Microorganisms exhibit immense diversity, occupying countless ecological niches throughout evolution. These microorganisms form complex microbial communities that significantly influence their environment, such as in the human gut, and host health. Identifying individual species within these communities is crucial for detecting disturbances and health-related issues. In this webinar, we will explore the application of nanoplate digital PCR (dPCR) for the accurate detection and quantification of key microbial target species. We will also discuss best practices for multiplexing multiple microbial assays within a single dPCR reaction, highlighting the advantages of this technology in advancing microbiome research.