TABLE 2.

Oligonucleotide probes used in this study

Probe	Specificity	Sequence (5′-3′) of probe	Targeta site (rRNA positions)	% FAb in situ	Reference
EUB338	Bacteria	GCTGCCTCCCGTAGGAGT	16S (338–355)	0–35	2
NON338		ACTCCTACGGGAGGCAGC	16S (338–355)	0–35	64
ALF968	Alpha subclass of Proteobacteria	GGTAAGGTTCTGCGCGTT	16S (968–986)	35	40
BET42a	Beta subclass of Proteobacteria	GCCTTCCCACTTCGTTT	23S (1027–1043)	35	32
GAM42a	Gamma subclass of Proteobacteria	GCCTTCCCACATCGTTT	23S (1027–1043)	35	32
CF319a	Cytophaga-Flavobacterium cluster of CFB phylum	TGGTCCGTGTCTCAGTAC	16S (319–336)	35	31
PLA886	Planctomycetales	GCCTTGCGACCATACTCCC	16S (886–904)	35	41
ARCH915	Archaea	GTGCTCCCCCGCCAATTCCT	16S (915–935)	20–35	58

^aEscherichia coli numbering (9). 

^bPercentage of formamide (FA) in in situ hybridization buffer.