Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis(ARDRA)

  • Arturo A. Massol-Deya
  • David A. Odelson
  • Robert F. Hickey
  • James M. Tiedje


The 16S and 23S rRNA genes have been utilized for phylogenetic analysis of both prokaryotic and eukaryotic organisms (see Section 3). In addition to direct comparison of the nucleic acid sequences [9], numerous groups have used the rapid method of polymerase chain reaction (PCR) amplification of this gene [6] as well as the complete rRNA locus [3, 4, 8] for a simple method for identification of bacterial genera and species. In these latter procedures, the amplified ribosomal gene (rONA) is subjected to restriction endonuclease digestion; this has been termed ARDRA (Amplified Ribosomal DNA Restriction Analysis [8]). The resulting restriction fragment pattern is then used as a fingerprint for the identification of bacterial genomes. This method is based on the principle that the restriction sites on the RNA operon are conserved according to phylogenetic patterns.


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  1. 1.
    Brosius J, Dull TJ, Sleeter, DD, Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148: 107–127.PubMedCrossRefGoogle Scholar
  2. 2.
    Hook LA, Odelson DA, Bogardt AH, Hemmingsen BB, Labeda DP, MacDonell MT (1991) Numerical analysis of DNA restriction fragment length polymorphisms and whole- cell protein banding patterns: a means of bacterial identification at the species and subspecies level. Newsletter (USFCC) 21(3): 1–10.Google Scholar
  3. 3.
    Jayarao BM, Dore JJE, Baumbach GA, Matthews KR, Oliver SP (1991) Differentiation of Streptococcus uteris from Streptococcus parauberis by polymerase chain reaction and restriction fragments length polymorphism analysis of 16S ribosomal DNA. J Clin Microbiol 29: 2774–2778.PubMedGoogle Scholar
  4. 4.
    Jensen MA, Webster JA, Straus N. (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 59: 945–952.PubMedGoogle Scholar
  5. 5.
    Maniatis T, Fritsch EF, Sambrook J (1982) Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press.Google Scholar
  6. 6.
    Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695–700.PubMedGoogle Scholar
  7. 7.
    Ulrike E, Rogall T, Blocker H, Emde M, Bottger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA Nucl Acid Res 17: 7843–7853.Google Scholar
  8. 8.
    Vaneechoutte M, Rossau R, De Vos P, Gillis M, Janssens D, Paepe N, De Rouck A, Fiers T, Claeys G, Kersters K (1992). Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol. Lett. 93: 227–234.CrossRefGoogle Scholar
  9. 9.
    Woese, C.R. 1987. Bacterial evolution. Microbial Rev 51: 221–271.Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1995

Authors and Affiliations

  • Arturo A. Massol-Deya
    • 1
    • 2
  • David A. Odelson
    • 2
    • 3
  • Robert F. Hickey
    • 2
    • 4
  • James M. Tiedje
    • 2
  1. 1.Department of BiologyUniversity of Puerto RicoMayagüezUSA
  2. 2.NSF Center for Microbial EcologyMichigan State UniversityE. LansingUSA
  3. 3.Department of BiologyCentral Michigan UniversityMt. PleasantUSA
  4. 4.Michigan Biotechnology InstituteLansingUSA

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