Table 2.

Oligonucleotide probes used in this study

ProbeSpecificitySequence (5′-3′) of probeTargeta site (rRNA positions)% FAb in situReference
EUB338BacteriaGCTGCCTCCCGTAGGAGT16S (338–355)0–352
NON338ACTCCTACGGGAGGCAGC16S (338–355)0–3564
ALF968Alpha subclass ofProteobacteriaGGTAAGGTTCTGCGCGTT16S (968–986)3540
BET42aBeta subclass ofProteobacteriaGCCTTCCCACTTCGTTT23S (1027–1043)3532
GAM42aGamma subclass ofProteobacteriaGCCTTCCCACATCGTTT23S (1027–1043)3532
CF319aCytophaga-Flavobacterium cluster of CFB phylumTGGTCCGTGTCTCAGTAC16S (319–336)3531
PLA886PlanctomycetalesGCCTTGCGACCATACTCCC16S (886–904)3541
ARCH915ArchaeaGTGCTCCCCCGCCAATTCCT16S (915–935)20–3558
  • a Escherichia coli numbering (9).

  • b Percentage of formamide (FA) in in situ hybridization buffer.