Bacterial species identification

See here for 16S rRNA alignment assistance.

For 16S rDNA species specific probes, see ProbeBase

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. DOI:10.1128/jb.173.2.697-703.1991 |
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. DOI:10.1128/jcm.28.9.1942-1946.1990 |
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 |
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. DOI:10.1016/j.mimet.2003.08.009 |
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. DOI:10.1016/s0167-7012(01)00220-2 |
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. DOI:10.1016/0378-1097(89)90386-8 |
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. DOI:10.1073/pnas.82.20.6955 |

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.

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. DOI:10.1128/AEM.68.2.673-690.2002 |
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. DOI:10.1128/aem.62.10.3557-3559.1996 |

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