Table 1.
Summary of qPCR assay primer and probe sequences, targets, annealing temperatures, and references.
| qPCR Assay | Primer and Probe Sequences (5′ → 3′) | Target | Anneal Temp | Reference |
|---|---|---|---|---|
| Entero1a | F: GAGAAATTCCAAACGAACTTG R: CAGTGCTCTACCTCCATCATT P: [FAM]TGGTTCTCTCCGAAATAGCTTTAGGGCTA[TAMRA] |
Enterococci | 60°C | (Ludwig and Schleifer 2000, Siefring et al. 2008) |
| EC23S857 | F: GGTAGAGCACTGTTTTGGCA R: TGTCTCCCGTGATAACTTTCTC P: [FAM]TCATCCCGACTTACCAACCCG[TAMRA] |
E. coli | 56 °C | (Chern et al. 2011) |
| HF183/ BacR287 | F: ATCATGAGTTCACATGTCCG R: CTTCCTCTCAGAACCCCTATCC P: [FAM]CTGAGAGGAAGGTCCCCCACATTGGA[MGB] PIAC: [VIC]AACACGCCGTTGCTACA[MGB] |
Human fecal waste | 60°C | (Green et al. 2014a) |
| HumM2 | F: CGTCAGGTTTGTTTCGGTATTG R: TCATCACGTAACTTATTTATATGCATTAGC P: [FAM]TATCGAAAATCTCACGGATTAACTCTTGTGTACGC[TAMRA] PIAC: [VIC]CCTGCCGTCTCGTGCTCCTCA[TAMRA] |
60°C | (Shanks et al. 2009) | |
| CPQ_056 | F: CAGAAGTACAAACTCCTAAAAAACGTAGAG R: GATGACCAATAAACAAGCCATTAGC P: [FAM]AATAACGATTTACGTGATGTAAC[MGB] |
60°C | (Stachler et al. 2017) | |
| CPQ_064 | F:TGTATAGATGCTGCTGCAACTGTACTC R: CGTTGTTTTCATCTTTATCTTGTCCAT P: [FAM]CTGAAATTGTTCATAAGCAA[MGB] |
60°C | ||
| Rum2Bac | F:ACAGCCCGCGATTGATACTGGTAA R: CAATCGGAGTTCTTCGTGAT P: [FAM]ATGAGGTGGATGGAATTCGTGGTGT[BHQ-1] |
Ruminant fecal waste | 60°C | (Mieszkin et al. 2010) |
| CowM2 | F: CGGCCAAATACTCCTGATCGT R: GCTTGTTGCGTTCCTTGAGATAAT P: [FAM]AGGCACCTATGTCCTTTACCTCATCAACTACAGACA[TAMRA] PIAC: [VIC]TAGGAACAGGCGGCGACGA[TAMRA] |
Cattle fecal waste | 60°C | (Shanks et al. 2008) |
| CowM3 | F: CCTCTAATGGAAAATGGATGGTATCT R: CCATACTTCGCCTGCTAATACCTT P: [FAM]TTATGCATTGAGCATCGAGGCC[TAMRA] |
60°C | ||
| DG3 | F: TGAGCGGGCATGGTCATATT R: TTTTCAGCCCCGTTGTTTCG P: [FAM]AGTCTACGCGGGCGTACT[MGB] |
Canine fecal waste | 60°C | (Green et al. 2014b) |
| DG37 | F: CTTGGTTATGGGCGACATTG R: TTTTCTCCCACGGTCATCTG P: [FAM]TTGAACGTTTAAAGGAGCAGGTGGCAG[TAMRA] |
60°C | ||
| Pig2Bac | F: GCATGAATTTAGCTTGCTAAATTTGAT R: ACCTCATACGGTATTAATCCGC P: [FAM]TCCACGGGATAGCC[MGB] |
Swine fecal waste | 60°C | (Mieszkin et al. 2009) |
| GFD | F: TCGGCTGAGCACTCTAGGG R: GCGTCTCTTTGTACATCCCA |
Avian fecal waste | 57 °C | (Green et al. 2012) |
‘Anneal Temp’ indicates qPCR assay annealing temperature.
PIAC denotes the internal amplification control (IAC) probe in multiplex qPCR assay.