TABLE 2.
Primers used in the qPCR assay.
| Target (amplicon size) | Primer | Sequence (5′–3′) | Annealing temperature (°C) | References |
| Campylobacter spp. (108 bp) | R-campF2 | CAC GTG CTA CAA TGG CAT AT | 62 | Lund et al., 2004 |
| R-campR2 | GGC TTC ATG CTC TCG AGT T | |||
| Blautia spp. (250 bp) | BlautiaF | TCTGATGTGAAAGGCTGGGGCTTA | 59 | Suchodolski et al., 2012 |
| BlautiaR | GGCTTAGCCACCCGACACCTA | |||
| Turicibacter spp. (140 bp) | TuriciF | CAGACGGGGACAACGATTGGA | 62 | Suchodolski et al., 2012 |
| TuriciR | TACGCATCGTCGCCTTGGTA | |||
| Clostridium cluster I (231 bp) | CloI-F | TACCHRAGGAGGAAGCCAC | 62 | Song et al., 2004 |
| CloI-R | GTTCTTCCTAATCTCTACGCAT | |||
| Clostridium cluster XIV (157 bp) | CloXIV-F | GAWGAAGTATYTCGGTATGT | 59 | Song et al., 2004 |
| CloXIV-R | CTACGCWCCCTTTACAC | |||
| Escherichia coli (340 bp) | Coli_F | GTTAATACCTTTGCTCATTGA | 59 | Malinen et al., 2003 |
| Coli_R | ACCAGGGTATCTAATCCTGTT | |||
| Ruminococcaceae (258 bp) | Rumi_F | ACTGAGAGGTTGAACGGCCA | 64 | Garcia-Mazcorro et al., 2012 |
| Rumi_R | CCTTTACACCCAGTAAWTCCGGA | |||
| Campylobacter jejuni (124 bp) | CjejF | TGCACCAGTGACTATGAATAACGA | 62 | He et al., 2010 |
| CjejR | TCCAAAATCCTCACTTGCCATT | |||
| Campylobacter lari (86 bp) | ClariF | TTAGATTGTTGTGAAATAGGCGAGTT | 59 | He et al., 2010 |
| ClariR | TGAGCTGATTTGCCTATAAATTCG |