Absence of a Consistent Gut or Oral Microbial Signature in Fibromyalgia Under Strictly Controlled Clinical Conditions: A Multi-Compartment 16S rRNA Analysis.

BACKGROUND

Fibromyalgia (FM) has been increasingly studied in the context of gut-brain-immune interactions, and several reports have suggested an association between FM and alterations in gut or oral microbial communities. However, prior studies have often suffered from heterogeneous comorbidities, inconsistent sampling procedures, and limited control for environmental factors, making it unclear whether FM is associated with a reproducible, site-independent microbial signature.

OBJECTIVES

To determine whether women with FM exhibit consistent alterations in gut or oral microbiota when evaluated under strictly standardized physiological, clinical, and environmental conditions.

STUDY

DESIGN

A prospective, observational, case-control study.

SETTING

The Department of Pain Medicine and Department of Medical Microbiology at Gazi University, Türkiye.

METHODS

The patient selection comprised 31 women (16 with FM; 15 healthy controls) who met rigorous inclusion and exclusion criteria, minimizing confounding from diet, metabolic disease, medications, hormonal status, and recent infections. No therapeutic intervention was performed; all patients provided paired oral mucosal and fecal samples during the follicular phase of the menstrual cycle. Sequencing of 16S rRNA V3-V4was performed on DNA extracted from all samples. Alpha and beta diversity metrics, taxonomic profiles, and differential abundance analyses (including LEfSe with FDR correction) were compared between groups. The clinical severity of FM was assessed using scores on the visual analog scale (VAS), Widespread Pain Index (WPI), and Symptom Severity Scale (SSS).

RESULTS

No statistically significant differences were observed between FM patients and controls in fecal or oral alpha diversity (Shannon, Simpson, Chao1, Observed OTU indices, all P > 0.05). Beta diversity analyses (Bray-Curtis PERMANOVA) revealed no between-group separation in either compartment (fecal R² = 0.032, P = 0.529; oral R² = 0.032, P = 0.464). Both groups displayed preserved core microbial communities in the gut, dominated by Firmicutes and Bacteroidota and, in the oral cavity, Streptococcus-enriched profiles. Minor genus-level variations were detected, but none remained significant after FDR correction. Cross-site analyses confirmed the expected ecological divergence between oral and fecal habitats but identified no FM-specific microbial pattern. Post hoc sensitivity analysis indicated that the study was powered to detect only moderate effect sizes (R² ≥ 0.11), suggesting that subtle differences might have remained undetected.

LIMITATIONS: A modest sample size, a lack of quantitative dietary assessment, and reliance on 16S rRNA sequencing limited the detection of subtle or functional microbial alterations. Additionally, the cross-sectional design precludes causal inference.

CONCLUSIONS

Under highly controlled sampling and exclusion conditions, FM was not associated with detectable alterations in the diversity or composition of gut or oral microbes. These findings suggest that previously reported dysbiosis may reflect comorbidity-driven or phenotype-specific variation rather than a universal microbial hallmark. Larger, multi-omic and phenotype-stratified studies are needed to clarify functional host-microbiome interactions in FM.