TABLE 1.
Primers and probes used in this study
| Oligonucleotide primer or probea | Final Rx concn (nM)b | Sequence (5′ to 3′) | Assay | No. of exact sequence matches/total no. of sequences (%)c
|
|||
|---|---|---|---|---|---|---|---|
| Enterobacterales | Proteobacteria (non-Enterobacterales) | Firmicutes | Bacterioidetes | ||||
| MGB_ENT_GG_Probe (FAM) | 250 | TACCTGGTCTTGACATCCA | Both | 62/319 (19.4) | 59/4,273 (1.4) | 0/2,438 (0) | 0/1,315 (0) |
| MGB_ENT_AC_Probe (FAM) | 250 | TTACCTACTCTTGACATCCA | Both | 212/319 (66.4) | 353/4,273 (8.3) | 0/2,438 (0) | 0/1,315 (0) |
| MGB_Uniprobe _p1 (VIC) | 250 | ACGAGCTGACGACARC | A | 314/319 (98.4) | 4,120/4,273 (96.4) | 2,357/2,438 (96.7) | 1,254/1,315 (95.4) |
| Uniprobe_B (VIC) | 250 | ATTGACGGGGRCCCGCACAAG | B | 315/319 (98.7) | 3,762/4,273 (88.0) | 2,327/2,438 (95.4) | 1,034/1,315 (78.6) |
| Forward primer A (P891F) | 900 | TGGAGCATGTGGTTTAATTCGA | A | 312/319 (97.8) | 3,214/4,273 (75.2) | 16,83/2,438 (69.0) | 818/1,315 (62.2) |
| Reverse primer A (p1022R) | 900 | TGCGGGACTTAACCCAACA | A | 316/319 (99.1) | 3,192/4,273 (75.3) | 2,259/2,438 (92.7) | 478/1,315 (36.3) |
| Forward primer B (F785) | 900 | GGATTAGATACCCTGGTAGTCC | B | 316/319 (99.1) | 4,138/4,273 (96.8) | 2,214/2,438 (90.8) | 1,194/1,315 (90.8) |
| Reverse primer B (R1097 – P2) | 900 | GAGCTGACGACARCCATGC | B | 314/319 (98.4) | 3,980/4,273 (93.1) | 2,329/2,438 (95.5) | 1,256/1,315 (95.5) |
a
FAM, 6-carboxyfluorescein.
b
Rx, reaction.
c
Matching 16S sequences from type strains, isolates, size ≥1,200, and good quality in RDP release 11.5.