TABLE 2.
Primers used for PCR amplification, sequence, specificity, and location on the rRNA operon
| Species | Primer | R/Fa | Sequence (5′-3′) | Specificity | Position | Reference |
|---|---|---|---|---|---|---|
| L. sakei | Ls | R | ATGAAACTATTAAATTGGTAC | Species | 16S-23S spacer region | Berthier and Ehrlich (8) |
| 16S | F | GCTGGATCACCTCCTTTC | 16S RNA gene | 3′-end 16S rRNA | ||
| L. curvatus | Lc | R | TTGGTACTATTTAATTCTTAG | Species | 16S-23S spacer region | Berthier and Ehrlich (8) |
| 16S | F | GCTGGATCACCTCCTTTC | 16S RNA gene | 3′-end 16S rRNA | ||
| L. plantarum | Lpl | R | ATGAGGTATTCAACTTATG | Species | 16S-23S spacer region | Berthier and Ehrlich (8) |
| 16S | F | GCTGGATCACCTCCTTTC | 16S RNA gene | 3′-end 16S rRNA | ||
| E. faecium | Ef | R | CACACAATCGTAACATCCTA | Species | 23S rRNA | Frahm et al. (29) |
| 16S | F | GCTGGATCACCTCCTTTC | 16S RNA gene | 3′-end 16S rRNA | Berthier and Ehrlich (8) | |
| L. lactis | Lac | F | GCTGAAGGTTGGTACTTGTA | Species | 16S rRNA (V1) | Klijn et al. (43) |
| 23S | R | AGTGCCAAGGCATCCACC | 23S RNA gene | 5′-end 23S rRNA | Berthier and Ehrlich (8) | |
| P. acidilactici | Pda | F | CTGAATGAGATTTTAACACGAA | Species | 16S rRNA (V1) | Cai et al. (11) |
| 23S | R | AGTGCCAAGGCATCCACC | 23S RNA gene | 5′-end 23S rRNA | Berthier and Ehrlich (8) | |
| S. camosus | ScaI | F | GAACCGCATGGTTCTGCAA | Species | 16S rRNA | Gory et al. (33) |
| ScaII | R | CCGTCAAGGTGCGCATAGT | Species | 16S rRNA | This study | |
| S. warneri | Swa | F | TAGTGAAAGGCGGCTTTGCTG | Species | 16S rRNA | Gory et al. (33) |
| Sta2 | R | CCGTCAAGATGTGCACAGT | Genera | 16S rRNA | This study | |
| K. varians | Kva | R | CACGTTTACCTCCCCGGATC | Species | 23S rRNA (insertion region) | This study |
| Kva2 | F | GGTTTGTCGCGTCTTCTGTG | 16S RNA gene | 16S rRNA (V3-559-578pb) | This study | |
| S. xylosus | Sxyl FA | F | AAGTCGGTTGAAAACCCAAA | Strain | 16S-23S spacer region | This study |
| Sxyl FB | F | AAAATCGGCTGAAAACCTAAA | Strain | 16S-23S spacer region | This study | |
| Sxyl RA | R | CATTGACATATTGTCTTCAG | Strain | |||
| Sxyl RB | R | CATTGACATATTGTATTCAG | Strain | |||
| S. simulans | Si1 | F | ATTCGGAACAGTTTCGCAG | Species | 16S-23S spacer region | Forsman et al. (25) |
| Si2 | R | ATTGTGAGTAATCGTTTGCC | Species | 16S-23S spacer region | ||
| S. epidermidis | Epi1 | F | TCTACGAAGATGAGGGATA | Species | 16S-23S spacer region | Forsman et al. (25) |
| Epi2 | R | TTTCCACCATATTTTGAATTGT | Species | 16S-23S spacer region |
a
R, reverse; F, forward.