Why Your Stool Test Doesn't Match Your Symptoms: The Mechanistic Limits of GI-MAP, BiomeFx, and Comprehensive Stool Analysis — Part 2: The Mechanistic Reasons Stool Tests Mislead in Chronic Illness

The First Problem: The Sequencing Methods Cannot See What They Are Not Looking For qPCR can only detect organisms in its primer panel. Most commercial panels include between forty and one hundred and fifty targets. The human gut harbors thousands of bacterial species, hundreds of archaeal species, an extensive fungal community, viruses including bacteriophages that dominate by number, and protozoa whose distribution is poorly characterized in non-clinical samples. If your pathology is being driven by an organism the panel does not target, the panel will not see it. This is not occasionally true. This is structurally true for every qPCR-based stool test, and it is invisible to the patient and frequently invisible to the practitioner reading the report. A clean GI-MAP report does not mean a clean gut. It means a gut with low abundance of the specific organisms in the GI-MAP primer panel. 16S sequencing avoids the primer-panel problem but introduces a different bias. 16S copy number per genome varies several-fold across bacterial species. Two organisms present in equal cell counts can appear at very different abundances on a 16S report because one species has six copies of the 16S gene per cell and another has one. Primer choice within the 16S variable region also matters: V3–V4 primers (the most common commercial choice) systematically under-represent some taxa and over-represent