Table 1.
Primer pairs and conditions of quantitative real-time PCR.
| Main target (target gene) | Designation | Oligonucleotide sequence (5′-> 3′) | Annealing temperature (°C) | Cycling | References |
|---|---|---|---|---|---|
| Fungi (18S rRNA) | Fungi2F Fungi2R |
F: ATT-GGA-GGG-CAA-GTC-TGG-TG R: CCG-ATC-CCT-AGT-CGG-CAT-AG |
55 | 60 cycles: 15 s at 95°C, 10 s at 55°C, 25 s at 72°C |
Einsele et al., 1997 |
| Staphylococcus (tuf) | TStaG422-F TStag765-R |
F: GGC-CGT-GTT-GAA-CGT-GGT-CAA-ATC-A R: TAT-HAC-CAT-TTC-AGT-ACC-TTC-TGG-TAA |
55 |
45 cycles: 20 s at 95°C, 30 s at 55°C, 1 min at 72°C |
Martineau et al., 2001 |
| Haemophilus (P6) | HI-IV | F: ACT-TTT-GGC-GGT-TAC-TCT-GT | 55 | van Ketel et al., 1990 | |
| HI-V | R: TGT-GCC-TAA-TTT-ACC-AGC-AT | ||||
| Universal archaea (16S rRNA) | ARC787F ARC1059R |
F: ATT-AGA-TAC-CCS-BGT-AGT-CC R: GCC-ATG-CAC-CWC-CTC-T |
60 | Yu et al., 2005 | |
| Lactobacillus (16S rRNA) | Lac774F Lac989R |
F: GCG-GTG-AAA-TTC-CAA-ACGR: GGG-ACC-TTA-ACT-GGT-GAT | 60 | 45 cycles: 15 s at 95°C, 30 s at 60°C, 1 min at 72°C |
Hermann-Bank et al., 2013 |
| Streptococcus (16S rRNA) | Strep488F | F: CTW-ACC-AGA-AAG-GGA-CGG-CT | 60 | Hermann-Bank et al., 2013 | |
| Strep824R | R: AAG-GRY-CYA-ACA-CCT-AGC | ||||
| Firmicutes (16S rRNA) | Lgc353 | F: GCA-GTA-GGG-AAT-CTT-CCG | 60 | Fierer et al., 2005 | |
| Eub518 | R: ATT-ACC-GCG-GCT-GCT-GG | ||||
| Bacteroidetes (16S rRNA) | 798cfbF cfb967R |
F: CRA-ACA-GGA-TTA-GAT-ACC-CT R: GGT-AAG-GTT-CCT-CGC-GTA-T |
61 | 45 cycles: 15 s at 95°C, 20 s at 61°C, 30 s at 72°C |
Bacchetti De Gregoris et al., 2011 |
| Universal prokaryotes (16S rRNA) | 926F | F: AAA-CTC-AAA-KGA-ATT-GAC-GG | 61 | Bacchetti De Gregoris et al., 2011 | |
| 1062R | R: CTC-ACR-RCA-CGA-GCT-GAC |