Background/objectivesResearch on irritable bowel syndrome (IBS) and the gut microbiome has expanded rapidly. However, the structural evolution of this literature has not been systematically characterized across major indexing platforms.MethodsWe performed a parallel bibliometric analysis of the Web of Science Core Collection (WoSCC, n = 1,502), Scopus (n = 1,163), and PubMed (n = 975). The analysis included English-language articles and reviews published from January 2000 to December 2025. WoSCC served as the primary dataset, and Scopus and PubMed were analyzed in parallel for cross-database comparison. Bibliometric mapping and visualization were performed using VOSviewer, CiteSpace, and bibliometrix.ResultsAnnual output increased from fewer than 10 articles per year before 2010 to 162 in 2025. This acceleration became marked after 2014 and was reproduced across all three databases. The United States and China led publication volume, whereas the UK output was concentrated in a small number of flagship centers. Our analysis suggests three developmental phases: compositional profiling and culture-dependent benchmarks (2000–2012), community-level characterization and interventional consolidation (2012–2017), and neuroendocrine and short-chain fatty acid mechanisms (2017–2025). Visceral hyperalgesia and hypothalamic–pituitary–adrenal axis dysregulation showed the strongest currently active keyword bursts. Diet-related and precision-oriented approaches also gained visibility.ConclusionIBS–gut microbiome research has shifted from descriptive profiling toward mechanistic, diet-related, and precision-medicine themes. These findings provide a structured overview of the field and help clarify priorities for its next phase.