Table 2.

Oligonucleotide probes used in this study

ProbeSpecificitySequence (5′-3′) of probeTargeta site (rRNA positions)% FAb in situReference
EUB338 Bacteria GCTGCCTCCCGTAGGAGT16S (338–355)0–35 2
NON338ACTCCTACGGGAGGCAGC16S (338–355)0–35 64
ALF968Alpha subclass ofProteobacteria GGTAAGGTTCTGCGCGTT16S (968–986)35 40
BET42aBeta subclass ofProteobacteria GCCTTCCCACTTCGTTT23S (1027–1043)35 32
GAM42aGamma subclass ofProteobacteria GCCTTCCCACATCGTTT23S (1027–1043)35 32
CF319a Cytophaga-Flavobacterium cluster of CFB phylumTGGTCCGTGTCTCAGTAC16S (319–336)35 31
PLA886 Planctomycetales GCCTTGCGACCATACTCCC16S (886–904)35 41
ARCH915 Archaea GTGCTCCCCCGCCAATTCCT16S (915–935)20–35 58
  • a Escherichia coli numbering (9).

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