Why Your Stool Test Doesn't Match Your Symptoms: The Mechanistic Limits of GI-MAP, BiomeFx, and Comprehensive Stool Analysis — Part 3: How to Actually Read a Stool Test

A stool test in front of you is not useless. It is a low-resolution probe of a complex system, and read carefully, it can contribute genuine information to a case analysis. Read carelessly, it generates expensive, wrong-layered treatment that consumes years. Here is how to read it. What the Test Can Legitimately Tell You Pathogen detection. If a stool test reports H. pylori, C. difficile, a parasite, a known enteric pathogen at meaningful abundance, this is information you can act on. The PCR sensitivity for specific pathogens is reasonable, and a clinically detected pathogen is a clinical pathogen regardless of methodological caveats. This is the highest-confidence signal on most stool tests. Extreme compositional findings. When a single organism dominates the composition far outside expected ranges — a stool that is forty percent Klebsiella, or one that shows the near-absence of any diversity, or one showing a clear sulfide-shifted signature — the test is reporting a community state extreme enough that the methodological caveats matter less. Even with all the biases, an extreme finding is probably an extreme finding. Functional biomarker direction across multiple panels. A single calprotectin reading is noisy. A calprotectin reading that has been consistently elevated across three panels over a year is signal. The same is true for sIgA, elastase, occult blood, and the inflamm