Background: The gut microbiota is emerging as a pivotal player in the pathogenesis of many non-communicable diseases. Thus, it has been proposed as a new diagnostic and therapeutic target. Aim and scope: This Special Issue will focus on the microbiome as a potential target of new personalized therapies or diagnostic tools. History: In recent decades, the gut microbiome has been deeply investigated, and many studies have provided new information on the role of dysbiosis in many gastrointestinal and extra-gastrointestinal diseases. Recently, in addition to its phylogenetic characterization, new information has become available regarding the function of the gut microbiota, thanks to proteomic and metabolomic analyses. Cutting-edge