3 Open in new tab rRNA-targeted...

Probe	Target group	Sequence (5′–3′) of probe	Target site^a	FA^b (%)	NaCl^c (mM)	Reference
EUB338^*	Domain Bacteria	GCTGCCTCCCGTAGGAGT	16S (338)	0–35	80–900	[73]
EUB338 II^*	Domain Bacteria	GCAGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
EUB338 III^*	Domain Bacteria	GCTGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
NON338	Control probe complementary to EUB338	ACTCCTACGGGAGGCAGC	16S	0–35	80–900	[75]
ARC915	Domain Archaea	GTGCTCCCCCGCCAATTCCT	16S (915)	20	225	[39]
ALF968	α-subclass of Proteobacteria	GGTAAGGTTCTGCGCGTT	16S (968)	35	80	[76]
BET42a	β-subclass of Proteobacteria	GCCTTCCCACTTCGTTT	23S (1027)	35	80	[77]
GAM42a	γ-subclass of Proteobacteria	GCCTTCCCACATCGTTT	23S (1027)	35	80	[77]
CF319A^**	Cytophaga–Flavobacterium cluster of CFB-phylum	TGGTCCGTGTCTCAGTAC	16S (319)	35	80	[77]
CF319B^**	Same as CF319A	TGGTCCGTATCTCAGTAC	16S (319)	35	80	[77]
HGC69a	Gram-positive bacteria with high GC content	TATAGTTACCACCGCCGT	23S (1901)	25	159	[78]
LGC354A^***	Gram-positive bacteria with low GC content	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354B^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354C^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]

Probe

Target group

Sequence (5′–3′) of probe

Target site^a

FA^b (%)

NaCl^c (mM)

Reference

EUB338^*

Domain Bacteria

GCTGCCTCCCGTAGGAGT

16S (338)

0–35

80–900

[73]

EUB338 II^*

Domain Bacteria

GCAGCCACCCGTAGGTGT

16S (338)

0–35

80–900

[74]

EUB338 III^*

Domain Bacteria

GCTGCCACCCGTAGGTGT

16S (338)

0–35

80–900

[74]

NON338

Control probe complementary to EUB338

ACTCCTACGGGAGGCAGC

16S

0–35

80–900

[75]

ARC915

Domain Archaea

GTGCTCCCCCGCCAATTCCT

16S (915)

225

[39]

ALF968

α-subclass of Proteobacteria

GGTAAGGTTCTGCGCGTT

16S (968)

[76]

BET42a

β-subclass of Proteobacteria

GCCTTCCCACTTCGTTT

23S (1027)

[77]

GAM42a

γ-subclass of Proteobacteria

GCCTTCCCACATCGTTT

23S (1027)

[77]

CF319A^**

Cytophaga–Flavobacterium cluster of CFB-phylum

TGGTCCGTGTCTCAGTAC

16S (319)

[77]

CF319B^**

Same as CF319A

TGGTCCGTATCTCAGTAC

16S (319)

[77]

HGC69a

Gram-positive bacteria with high GC content

TATAGTTACCACCGCCGT

23S (1901)

159

[78]

LGC354A^***

Gram-positive bacteria with low GC content

TGGAAGATTCCCTACTGC

16S (354)

[79]

LGC354B^***

Same as LGC354A

TGGAAGATTCCCTACTGC

16S (354)

[79]

LGC354C^***

Same as LGC354A

TGGAAGATTCCCTACTGC

16S (354)

[79]

Probe	Target group	Sequence (5′–3′) of probe	Target site^a	FA^b (%)	NaCl^c (mM)	Reference
EUB338^*	Domain Bacteria	GCTGCCTCCCGTAGGAGT	16S (338)	0–35	80–900	[73]
EUB338 II^*	Domain Bacteria	GCAGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
EUB338 III^*	Domain Bacteria	GCTGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
NON338	Control probe complementary to EUB338	ACTCCTACGGGAGGCAGC	16S	0–35	80–900	[75]
ARC915	Domain Archaea	GTGCTCCCCCGCCAATTCCT	16S (915)	20	225	[39]
ALF968	α-subclass of Proteobacteria	GGTAAGGTTCTGCGCGTT	16S (968)	35	80	[76]
BET42a	β-subclass of Proteobacteria	GCCTTCCCACTTCGTTT	23S (1027)	35	80	[77]
GAM42a	γ-subclass of Proteobacteria	GCCTTCCCACATCGTTT	23S (1027)	35	80	[77]
CF319A^**	Cytophaga–Flavobacterium cluster of CFB-phylum	TGGTCCGTGTCTCAGTAC	16S (319)	35	80	[77]
CF319B^**	Same as CF319A	TGGTCCGTATCTCAGTAC	16S (319)	35	80	[77]
HGC69a	Gram-positive bacteria with high GC content	TATAGTTACCACCGCCGT	23S (1901)	25	159	[78]
LGC354A^***	Gram-positive bacteria with low GC content	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354B^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354C^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]

Open in new tab

rRNA-targeted oligonucleotide probes used for hybridisation

Probe	Target group	Sequence (5′–3′) of probe	Target site^a	FA^b (%)	NaCl^c (mM)	Reference
EUB338^*	Domain Bacteria	GCTGCCTCCCGTAGGAGT	16S (338)	0–35	80–900	[73]
EUB338 II^*	Domain Bacteria	GCAGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
EUB338 III^*	Domain Bacteria	GCTGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
NON338	Control probe complementary to EUB338	ACTCCTACGGGAGGCAGC	16S	0–35	80–900	[75]
ARC915	Domain Archaea	GTGCTCCCCCGCCAATTCCT	16S (915)	20	225	[39]
ALF968	α-subclass of Proteobacteria	GGTAAGGTTCTGCGCGTT	16S (968)	35	80	[76]
BET42a	β-subclass of Proteobacteria	GCCTTCCCACTTCGTTT	23S (1027)	35	80	[77]
GAM42a	γ-subclass of Proteobacteria	GCCTTCCCACATCGTTT	23S (1027)	35	80	[77]
CF319A^**	Cytophaga–Flavobacterium cluster of CFB-phylum	TGGTCCGTGTCTCAGTAC	16S (319)	35	80	[77]
CF319B^**	Same as CF319A	TGGTCCGTATCTCAGTAC	16S (319)	35	80	[77]
HGC69a	Gram-positive bacteria with high GC content	TATAGTTACCACCGCCGT	23S (1901)	25	159	[78]
LGC354A^***	Gram-positive bacteria with low GC content	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354B^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354C^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]

Probe	Target group	Sequence (5′–3′) of probe	Target site^a	FA^b (%)	NaCl^c (mM)	Reference
EUB338^*	Domain Bacteria	GCTGCCTCCCGTAGGAGT	16S (338)	0–35	80–900	[73]
EUB338 II^*	Domain Bacteria	GCAGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
EUB338 III^*	Domain Bacteria	GCTGCCACCCGTAGGTGT	16S (338)	0–35	80–900	[74]
NON338	Control probe complementary to EUB338	ACTCCTACGGGAGGCAGC	16S	0–35	80–900	[75]
ARC915	Domain Archaea	GTGCTCCCCCGCCAATTCCT	16S (915)	20	225	[39]
ALF968	α-subclass of Proteobacteria	GGTAAGGTTCTGCGCGTT	16S (968)	35	80	[76]
BET42a	β-subclass of Proteobacteria	GCCTTCCCACTTCGTTT	23S (1027)	35	80	[77]
GAM42a	γ-subclass of Proteobacteria	GCCTTCCCACATCGTTT	23S (1027)	35	80	[77]
CF319A^**	Cytophaga–Flavobacterium cluster of CFB-phylum	TGGTCCGTGTCTCAGTAC	16S (319)	35	80	[77]
CF319B^**	Same as CF319A	TGGTCCGTATCTCAGTAC	16S (319)	35	80	[77]
HGC69a	Gram-positive bacteria with high GC content	TATAGTTACCACCGCCGT	23S (1901)	25	159	[78]
LGC354A^***	Gram-positive bacteria with low GC content	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354B^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]
LGC354C^***	Same as LGC354A	TGGAAGATTCCCTACTGC	16S (354)	35	80	[79]

^*–^***, Probes marked with the same amount of ^* are applied in equimolar mixtures.

^aEscherichia coli numbering.

^bPercentage (vol/vol) of formamide in the hybridisation buffer.

^cPercentage (vol/vol) of NaCl in the washing buffer.

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