Abstract
Fibromyalgia (FM) is a chronic pain syndrome characterized by widespread musculoskeletal pain, fatigue, sleep disturbances, and cognitive and gastrointestinal symptoms. It is classified as a central sensitization syndrome, involving altered pain processing in the absence of structural damage. Despite its high prevalence—affecting 2–4% of the global population, predominantly women—its pathophysiology remains poorly understood, and diagnosis is often delayed due to the lack of reliable biomarkers. Emerging evidence suggests that gut microbiota alterations may contribute to FM symptoms through immune dysregulation, neuroinflammation, and disruption of the gut-brain axis. Further studies controlling for these variables are needed to clarify the relationship. This study aimed to characterize the gut microbiota of women with FM, examine associated lifestyle and psychosocial factors, and compare them with healthy controls (HC). In this cross-sectional study, FM patients and HC underwent 16 S rRNA sequencing. Microbiota diversity were analyzed using QIIME2 and R. Thirty-seven FM patients and 46 HC participated in this study. FM patients reported greater pain (NRS-11: 5.92 vs. 1.05, p-value < 0.001), lower muscle mass (p-value: 0.021), and poorer nutrition (p-value: 0.021). They showed reduced α-diversity (Shannon index, p-value: 0.009) and distinct β-diversity (p-value < 0.001). SIBO prevalence was higher in FM (59.5% vs. 32.6%, p < 0.001), with methanogen dominance. FM patients had increased Akkermansia, Oscillospira, Methanobrevibacter, and Christensenellaceae. Network analysis revealed altered microbial interactions. Women with FM show less diverse gut microbiota and different microbial profiles. These findings suggest that the microbiota could represent a potential target for future diagnostic and therapeutic strategies, although further studies are needed to establish causal relationships. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-32101-y.