Microbial geography of the oral cavity

J Dent Res. 2013 Jul;92(7):616-21. doi: 10.1177/0022034513488119. Epub 2013 May 14.


We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40% to 70% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.

Keywords: dental plaque; gingival sulcus; human microbiome; massively parallel sequencing; saliva; sampling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinobacillus / classification
  • Actinomycetaceae / classification
  • Adult
  • Bacteria / classification*
  • Bicuspid / microbiology
  • Capnocytophaga / classification
  • Cuspid / microbiology
  • DNA, Bacterial / analysis
  • Dental Plaque / microbiology
  • Fusobacterium / classification
  • Gingiva / microbiology
  • Haemophilus / classification
  • Humans
  • Incisor / microbiology
  • Male
  • Molar / microbiology
  • Mouth / microbiology*
  • Mouth Mucosa / microbiology
  • Palate / microbiology
  • Polymerase Chain Reaction
  • Prevotella / classification
  • RNA, Bacterial / analysis
  • RNA, Ribosomal, 16S / analysis
  • Saliva / microbiology
  • Streptococcus / classification
  • Tongue / microbiology
  • Veillonella / classification
  • Young Adult


  • DNA, Bacterial
  • RNA, Bacterial
  • RNA, Ribosomal, 16S