Difference between revisions of "Bacterial species identification"

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PMID 1987160
+
See [http://www.ccg.unam.mx/~vinuesa/Using_the_GreenGenes_and_RDPII_servers.html here] for 16S rRNA alignment assistance.
  
PMID 2095137
+
For 16S rDNA species specific probes, see [http://www.microbial-ecology.de/probebase/ ProbeBase]
  
PMID 14967233
+
A comprehensive database of 16s and 23s ribosomal sequences can be found here: [http://www.arb-silva.de/ Silva]
  
PMID 14607398
 
  
PMID 11240048
+
==References==
  
PMID 1987160
+
<biblio>
 +
#Weisburg91  pmid=1987160
  
PMID 2095137
+
#Wilson90  pmid=2095137
  
PMID 2482222
+
#Rivas04 pmid=14967233
  
 +
#Baker03  pmid=14607398
  
Mycoplasma universal primers
+
#Watanabe01  pmid=11240048
  
Johansson K-E, Characterization of mycoplasmas by PCR and sequence analysis iwth universal 16S rDNA primers, Chapter 18, Mycoplasma Protocols, 1998.
+
#Bottger89  pmid=2482222
  
U1F 12-27  ttg atc ctg gct cag gay daa cg
+
#Lane85 pmid=2413450
  
U2F  327-348  cca rac tcc tac ggr agg c
+
#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.
  
U3R  512-527  att acc gcg gck gct g
+
#Leser02 pmid=11823207
  
U4F  792-810  gta gtc cac gcc gta aac g
+
#Alm96 pmid=8837410
  
U5R  902-924  ctt gtg cgg gyy ccc gtc aa
+
</biblio>
  
U6F  1154-1172  gag gaa ggy grg gay gay g
 
  
U7R  1359-1374  aca agr ccc gag aac g
+
==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
  
U8R  1502-1524  gaa agg agg trw tcc ayc csc ac
 
  
 +
==Universal primers from Leser02==
 +
* Edited from Lane91, naming from Alm96, PMID 8837410
  
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.
+
* 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.
  
27f 5'AGAGTTTGATCMTGGCTCAG
+
* U1F  12-27  ttg atc ctg gct cag gay daa cg
342r 5'CTGCTGCSYCCCGTAG
+
* U2F  327-348  cca rac tcc tac ggr agg c
357f 5'CTCCTACGGGAGGCAGCAG
+
* U3R  512-527  att acc gcg gck gct g
519r 5'GWATTACCGCGGCKGCTG
+
* U4F  792-810  gta gtc cac gcc gta aac g
530f 5'GTGCCAGCMGCCGCGG
+
* U5R  902-924  ctt gtg cgg gyy ccc gtc aa
1100r 5'GGGTTGCGCTCGTTG
+
* U6F  1154-1172  gag gaa ggy grg gay gay g
1114f 5'GCAACGAGCGCAACCC
+
* U7R  1359-1374  aca agr ccc gag aac g
1392r 5'ACGGGCGGTGTGTRC
+
* U8R  1502-1524  gaa agg agg trw tcc ayc csc ac
1406f 5'TGYACACACCTCCCGT
 
1492r 5'TACGGYTACCTTGTTACGACTT
 
1525r 5'AAGGAGGTGWTCCARCC
 

Latest revision as of 04:49, 25 March 2012

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


References

  1. Weisburg WG, Barns SM, Pelletier DA, and Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697-703. PubMed ID:1987160 | HubMed [Weisburg91]
  2. Wilson KH, Blitchington RB, and Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol. 1990 Sep;28(9):1942-6. PubMed ID:2095137 | HubMed [Wilson90]
  3. Rivas R, Velázquez E, Zurdo-Piñeiro JL, Mateos PF, and Martínez Molina E. Identification of microorganisms by PCR amplification and sequencing of a universal amplified ribosomal region present in both prokaryotes and eukaryotes. J Microbiol Methods. 2004 Mar;56(3):413-26. DOI:10.1016/j.mimet.2003.11.007 | PubMed ID:14967233 | HubMed [Rivas04]
  4. Baker GC, Smith JJ, and Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods. 2003 Dec;55(3):541-55. PubMed ID:14607398 | HubMed [Baker03]
  5. Watanabe K, Kodama Y, and Harayama S. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods. 2001 Apr;44(3):253-62. PubMed ID:11240048 | HubMed [Watanabe01]
  6. Böttger EC. Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol Lett. 1989 Nov;53(1-2):171-6. PubMed ID:2482222 | HubMed [Bottger89]
  7. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, and Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955-9. PubMed ID:2413450 | 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. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol. 2002 Feb;68(2):673-90. PubMed ID:11823207 | HubMed [Leser02]
  10. Alm EW, Oerther DB, Larsen N, Stahl DA, and Raskin L. The oligonucleotide probe database. Appl Environ Microbiol. 1996 Oct;62(10):3557-9. PubMed ID:8837410 | 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

  • Edited from Lane91, naming from Alm96, PMID 8837410
  • 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