TABLE 2.
Oligonucleotide primers used for gene amplification and DNA sequencing
| Gene and primera | Sequence (5′ to 3′)b or description | Base positions |
|---|---|---|
| vtp | Amplicon size for DAH, 836 bp; ORF, 627 | |
| Vtp sp-7 | TGATAATATTTTTGTTTTGTAAAATTATTTACG | −115 to −83 |
| Vtp sp-12 | GCTTTCTATTTATTGACTTTATTTTTCCAG | +91 to +62 |
| 16S rRNA | Amplicon size1489 bp; Trimmed: 1273 bp | |
| FD3* | AGAGTTTGATCCTGGCTTAG | −89 to −70 |
| T50* | GTTACGACTTCACCCTCCT | +127 to +109 |
| Rec4* | ATGCTAGAAACTGCATGA | 533 to 550 |
| Rec9* | TCGTCTGAGTCCCCATCT | 1052 to 1035 |
| 16s (−) | TAGAAGTTCGCCTTCGCCTCTG | 641 to 620 |
| 16s (+) | TACAGGTGCTGCATGGTTGTCG | 939 to 960 |
| flaB | Amplicon size, 1,285 bp; ORF, 1,002 bp | |
| Bh fla 5′ | AATCTTTGAATTTACAGCGACAAAACAGG | −155 to −127 |
| Bh fla 3′ | AAACTCCAATGCGAAAACATTACAATCC | +125 to +98 |
| Fla +1 | AGAGCTTGGAATGCAACCCG | 447 to 466 |
| Fla −1 | TGCCTCATCCTGATTTGCG | 552 to 534 |
| gyrB | Amplicon size, 2,141 bp; ORF, 1902 bp | |
| gyrB 5′ A-1 | TTTATTGGTTTTAAGTCAAGTTGAATATGTC | −120 to −90 |
| gyrB 3′ | GGCTCTTGAAACAATAACAGACATCGC | +116 to +90 |
| gyrB 5′ | GGTTTATGAGTTATGTTGCTAGTAATATTCAAGTGC | −5 to 31 |
| gyrB 5′+1 | TTATCAAAGAGACTTAGGGAACTTGC | 547 to 572 |
| gyrB 5′+2 | GAAAGATGTTCCAAGTCTTACATTAGATG | 906 to 934 |
| gyrB 5′+3 | GCTGATGCTGATGTTGATGG | 1480 to 1499 |
| gyrB 3′+1 | TGCCCATTCTCAATTAACTCCC | 1568 to 1547 |
| gyrB 3′+2 | CATCATGCACAATAGTTTCAACG | 1060 to 1038 |
| gyrB 3′+3 | TTCTCTTTTCCCGATCTCCTATC | 629 to 607 |
| glpQ | Amplicon size, 1,396 bp; ORF, 1,020 and 1,026 bp | |
| glpQ F+1 | GGGGTTCTGTTACTGCTAGTGCCATTAC | −252 to −225 |
| Rev-2 | CAATACTAAGACCAGTTGCTCCTCCGCC | +121 to +94 |
| Rev-1 | GCACAGGTAGGAATGTTGGAATTTATCCTG | 482 to 511 |
| glpQ F-1 | CAATTTTAGATATGTCTTTACCTTGTTGTTTATGCC | 565 to 530 |
a
*, For flaB, gyrB, and glpQ, the minus (−) numbers represent positions upstream of the A in the ATG start codon; positive (+) numbers represent positions downstream of the last base in the stop codon; numbers with no “+” or “−” are within the ORF, beginning with the A in the start codon. For 16S rRNA, minus (−) and positive (+) positions flank the sequence used in the analysis.