TABLE 1.

Oligonucleotide probes used for quantification of unmethylated ribosomes and microbial community analysis

ProbeSystematic nameLabel (5′)Target organismsTarget molecule% FormamideaSpecificity (%)bCoverage (%)cProbe sequence (5′-3′)Reference
MLSBL-*-MLSS-2053-a-S-13Cy3MLSB-sensitive bacteriad23S rRNA12.5NA97.5GGG TCT TTC CGT CThis study
ClostXIVaS-*-Clos-0129-a-A-15FAMe Clostridium cluster XIVa16S rRNA3099.8f9.4fCTG TAT GAG GCA GGT 36
ALF1BS-Sc-aProt-0019-a-A-17Cy3 Alphaproteobacteria 16S rRNA2052.268gCGT TCG YTC TGA GCC AG 24
BET42aL-C-bProt-1027-a-A-17FAM Betaproteobacteria 23S rRNA35NA92.6GCC TTC CCA CTT CGT TT 24
GAM42aL-C-gProt-1027-a-A-17FAM Gammaproteobacteria 23S rRNA35NA90.8GCC TTC CCA CAT CGT TT 24
Bact0338S-D-Bact-0338-a-A-18Cy3 Bacteria 16S rRNA2099.990gGCT GCC TCC CGT AGG AGT 3
  • a % Formamide, the percentage of formamide in the hybridization buffer for optimal hybridization conditions in FISH experiments.

  • b Specificity, the percentage of sequences matching the probe within the target group over the total number of sequences matching the probe. Source, Ribosomal Database Project (http://rdp.cme.msu.edu/index.jsp , accessed on 11 November 2008). NA, not available.

  • c Coverage, the percentage of sequences matching the probe within the target group over the total number of sequences in the target group. Source, Ribosomal Database Project (http://rdp.cme.msu.edu/index.jsp , accessed on 11 November 2008), except where noted.

  • d For the calculations presented here, MLSB-sensitive bacteria are defined as all bacteria that contain G2057 and are unmethylated at position A2058.

  • e FAM, 6-carboxyfluorescein.

  • f Specificity and coverage were calculated for the target order Clostridiales.

  • g Source, probeBase (23; http://www.microbial-ecology.net/probebase/default.asp ).