title: Clonality of bacterial consortia in root canals and subjacent gingival crevices.
abstract: OBJECTIVE
  No oral niche can be considered to be segregated from the subjacent milieu because of the complex community behavior and nature of the oral biofilms. The aim of this study was to address the paucity of information on how these species are clonally related to the subjacent gingival crevice bacteria.
  
  
  METHODS
  We utilized a metagenomic approach of amplifying 16S rDNA from genomic DNA, cloning, sequencing and analysis using LIBSHUFF software to assess the genetic homogeneity of the bacterial species from two infected root canals and subjacent gingival crevices.
  
  
  RESULTS
  The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. Further, 42% of the clones were of hitherto unknown phylotypes indicating the extent of bacterial diversity, especially in infected root canals and subjacent gingival crevices.
  
  
  CONCLUSIONS
  We believe data generated through this novel analytical tool shed new light on understanding oral microbial ecosystems.
authors.affiliation: Department of Oral Bio-Sciences, Faculty of Dentistry and Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.
authors.forename: Nipuna B
authors.initials: NB
authors.lastname: Parahitiyawa
authors.forename: Frederick C S
authors.initials: FC
authors.lastname: Chu
authors.forename: Wai K
authors.initials: WK
authors.lastname: Leung
authors.forename: Wing C
authors.initials: WC
authors.lastname: Yam
authors.forename: Li Jian
authors.initials: LJ
authors.lastname: Jin
authors.forename: Lakshman P
authors.initials: LP
authors.lastname: Samaranayake
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D044822:Biodiversity; D004269:DNA, Bacterial / Q000032:analysis; D003773:Dental Plaque / Q000382:microbiology*; D003786:Dental Pulp Cavity / Q000382:microbiology*; D003789:Dental Pulp Exposure / Q000382:microbiology; D064349:Genome, Microbial / Q000235:genetics; D005881:Gingiva / Q000382:microbiology*; D006801:Humans; D007180:Incisor / Q000293:injuries; D008297:Male; D054892:Metagenome / Q000235:genetics; D059013:Microbial Consortia / Q000502:physiology*; D010483:Periapical Diseases / Q000382:microbiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014082:Tooth Fractures / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: clonality; diversity; gingival crevice; root-canal bacteria; sequencing