Bacterial species identification

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. 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