TABLE 1.

Oligonucleotides used in this study

Name	Target organisms	Sequence (5′-3′)	Target site	% Formamidef	Reference
GM3Fa	Bacteria	AGA GTT TGA TCM TGG C	16S (8-24)	NA	18
GM4Ra	Bacteria	TAC CTT GTT ACG ACT T	16S (1492-1507)	NA	18
341F-GCa,b	Bacteria	CC TAC GGG AGG CAG CAG	16S (341-357)	NA	23
907RMa	Bacteria	CCG TCA ATT CMT TTG AGTT T	16S (907-927)	NA	23
ALF1bc	α-Proteobacteria	CGT TCG YTC TGA GCC AG	16S (19-35)	20	15
ALF968c	α-Proteobacteria	GGT AAG GTT CTG CGC GTT	16S (968-986)	20	20
BET42ac,d	β-Proteobacteria	GCC TTC CCA CTT CGT TT	23S (1027-1043)	35	15
GAM42ac,d	γ-Proteobacteria	GCC TTC CCA CAT CGT TT	23S (1027-1043)	35	15
CF319ac	Cytophaga-Flavobacterium cluster	TGG TCC GTG TCT CAG TAC	16S (319-336)	35	16
FB648c	T. danicus and strain DK4	ACC TCT CCC ATG GTC TAG TT	16S (648-668)	40	This study
FB741c	T. danicus and strain DK4	CCT CAG CGT CAG CTA TGT TC	16S (741-761)	40	This study
FB842c	Strain DK4	ACT GTG TTA CTG CAG CCT CT	16S (842-862)	40	This study
ARC94c	Arcobacter spp.	TGC GCC ACT TAG CTG ACA	16S (94-112)	20	24
ARC1430c	Arcobacter spp.	TTA GCA TCC CCG CTT CGA	16S (1430-1448)	20	24
EUB338c	Most bacteria	GCT GCC TCC CGT AGG AGT	16S (338-356)	35	2
EUB338IIc,e	Planctomycetales	GCA GCC ACC CGT AGG TGT	16S (338-356)	35	7
EUB338IIIc,e	Verrucomicrobiales	GCT GCC ACC CGT AGG TGT	16S (338-356)	35	7

^aOligonucleotide used as primer in the PCR.

^bThe GC clamp (5′-CGC CCG CCG CGC CCC GCG CCC GTC CCG CCG CCC CCG CCC G-3′) was incorporated at the 5′ end of this primer.

^cOligonucleotide used as probe in whole-cell hybridization.

^dProbe GAM42a was applied together with the unlabeled BET42a to prevent unspecific hybridization to possible β-Proteobacteria.

^eProbes EUB338II and EUB338III were used together with EUB338 to cover all Bacteria. The combination of the three probes is named EUB338mix.

^fNA, not applicable.