Characterization of microbial diversity and eosinophilic otitis media biomarkers using next-generation sequencing

Eosinophilic otitis media (EOM) is a chronic eosinophilic inflammatory disease linked to bronchial asthma and nasal polyps. EOM is often accompanied by tympanic membrane perforation. Although the primary treatment, steroid therapy, is generally effective, its efficacy may be limited in advanced cases, particularly those involving significant thickening of the middle ear mucosa. Despite its clinical importance, details regarding the pathogenesis of EOM have not been elucidated. Our study aimed to characterize the microbiome associated with EOM and explore changes with and without tympanic membrane perforation.

We enrolled 27 patients clinically diagnosed with EOM, 25 controls without middle ear infections, and 10 patients with chronic suppurative otitis media (CSOM) [1] [2]. Specimens were collected by swabbing the middle ear, nasopharynx, and external auditory canal (EAC) of subjects in the EOM and control groups, whereas CSOM specimens were collected only from the middle ear. The V3-V4 regions of the 16S ribosomal RNA genes were amplified and subjected to high-throughput sequencing. We evaluated alpha and beta diversity indices between the EOM and control subjects, followed by Linear discriminant analysis Effect Size (LEfSe) analysis to identify potential biomarkers. Additionally, co-occurrence patterns were analyzed to explore the associated microbial interactions. To assess whether similar biomarkers were identified between the EOM and CSOM subjects, LEfSe analysis was conducted for these two groups.

Compared with controls, EOM patients were significantly enriched in Nocardioides in the middle ear, nasopharynx, and EAC, highlighting a distinct microbiological feature. Both alpha and beta diversity were significantly reduced in EOM patients with tympanic membrane perforation. When comparing the EOM and CSOM groups, Nocardioides was consistently identified as a significant biomarker for EOM, confirming its distinct association with EOM. In co-occurrence analysis, Nocardioides showed notable positive co-occurrence with several other genera.

This study reports the first detailed exploration of the EOM microbiome and identified Nocardioides as a new biomarker. The significant shift in microbial co-occurrence associated with tympanic membrane perforation may contribute to the disease's refractory nature, suggesting new avenues for understanding and managing EOM.