Cholesteatoma has an altered microbiota with a higher abundance of Staphylococcus species

OBJECTIVE: To compare the microbiota between cholesteatoma and chronic suppurative otitis media (COM) and to identify potential pathogens that explain the relevant phenotypes of cholesteatoma. STUDY DESIGN: Prospective cohort study. METHODS: Surgical specimens collected from 20 cholesteatomas and nine COMs were treated to dissolve biofilms and subjected to 16S ribosomal RNA (rRNA) gene sequencing and amplicon sequence variant‐level analysis for microbiota profiling and quantitative comparison. Correlations between the relative abundance of potential pathogens and the volume of the primary resected cholesteatomas were examined. RESULTS: Differences in bacterial composition (beta diversity) were observed between cholesteatomas and COM (p = .002), with a higher abundance of Staphylococcus in cholesteatomas than in COM (p = .005). Common genera in the external auditory canal (EAC) flora, such as Staphylococcus, Corynebacterium, and Cutibacterium, were predominant in both cholesteatoma and COM; Staphylococcus aureus and Pseudomonas aeruginosa were increased in both diseases compared with the EAC flora. Furthermore, coagulase‐negative staphylococci (CoNS) were more abundant in cholesteatomas than in COM (p = 0.002). Linear discriminant analysis coupled with effect size measurements (LEfSe) identified four CoNS as potential biomarkers for cholesteatoma. The relative abundance of S. aureus, a potential pathogen, was positively correlated with cholesteatoma volume (r = .60, p = .02). CONCLUSION: The microbiota of cholesteatoma and COM originated from EAC flora, but the bacterial composition was largely altered. Our results suggested that S. aureus infection is involved in cholesteatoma progression. LEVEL OF EVIDENCE: 3b