Bacterial species identification

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See here for 16S rRNA alignment assistance.

For 16S rDNA species specific probes, see ProbeBase


Contents

References

  1. Weisburg WG, Barns SM, Pelletier DA, and Lane DJ. . pmid:1987160. PubMed HubMed [Weisburg91]
  2. Wilson KH, Blitchington RB, and Greene RC. . pmid:2095137. PubMed HubMed [Wilson90]
  3. Rivas R, Velázquez E, Zurdo-Piñeiro JL, Mateos PF, and Martínez Molina E. . pmid:14967233. PubMed HubMed [Rivas04]
  4. Baker GC, Smith JJ, and Cowan DA. . pmid:14607398. PubMed HubMed [Baker03]
  5. Watanabe K, Kodama Y, and Harayama S. . pmid:11240048. PubMed HubMed [Watanabe01]
  6. Böttger EC. . pmid:2482222. PubMed HubMed [Bottger89]
  7. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, and Pace NR. . pmid:2413450. PubMed HubMed [Lane85]
  8. Lane DJ (1991) 16S/23S rRNA sequencing. in Nucleic Acid Techniques in Bacterial Systematics, eds Stackebrandt E, Goodfellow M (Wiley, New York), pp 115–175.

    [Lane91]

  9. Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, and Møller K. . pmid:11823207. PubMed HubMed [Leser02]
  10. Alm EW, Oerther DB, Larsen N, Stahl DA, and Raskin L. . pmid:8837410. PubMed HubMed [Alm96]
All Medline abstracts: PubMed HubMed

Universal Bacterial Primers

Lane, D. J. (1991). 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. E. Stackebrandt and M. Goodfellow, eds. New York, NY, John Wiley and Sons: 115-175.

  • 27f 5'AGAGTTTGATCMTGGCTCAG
  • 342r 5'CTGCTGCSYCCCGTAG
  • 357f 5'CTCCTACGGGAGGCAGCAG
  • 519r 5'GWATTACCGCGGCKGCTG
  • 530f 5'GTGCCAGCMGCCGCGG
  • 1100r 5'GGGTTGCGCTCGTTG
  • 1114f 5'GCAACGAGCGCAACCC
  • 1392r 5'ACGGGCGGTGTGTRC
  • 1406f 5'TGYACACACCTCCCGT
  • 1492r 5'TACGGYTACCTTGTTACGACTT
  • 1525r 5'AAGGAGGTGWTCCARCC

Universal primers from Leser02

  • S-*-Univ-1492-a-A-19 GGTTACCTTGTTACGACTT-3
  • S-D-Bact-0008-a-S-20 AGAGTTTGATCMTGGCTCAG-3
  • S-D-Bact-0907-a-S-20 AAACTCAAAGGAATTGACGG-3
  • S-*-Univ-0519-a-A-18 GTATTACCGCGGCTGCTG-3
  • S-D-Bact-0786-a-A-20 GACTACCAGGGTATCTAATC-3
  • S-D-Bact-1054-a-A-20 ACGAGCTGACGACAGCCATG-3

Mycoplasma universal primers

Johansson K-E, Characterization of mycoplasmas by PCR and sequence analysis with universal 16S rDNA primers, Chapter 18, Mycoplasma Protocols, 1998.

  • U1F 12-27 ttg atc ctg gct cag gay daa cg
  • U2F 327-348 cca rac tcc tac ggr agg c
  • U3R 512-527 att acc gcg gck gct g
  • U4F 792-810 gta gtc cac gcc gta aac g
  • U5R 902-924 ctt gtg cgg gyy ccc gtc aa
  • U6F 1154-1172 gag gaa ggy grg gay gay g
  • U7R 1359-1374 aca agr ccc gag aac g
  • U8R 1502-1524 gaa agg agg trw tcc ayc csc ac
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