Primer
|
Sequence 5' to 3'
|
Targeted site
|
Amplicon size (bp)
|
Reference
|
---|
SG-F
|
GGGTTGTCTGCGAAAGCGAAa
|
ITS-G
|
282
|
Liu et al., [44]
|
SG-R
|
GTCTTCGTGCTGCGAGTTTG
|
ITS-G & ITS-IA
| | |
SI-F
|
CAGGAGTTGAAGAGGTTTAACTb
|
ITS-IA
|
251
|
Liu et al., [44]
|
SI-R
|
GTGCTGCGAGTTTGAGAGACTC
|
ITS-G & ITS-IA
| | |
Saka 1a
|
ACAGGGAGCAGCTTGCTGCc
|
V1g
|
952
|
Hassan et al., [45]
|
Saka 2b
|
TCCCGCATCTCTGCAGGA
|
V3h
| | |
Zpx F
|
GAAAGCGTATAAGCGCGATTCd
|
zpx
|
94
|
Kothary et al., [13]
|
Zpx R
|
GTTCCAGAAGGCGTTCTGGT
| | | |
BAM122
|
AWATCTATGACGCGCAGAACCGe
|
zpx
|
350
|
Kothary et al., [13]
|
BAM123
|
AAAATAGATAAGCCCGGCTTCG
| | | |
EsgluAf
|
TGAAAGCAATCGACAAGAAGf
|
gluA
|
1680
|
Lehner et al., [3]
|
EsgluAr
|
ACTCATTACCCCTCCTGATG
| | | |
EsgluBf
|
TGAGTGAAGCACCGACGCAGf
|
gluB
|
1720
|
Lehner et al., [47]
|
EsgluBr
|
GTTACGTCACAGGTTTTGAT
| | | |
ESSF
|
GGATTTAACCGTGAACTTTTCCi
|
ompA
|
469
|
Nair and Venkitanarayanan [46]
|
ESSR
|
CGCCAGCGATGTTAGAAGA
| | | |
- a&b Running conditions; 94°C for 10 min; 30 cycles of 94°C for 30 sec each; 57°C for 1 min; 72°C for 1 min; a final extension period of 5 min at 72°C.
- c Running conditions; 95°C for 4 min; 30 cycles of 95°C for 60 sec each; 50°C for 1 min; 72°C for 90 sec; final extension period of 4 min at 72°C.
- d&e Running conditions; The hot start polymerase was activated by incubation for 15 min at 95°C; followed by 35 cycles of 1 min at 95°C; 62°C for zpx primers (50.5°C was used for 8 isolates) or 50°C for BAM primers for 1 min; 72°C for 1 min; final extension of 10 min at 72°C for zpx and 7 min for BAM primers.
- f Running conditions were as described by Lehner et al. [3, 47]; The hot start polymerase was activated by incubation for 15 min at 95°C; followed by 30 cycles of 30 s at 94°C; 56°C (gluA) or 58°C (gluB) for 1 min; 72°C for 1.5 min; final extension period of 5 min at 72°C.
- g&h: Variable regions of the 16S rRNA gene.
- i Running conditions: 94°C for 2 min; 30 cycles 94°C for 15 sec each; 60°C for 15 sec; 72°C for 30 sec; final extension period of 5 min at 72°C.