TABLE 1.
Primer | Sequence (5′→3′) | Annealing positiona | Target | Annealing temp (°C) | Amplicon length (bp)b | Reference |
---|---|---|---|---|---|---|
27f | AGA GTT TGA TCM TGG CTC AG | 8–27 | Most bacteria | 54 | 1,535 | 38 |
1525r | AAG GAG GTG WTC CAR CC | 1,525–1,542 | ||||
340f | TCC TAC GGG AGG CAG CAG T | 340–258 | Most bacteria | 60 | 467 | 76 |
806r | GGA CTA CCA GGG TAT CTA ATC CTG TT | 781–806 | ||||
TaqMan probe | 6-FAM-5′-CGT ATT ACC GCG GCT GCT GGC AC-3′-TAMRA | 515–537 | ||||
Bac303f | GAA GGT CCC CCA CAT TG | 302–318 | Bacteroides | 56 | 418 | 41 |
Bac708r | CAA TCG GAG TTC TTC GTG | 708–725 | 77 | |||
Bif164f | GGG TGG TAA TGC CGG ATG | 164–181 | Bifidobacterium | 60 | 530 | 78 |
Bif662rc | CCA CCG TTA CAC CGG GAA | 676–693 | ||||
ECA75f | GGA AGA AGC TTG CTT CTT TGCT GAC | 75–99 | E. coli | 56 | 545 | 44 |
ECR619r | AGC CCG GGG ATT TCA CAT CTG ACT TA | 594–619 | ||||
Cdif-706f | ATT AGG AGG AAC ACC AGT TG | 164–181 | C. difficile | 54 | 307 | 43 |
Cdif-994r | AGG AGA TGT CAT TGG GAT GT | 994–1,012 | ||||
BiLON-1 | TTC CAG TTG ATC GCA TGG TC | 186–207 | B. longum | 63 | 831 | 42 |
BiLON-2 | GGG AAG CCG TAT CTC TAC GA | 1,009–1,028 | ||||
ERIC 1 | ATG TAA GCT CCT GGG GAT TCA C | Variable | Bacteria | 52 | Variable | 37 |
ERIC 2 | AAG TAA GTG ACT GGG GTG AGC G |
Based on numbering of the rrs gene of Bacteroides.
Calculated based on the rrs gene of Bacteroides.
When used in PCR-DGGE, a 40-bp GC clamp (5′-CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG G-3′) was attached to the primer at the 5′ end.