Pengrui Feng, Xiao Fu, Chaoyi Zhang, Dong Wang, Zan Chen, Guanglin Wang
Background The gut microbiota is recognized as essential for maintaining immune homeostasis, and dysbiosis of the gut microbiota has been increasingly associated with the pathogenesis of various autoimmune diseases. Emerging evidence suggests that alterations in gut microbial composition may contribute to dysregulation of the immune system, thereby promoting inflammatory responses and autoimmunity. Despite growing interest in this field, a comprehensive bibliometric analysis integrating global research trends, influential publications, and key contributors, as well as clinical translation perspectives, remains lacking. This study aims to systematically evaluate the research landscape on the relationship between the gut microbiota and autoimmune diseases, thereby providing insights into research development, emerging hotspots, and future directions. Methods Global publications on gut microbiota and autoimmune diseases were systematically retrieved and extracted from the Web of Science Core Collection (WOSCC) database, covering the period from January 2000 to February 2025. The literature search and data extraction were conducted in February 2025, which was predefined as the cutoff date for data collection, thereby ensuring dataset reproducibility. Publications from 2025 were treated as partial-year data due to incomplete annual coverage and were excluded from longitudinal trend analyses to minimize temporal bias. In addition, a separate search of the PubMed database was conducted to identify clinical trials in this field. Bibliometric analyses and visualization were performed using VOSviewer, CiteSpace, and R version 4.4.0. Results A total of 3,004 publications were retrieved from the Web of Science Core Collection and 85 clinical trials from PubMed, covering the period from 2000 to 2025. The overall number of publications has steadily increased over time. Citation analysis indicates that the United States and China are the leading countries in terms of publication output and citation frequency. Harvard Medical School was identified as the most productive institution, while New York University received the highest citation counts. Ochoa-Reparaz, J was the most prolific author, whereas citation frequency was highest for Atarashi, K, followed by Ochoa-Reparaz, J. Frontiers in Immunology published the highest number of articles in this field. Keyword and literature analyses identified mechanistic links between gut dysbiosis and autoimmune diseases, clinical relevance, and causal inference as major research themes. Integration of clinical trial evidence revealed that these basic research themes have progressively translated into disease-specific investigations, particularly in type 1 diabetes mellitus, multiple sclerosis, and rheumatoid arthritis. Probiotic supplementation, dietary modulation, and fecal microbiota transplantation represented emerging microbiota-targeted strategies, highlighting the transition of this field from mechanistic exploration toward clinical intervention. Conclusion While previous bibliometric studies have primarily relied on a single database, the present study integrates bibliometric data from the Web of Science Core Collection with supplementary clinical trial data retrieved from PubMed. This study provides valuable reference for identifying research foci and highlighting future research directions.