Examining the evidence for an adult healthy middle ear Microbiome

Jake Jervis-Bardy, Lex E.X. Leong, Lito E. Papanicolas, Kerry L. Ivey, Sharad Chawla, Charmaine M. Woods, Claire Frauenfelder, Eng H. Ooi, Geraint B. Rogers

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Otitis media (OM) is a cluster of diseases of the middle ear that commonly result from bacterial infection. OM subtypes in which the tympanic membrane is intact (acute otitis media and otitis media with effusion) are presumed to result from pathogen translocation through the eustachian tube. Recent molecularbased studies have suggested that a diverse middle ear microbiome exists in the absence of disease. These have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. Middle ear (ME), nasopharynx (NP), and external ear canal (EC) swabs were collected from a total of 25 adult patients undergoing cochlear implant, stapedotomy, or translabyrinthine vestibular schwannoma resection. Diagnostic culture, microscopy, quantitative PCR, and 16S rRNA gene amplicon sequencing were used to assess sample bacterial content. EC and NP microbiota were consistent with previous reports. In contrast, bacterial levels in ME samples were not significantly above those in unused control swabs. Commonly detected taxa were among recognized sequencing contaminants (Methylobacterium, Pseudomonas, and Acinetobacter). Linear regression of dominant ME taxa confirmed a negative relationship between relative abundance and bacterial load, consistent with contamination. No bacteria were detected by microscopy or diagnostic culture in any middle ear sample. Our findings cast substantial doubt on previous reports identifying a healthy middle ear microbiome using 16S amplicon sequencing.

Original languageEnglish
Article numbere00456-19
Issue number5
Publication statusPublished or Issued - 1 Sep 2019


  • Microbiome
  • Middle ear
  • Otitis media

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

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