TABLE 1.
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 |
Oligonucleotide used as primer in the PCR.
The 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.
Oligonucleotide used as probe in whole-cell hybridization.
Probe GAM42a was applied together with the unlabeled BET42a to prevent unspecific hybridization to possible β-Proteobacteria.
Probes EUB338II and EUB338III were used together with EUB338 to cover all Bacteria. The combination of the three probes is named EUB338mix.
NA, not applicable.