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

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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.

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