Microbiome Analysis of Cholesteatoma by Gene Sequencing

Objective: To compare the microbial flora of cholesteatoma and normal middle ears using gene-based sequencing analysis. Study Design: Controlled ex vivo human study. Setting: Academic, tertiary medical center. Subjects and Methods: Brush, swab, and tissue samples were each taken from cholesteatoma matrix and uninvolved tissue in patients with previously untreated, acquired cholesteatoma (n=19) or middle ear mucosa from patients undergoing cochlear implantation with no history of cholesteatoma or previous middle ear surgery (control; n=12). DNA was isolated from specimens then 16S rRNA gene sequencing was performed. Results: There was no difference in microbial yield between the sampling methods. Cholesteatoma specimens had lower relative abundance of 14 bacterial species compared with controls including Acidovorax sp., Bacillus sp., Masillia sp., Moraxella osloensis, Phenylobacterium conjunctum, Sphingomonas sp., and Staphylococcus epidermidis (all p <0.05). Alternaria sp. were present on nearly all the specimens. Alternaria sp. and Cladosporium herbarum (both p <= 0.05) were lower in the cholesteatoma compared with control group. There was no difference in the relative abundance of any bacteria or fungi between the cholesteatoma matrix and uninvolved middle ear mucosa. Conclusions: Microbiome of cholesteatoma matrix is largely similar to adjacent mucosa. This differs from healthy ears. Further study is needed to understand if middle ear microbiome may impact cholesteatoma pathogenesis or treatment.