Table 2.

Oligonucleotide probes used in this study

ProbeSpecificityProbe sequence (5′ to 3′)Target sitea (rRNA positions)% FA in situbReference
EUB338BacteriaGCTGCCTCCCGTAGGAGT16S (338–355)01
ALF1bAlpha subclass and several members of delta subclass ofProteobacteria, most spirochetesCGTTCGYTCTGAGCCAG16S (19–35)2021
BET42aBeta subclass ofProteobacteria GCCTTCCCACTTCGTTT23S (1027–1043)3521
GAM42aGamma subclass ofProteobacteria GCCTTCCCACATCGTTT23S (1027–1043)3521
HGC69aGram-positive bacteria with high G+C DNA contentTATAGTTACCACCGCCGT23S (1901–1918)3530
ALBO34aBordetella spp., Alcaligenes spp. (sensu stricto)CGTGCCTTCAACCTGGCC23S (699–716)60This study
Bcv13bBurkholderia vietnamiensis,Burkholderia cepaciaGCTCATCCCATTTCGCTC23S (255–277)20This study
SUBU1237Burkholderia spp. and Sutterellaspp.CCCTCTGTTCCGACCATT16S (1237–1254)35This study
BONE23aBeta1 subgroup ofProteobacteria GAATTCCATCCCCCTCT16S (663–679)354
PS56aMost true Pseudomonasspp.GCTGGCCTAGCCTTC23S (1432–1446)031
Ppu56aP. putida, P. mendocinaGCTGGCCTAACCTTC23S (1432–1446)031
BTWO23aCompetitor for BONE23aGAATTCCACCCCCCTCT16S (663–679)354
  • a Escherichia coli numbering (13).

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