The aim of this review was to provide a general overview to the topic of this special issue. In this study the available categories of biotics were defined (i.e., probiotics, prebiotics, postobiotics and synbiotics) as first actors of therapies that target the gut flora, with the aim to modify it in a specific direction, generally with the goal of controlling inflammatory phenomena. The points that must be considered when evaluating the results of these interventions, and, specifically, the changes in gut microbiota following the assumption of biotics were analyzed. This context typically represented the one of clinical trials aimed at inducing or maintaining remission in pediatric autoimmune inflammatory diseases, that often yield conflicting results. We finally attempted to draft possible research developments for the next years.