Metagenomics and Community Profiling: Culture-Independent Techniques in the Clinical Laboratory

Clinical diagnostics for microbial pathogens often rely on culture or performing targeted molecular assays for identification. High-throughput culture-independent techniques offer a method to characterize individual isolates, as well as total microbial communities, without the need for cultivation or a priori knowledge of the organisms that may be present. Community profiling exploits universal marker genes present in bacteria, archaea, and fungi to explore diversity. Using bulk DNA/RNA sequencing, metagenomics can be applied to microbial populations. Here, we review these methods and their use to describe microbial and viral communities associated with the human body, with a special focus on clinical applications.