Culture-independent molecular analysis of microbial constituents of the healthy human outer ear

J Clin Microbiol. 2003 Jan;41(1):295-303. doi: 10.1128/JCM.41.1.295-303.2003.


Molecular-phylogenetic sequence analyses have provided a new perspective on microbial communities by allowing the detection and identification of constituent microorganisms in the absence of cultivation. In this study we used broad-specificity amplification of ribosomal DNA (rDNA) genes to survey organisms present in the human outer ear canal. Samples were obtained from 24 individuals, including members of three extended families, in order to survey the resident microbiota and to examine microbial population structures in individuals related by familial or household associations. To examine the stability of the microbial populations, one individual was sampled four times and another twice over a 14-month period. We found that a distinct set of microbial types was present in the majority of the subjects sampled. The two most prevalent rDNA sequence types that were identified in multiple individuals corresponded closely to those of Alloiococcus otitis and Corynebacterium otitidis, commonly thought to be associated exclusively with infections of the middle ear. Our results suggest, therefore, that the outer ear canal may serve as a reservoir for normally commensal microbes that can contribute to pathogenesis upon introduction into the middle ear. Alternatively, culture analyses of diseases of the middle ear may have been confounded by these contaminating commensal organisms.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Cell Culture Techniques
  • DNA, Bacterial / analysis
  • Ear Canal / microbiology*
  • Humans
  • RNA, Ribosomal / analysis*
  • RNA, Ribosomal / genetics
  • Reverse Transcriptase Polymerase Chain Reaction


  • DNA, Bacterial
  • RNA, Ribosomal