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The role of gut microbiota in influencing the efficacy and side effect profile of biological therapies for autoimmune diseases has gained increasing attention. Understanding these interactions is crucial for optimizing treatment outcomes and minimizing adverse events associated with biological therapies. This systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We comprehensively analyzed studies involving human subjects with autoimmune diseases treated with biological therapies. Data on gut microbiota composition, therapeutic efficacy, and side effect profiles were extracted and synthesized to assess the impact of microbiota on treatment outcomes. Our review identified a significant relationship between gut microbiota composition and the efficacy of biological therapies. Specific bacterial taxa, such as Clostridiales and Roseburia inulinivorans , were associated with improved therapeutic responses, while alterations in microbiota were linked to increased adverse events. The predictive potential was demonstrated with microbiota signatures correlating with treatment success and side effects, highlighting the relevance of microbial profiles in therapeutic outcomes. The findings suggest that gut microbiota plays a pivotal role in modulating the efficacy and side effect profile of biological therapies for autoimmune diseases. Integrating microbiota assessments into clinical practice could enhance personalized treatment strategies and improve patient outcomes., Competing Interests: Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Qusty et al.)