Same Sample, Different Story: Why qPCR and Shotgun Microbiome Tests Don’t Always Match

“Same gut, different story.” It’s a phrase I’ve come to know well. Clients are often puzzled when microbes flagged as high on one test vanish from the next. But this isn’t a mistake - it’s a reflection of how different microbiome testing technologies work. qPCR panels like GI-MAP are selective and targeted. Shotgun metagenomics? Expansive and ecosystem-wide. Each test tells a different story because it’s asking a different question. Understanding these differences is essential - not just for interpreting results, but for making meaningful, clinically-relevant decisions.