Bacterial species identification

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See [http://www.ccg.unam.mx/~vinuesa/Using_the_GreenGenes_and_RDPII_servers.html here] for 16S rRNA alignment assistance.
See [http://www.ccg.unam.mx/~vinuesa/Using_the_GreenGenes_and_RDPII_servers.html here] for 16S rRNA alignment assistance.
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For 16S rDNA species specific probes, see [http://www.microbial-ecology.de/probebase/ ProbeBase]
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A comprehensive database of 16s and 23s ribosomal sequences can be found here: [http://www.arb-silva.de/ Silva]
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==References==
==References==
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#Lane85  pmid=2413450
#Lane85  pmid=2413450
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#Lane91 Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. in Nucleic Acid Techniques in Bacterial Systematics, eds Stackebrandt
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#Lane91 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.
E, Goodfellow M (Wiley, New York), pp 115–175.
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</biblio>
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#Leser02 pmid=11823207
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==Mycoplasma universal primers==
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#Alm96 pmid=8837410
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Johansson K-E, Characterization of mycoplasmas by PCR and sequence analysis with universal 16S rDNA primers, Chapter 18, Mycoplasma Protocols, 1998.
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</biblio>
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* 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
 
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* U6F  1154-1172  gag gaa ggy grg gay gay g
 
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* U7R  1359-1374  aca agr ccc gag aac g
 
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* U8R  1502-1524  gaa agg agg trw tcc ayc csc ac
 
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==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.
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.
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* 1492r 5'TACGGYTACCTTGTTACGACTT
* 1492r 5'TACGGYTACCTTGTTACGACTT
* 1525r 5'AAGGAGGTGWTCCARCC
* 1525r 5'AAGGAGGTGWTCCARCC
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 +
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==Universal primers from Leser02==
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* Edited from Lane91, naming from Alm96, PMID 8837410
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* S-*-Univ-1492-a-A-19 GGTTACCTTGTTACGACTT-3
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* S-D-Bact-0008-a-S-20 AGAGTTTGATCMTGGCTCAG-3
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* S-D-Bact-0907-a-S-20 AAACTCAAAGGAATTGACGG-3
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* S-*-Univ-0519-a-A-18 GTATTACCGCGGCTGCTG-3
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* S-D-Bact-0786-a-A-20 GACTACCAGGGTATCTAATC-3
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* S-D-Bact-1054-a-A-20 ACGAGCTGACGACAGCCATG-3
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 +
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==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

Current revision

See here for 16S rRNA alignment assistance.

For 16S rDNA species specific probes, see ProbeBase

A comprehensive database of 16s and 23s ribosomal sequences can be found here: Silva


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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