing results with your gastroenterologist is helpful for context, though there aren’t evidence-based interventions yet. That said, the gut microbiome is clearly important in health and disease—the science just needs to move from describing what’s there to understanding what it actually does before these tests become clinically useful.