The global incidence of numerous immune-mediated, metabolic, neurodegenerative, and psychiatric diseases is steadily increasing [1,2,3]. The increased morbidity of human populations makes them more vulnerable to additional burdens, including infectious diseases. For example, the mortality rate of diabetics infected with the original variant of the SARS Co-2 virus was about twice that of the general population [4,5]. It is becoming increasingly clear that the gut microbiota plays an important role in the development of many, if not all, of these diseases [2,6,7]. Many of these diseases, including COVID-19 infection [8], are associated with alterations in gut microbiota composition and function, i.e., dysbiosis [9,10]. The most typical features of dysbiosis are a decrease in the diversity of the microbiota, a loss of beneficial microbiota, or an overgrowth of harmful microbiota. The term “gut microbiota” includes all microorganisms, i.e., not only bacteria, but also fungi, protists, archaea, and viruses that live in the gastrointestinal tract. The focus of this Special Issue was on all possible triggers of gut microbiota dysbiosis [11] and exploring ways to restore the gut microbiota, such as dietary interventions [12,13,14], probiotics, and FMT, to identify disease-associated microbiota signatures, elucidate pathogenetic mechanisms [15], find new diagnostic and prognostic markers, and develop novel and promising microbiota-based treatments. CLICK TO REVIEW