Characterization of the Middle Ear Microbiome in Meniere's Disease by 16S rRNA Gene Sequencing Compared to Chronic Suppurative Otitis Media

ABSTRACT Objective To investigate the middle ear microbiome in Meniere's disease (MD) patients. Methods Middle ear smears from 10 MD patients (ME group) and 10 chronic suppurative otitis patients (OE group) were collected during surgery and processed via 16S rRNA gene sequencing. Results The ME group demonstrated significant differences in alpha diversity (Shannon/Simpson index, p < 0.01) and beta diversity (ANOSIM/PERMANOVA, the Bray‐Curtis distance matrix, R = 0.144, p < 0.05; R 2 = 0.107, p < 0.05) compared to OE group, and the PERMDISP showed lower heterogeneity in the ME group ( p < 0.01). Ruminococcus, Ochrobactrum , and Halomonas at the genus level were enriched in the ME group, and the difference reached marginal significance. The linear discriminant analysis effect size analysis (LefSe) identified Bacteroides, Halomonas , and Prevotella as significantly enriched in ME, while Neisseriales was downregulated (|LDA| > 2, p < 0.05). BugBase phenotype analysis revealed that facultatively anaerobic bacteria and bacteria containing mobile genetic elements were significantly reduced in the ME group compared to the OE group ( p < 0.05). The proportion of anaerobes was higher in the ME group ( p = 0.123). Nine KEGG metabolic pathways were enriched in the ME group, though the difference was not significant after correction. Conclusion These findings suggested that inner ear inflammation resulted from middle ear dysbiosis may contribute to MD pathogenesis, offering novel perspectives for MD etiology and therapies.