TABLE 1.
Primers and probes used for qPCR assays
| Assay name | Primer or probe | Primer or probe sequence (5′–3′)a | Target organism | Reference |
|---|---|---|---|---|
| Salmon | Forward primer | GGTTTCCGCAGCTGGG | Salmon (Oncorhynchus keta) testes | 56 |
| Reverse primer | CCGAGCCGTCCTGGTCTA | |||
| Probe | FAM-AGTCGCAGGCGGCCACCGT-TAMRA | |||
| Entero1 | Forward primer | AGAAATTCCAAACGAACTTG | Enterococcus | 57 |
| Reverse primer | CAGTGCTCTACCTCCATCATT | |||
| Probe | FAM-TGGTTCTCTCCGAAATAGCTTTAGGGCTA-TAMRA | |||
| EPA-EC 23S | Forward primer | GGTAGAGCACTGTTTTGGCA | E. coli | 58 |
| Reverse primer | TGTCTCCCGTGATAACTTTCTC | |||
| Probe | FAM-TCATCCCGACTTACCAACCCG-TAMRA | |||
| Genbac | Forward primer | GGGGTTCTGAGAGGAAGGT | Bacteroidales | 28 |
| Reverse primer | CCGTCATCCTTCACGCTACT | |||
| Probe | VIC-CAATATTCCTCACTGCTGCCTCCCGTA-Iowa Black | |||
| CowM3 | Forward primer | CCTCTAATGGAAAATGGATGGTATCT | Cattle-associated microbial population | 29 |
| Reverse primer | CCATACTTCGCCTGCTAATACCTT | |||
| Probe | FAM-TTATGCATTGAGCATCGAGGCC-TAMRA | |||
| Rum-2-bac | Forward primer | ACAGCCCGCGATTGATACTGGTAA | Ruminant-associated microbial population | 30 |
| Reverse primer | CAATCGGAGTTCTTCGTGAT | |||
| Probe | FAM-ATGAGGTGGATGGAATTCGTGGTGT- TAMRA |
a
FAM, 6-carboxyfluorescein; TAMRA, 6-carboxytetramethylrhodamine.