Many animals rely on long-term symbiotic relationships with bacterial communities that are essential for normal physiology, however, traditional methods such as CFU plating have high limits of detection and fail to accurately quantify strain-level abundance. This project addresses these limitations by leveraging qPCR as an alternative quantitative. Here, we demonstrate that qPCR provides a more sensitive approach to determining bacterial abundance in vivo; providing a valuable tool for studying microbiome dynamics.