TABLE 1.
Primers used in this study for the species-specific PCR assays
| Target | Primers | Sequence (5′-3′) | Annealing temp (°C) | Source or referencea |
|---|---|---|---|---|
| Brevibacterium casei | Brevib, Bcas | Unpublished data | 64 | Furlan |
| Brevibacterium linens | Brevib, Blin | Unpublished data | 64 | Furlan |
| Corynebacterium variabile | Cvar, Corb | Unpublished data | 60 | Furlan |
| Escherichia coli | Eco 223 | ATCAACCGAGATTCCCCCAGT | ||
| Eco 455 | TCACTATCGGTCAGTCAGGAG | 64 | 46 | |
| Enterococcus casseliflavus | EC1, EC2 | Unpublished data | 52 | Firmesse |
| Enterococcus durans | ED1, ED2 | Unpublished data | 52 | Firmesse |
| Enterococcus faecalis | EFS1, EFS2 | Unpublished data | 52 | Firmesse |
| Enterococcus faecium | EFM1, EFM2 | Unpublished data | 52 | Firmesse |
| Enterococcus hirae | EH1, EH2 | Unpublished data | 52 | Firmesse |
| Lactococcus garvieae | 1RL LgR | TTTGAGAGTTTGATCCTGG AAGTAATTTTCCACTCTACTT | 45 | 42 |
| Lactococcus lactis | 1RL LacreR | TTTGAGAGTTTGATCCTGG GGGATCATCTTTGAGTGAT | 45 | 42 |
| Lactococcus lactis subsp. cremoris | CreF LacreR | GTGCTTGCACCGATTTGAA GGGATCATCTTTGAGTGAT | 58 | 42 |
| Lactococcus lactis subsp. lactis | LacF LacreR | GTACTTGTACCGACTGGAT GGGATCATCTTTGAGTGAT | 58 | 42 |
| Lactococcus raffinolactis | 1RL PipLraR | TTTGAGAGTTTGATCCTGG CGTCACTGAGGGCTGGAT | 45 | 42 |
| Lactobacillus acidophilus | Laci01 Laci02 | GACCGCATGATCAGCTTATA AGTCTCTCAACTCGGCTATG | 55 | 25 |
| Lactobacillus brevis | LbBreF LbBreR | CTTGCACTGATTTTAACA GGGCGGTGTGTACAAGGC | 40 | 26 |
| Lactobacillus casei | PrI 16S-23S CasII | CAGACTGAAAGTCTGACGG GCGATGCGAATTTCTTTTTC | 55 | 50 |
| Lactobacillus gasseri | GasI GasII | GAGTGCGAGAGCACTAAAG CTATTTCAAGTTGAGTTTCTCT | 55 | 50 |
| Lactobacillus johnsonii | Joh 16SI 16SII | GAGCTTGCCTAGATGATTTTA ACTACCAGGGTATCTAATCC | 57 | 50 |
| Lactobacillus plantarum | Lfpr16S-23S PlanII | GCCGCCTAAGGTGGGACAGAT TTACCTAACGGTAAATGCGA | 55 | 50 |
| Leuconostoc citreum | Lcit-f Lcit-r | AAAACTTAGTATCGCATGATATC CTTAGACGACTCCCTCCCG | 60 | 30 |
| Leuconostoc mesenteroides | Lnm1 Lnm2 | TGTCGCATGACACAAAGTTA ATCATTTCCTATTCTAGCTG | 58 | 4 |
| Pseudomonas aeruginosa | Paer16SH | AGGGCAGTAAGTTAATACCTTGCTG | 65 | 51 |
| Paer16SIR | CCACCTCTACCGTACTCTAGCTCAG | |||
| Serratia marcescens | Smar16SV | GGGAGCTTGCTCACTGGGTG | ||
| Smar16SWR | GCGAGTAACGTCAGTTGATGAGCGTATTA | 66 | 51 | |
| Staphylococcus aureus | STAA-AuI | TCTTCAGAAGATGCGGAATA | ||
| STAA-AuII | TAAGTCAAACGTTAACATACG | 55 | 24 | |
| Staphylococcus chromogenes | STAC-ChrI | ACGGAATATCGCTTTTAAGC | ||
| STAC-ChrII | CGTTTACATTCGGCTTTCG | 52 | 24 | |
| Staphylococcus epidermidis | STAE-EpI | TCTACGAAGATGAGGGATA | ||
| STAE-EpII | TTTCCACCATATTTTGAATTGT | 52 | 24 | |
| Staphylococcus saprophyticus | fStSap | TCAAAAAGTTTTCTAAAAAATTTAC | ||
| rStSap | ACGGGCGTCCACAAAATCAATAGGA | 55 | 33 | |
| Staphylococcus simulans | STAS-SiI | ATTCGGAACAGTTTCGCAG | ||
| STAS-SiII | ATTGTGAGTAATCGTTTGCC | 55 | 24 | |
| Staphylococcus xylosus | STAX-XyI | TCTTTAGAAGATGACAGAGG | ||
| STAX-XyII | TGACTTTTAACACGACGAAG | 55 | 24 | |
| Streptococcus thermophilus | Sther03 | TTATTTGAAAGGGGCAATTGCT | ||
| Sther08 | GTGAACTTTCCACTCTCACAC | 55 | 25 |
a
Firmesse, O. Firmesse et al., unpublished data; Furlan, S. Furlan et al., unpublished data.