Table 2.

Oligonucleotide probes used in this study

ProbeSpecificitySequence (5′ to 3′) of probeTarget site (rRNA positions)a% FA in situbReference
EUB338BacteriaGCTGCCTCCCGTAGGAGT16S, 338–3550–35 4
NON338ACTCCTACGGGAGGCAGC16S, 338–3550–35 62
HGC69aActinobacteriaTATAGTTACCACCGCCGT23S, 1901–198120 53
HGC236ActinobacteriaAACAAGCTGATAGGCCGC16S, 235–25310 19
HGC664ActinobacteriaAGGAATTCCAGTCTCCCC16S, 663–68130 19
HG1-840HG1 cluster of the class Actinobacteria TCGCA(C/G)AAACCGTGGAAG16S, 840–84610This study
HG1-654HG1 cluster of the classActinobacteria (without FukuN105, 1605-10, 1405-72, and 25-4-33); “cross-reaction” with some CFBcAGTCTCCCCTACCAAACTC16S, 654–67235This study
HGC270HHelper for HGC236ACCCGTCG(T/A/C)(C/A)GCCTTGGT16S, 270–28710This study
HGC697HHelper for HGC664GTTCCTCCTGATATCTGCGCA16S, 697–71730This study
HG1-810HHelper for HGC840CTAG(C/T)GCCCA(C/T)CGTTTACGG16S, 810–82910This study
HG1-820HHelper for HGC840GTTC(G/C)CACAACTAG(C/T)GCCCA16S, 820–83910This study
HG1-859HHelper for HGC840GGGGC(G/A)CTTAATGCGTTAGCTG16S, 859–88010This study
  • a E. coli numbering (11).

  • b Percent formamide (FA) in in situ hybridization buffer.