title: Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque.
abstract: OBJECTIVE
  Denaturing gradient gel electrophoresis (DGGE) was applied to the microbiologic examination of subgingival plaque.
  
  
  METHODS
  The PCR primers were designed from conserved nucleotide sequences on 16S ribosomal RNA gene (16SrDNA) with GC rich clamp at the 5'-end. Polymerase chain reaction (PCR) was performed using the primers and genomic DNAs of typical periodontal bacteria. The generated 16SrDNA fragments were separated by denaturing gel.
  
  
  RESULTS
  Although the sizes of the amplified DNA fragments were almost the same among the species, 16SrDNAs of the periodontal bacteria were distinguished according to their specific sequences. The microflora of clinical plaque samples were profiled by the PCR-DGGE method, and the dominant 16SrDNA bands were cloned and sequenced. Simultaneously, Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Prevotella intermedia were detected by an ordinary PCR method. In the deep periodontal pockets, the bacterial community structures were complicated and P. gingivalis was the most dominant species, whereas the DGGE profiles were simple and Streptococcus or Neisseria species were dominant in the shallow pockets. The species-specific PCR method revealed the presence of A. actinomycetemcomitans, P. gingivalis and P. intermedia in the clinical samples. However, corresponding bands were not always observed in the DGGE profiles, indicating a lower sensitivity of the DGGE method.
  
  
  CONCLUSIONS
  Although the DGGE method may have a lower sensitivity than the ordinary PCR methods, it could visualize the bacterial qualitative compositions and reveal the major species of the plaque. The DGGE analysis and following sequencing may have the potential to be a promising bacterial examination procedure in periodontal diseases.
authors.affiliation: Department of Patho-Physiology, Division of Periodontal Science, Okayama University Graduate School of Medicine and Dentistry, Okayama, Japan.
authors.forename: C
authors.initials: C
authors.lastname: Fujimoto
authors.forename: H
authors.initials: H
authors.lastname: Maeda
authors.forename: S
authors.initials: S
authors.lastname: Kokeguchi
authors.forename: S
authors.initials: S
authors.lastname: Takashiba
authors.forename: F
authors.initials: F
authors.lastname: Nishimura
authors.forename: H
authors.initials: H
authors.lastname: Arai
authors.forename: K
authors.initials: K
authors.lastname: Fukui
authors.forename: Y
authors.initials: Y
authors.lastname: Murayama
mesh_terms: D024506:5' Flanking Region / Q000235:genetics; D000293:Adolescent; D000368:Aged; D016976:Aggregatibacter actinomycetemcomitans / Q000145:classification; D010520:Aggressive Periodontitis / Q000382:microbiology; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D003773:Dental Plaque / Q000382:microbiology*; D004591:Electrophoresis, Polyacrylamide Gel; D005260:Female; D020862:GC Rich Sequence / Q000235:genetics; D016680:Genome, Bacterial; D006801:Humans; D008297:Male; D008875:Middle Aged; D009343:Neisseria / Q000145:classification; D010514:Periodontal Pocket / Q000382:microbiology; D016133:Polymerase Chain Reaction; D016966:Porphyromonas gingivalis / Q000145:classification; D018713:Prevotella intermedia / Q000145:classification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013291:Streptococcus / Q000145:classification
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S