The cat gut-inhabitant conjoint microbiota is a peculiar ecosystem in relationship with several bodily functions and immunity. Gut microbiota dysbiosis could participate within autoimmune disease pathogenesis, whereas its niche, whether causative or influencing role regarding systemic immunity in autoimmune diseases, remains fugitive. The purpose of the present study was to identify gut microbiota alterations and probable mechanisms that participated in the development of Pemphigus foliaceus for a better understanding of future effective therapeutical armamentarium based on gut microbiota. In the present article, the authors investigated gut microbiota alterations to those of eight cats diagnosed with Pemphigus foliaceus. Furthermore, the study thoroughly analyzed pathogenic bacteria species as triggers of autoimmunity. The diagnostic algorithm involved two distinct sides: i) on referral with the first criteria was proof of evidence for possible autoimmunity, and ii) Pemphigus foliaceus diagnosis with relevant analytes. A total of eight cats were enrolled, and gut microbiomes were detected by the use of the MIDOG All-in-One Microbial Test targeting Next-Generation DNA Sequencing. By this methodology, we analyzed the dysbiosis network for bacterial kingdoms and determined the relationship between disease activity related to Pemphigus foliaceus and gut microbiota. The data showed increasing abundances of Collinsella, Lachnospiroceae, and Escherichia coli and decreasing Desulfovibrio piger, Prevotella copri, and Helicobacter cianedi among cats with pemphigus foliaceus. For the first time in Turkey, the gut microbiota of cats with pemphigus foliaceus were detected, the results of which could be cautiously taken into consideration for novel and effective therapeutical approaches.