The Otologic Microbiome: A Study of the Bacterial Microbiota in a Pediatric Patient With Chronic Serous Otitis Media Using 16SrRNA Gene-Based Pyrosequencing

OBJECTIVE To characterize bacterial microbiota in middle ear, adenoid, and tonsil specimens using 16SrRNA gene-based pyrosequencing analysis. DESIGN Cross-sectional study of bacterial microbiota in middle ear, adenoid, and tonsil specimens from a pediatric patient with chronic serous otitis media. Middle ear, adenoid, and tonsil specimens from a pediatric patient were collected and underwent cell lysis and DNA isolation. Pyrosequencing was performed on the 454 Life Sciences GS FLX platform (Roche Diagnostics Corp, Branford, Connecticut). Pyrosequencing data were processed, quality-checked, and taxonomically classified to generate an abundance-based matrix. Ecological analyses were performed. SETTING Academic, tertiary referral center. MAIN OUTCOME MEASURES Comparative microbiome analysis. RESULTS We detected a total of 17 unique bacterial families, with 9, 9, and 12 bacterial families from the middle ear, tonsil, and adenoid specimens, respectively. Pseudomonadaceae dominated the middle ear microbiota at 82.7% relative abundance, whereas Streptococcaceae dominated the tonsil microbiota at 69.2%. Multiple bacteria, including Pseudomonadaceae, Streptococcaceae, Fusobacteriaceae, and Pasteurellaceae, dominated the adenoid microbiota. Overlap between the middle ear and the tonsil microbiota was minimal. In contrast, the adenoid microbiota encompassed bacteria detected from middle ear and tonsil. CONCLUSIONS Bacterial community analysis using pyrosequencing analysis revealed diverse, previously unknown bacterial communities in a set of pediatric middle ear, tonsil, and adenoid specimens. Our findings suggest that the adenoid may be a source site for both the middle ear and tonsil microbiota. An ecological framework is appropriate in comparative analysis of microbiota from nonsterile body sites.