Table 2.
Primers used in the qPCR assay.
| Target species | Primer | Sequence (5′→3′) | Annealing temperature (°C) | Reference |
|---|---|---|---|---|
| Total bacteria (194 bp) | UniF | CCTACGGGAGGCAGCAG | 62 | Muyzer de Waal and Uitterlinden (1993) |
| UniR | ATTACCGCGGCTGCTGG | |||
| Clostridium cluster I (231 bp) | CI-F1 | TACCHRAGGAGGAAGCCA | 59 | Song, Liu and Finegold (2004) |
| CI-R2 | GTTCTTCCTAATCTCTACGCAT | |||
| Lactobacillus spp. (341 bp) | LacF | AGCAGTAGGGAATCTTCCA | 64 | Malinen et al. (2005) |
| LacR | CACCGCTACACATGGAG | |||
| Bifidobacterium spp. (243 bp) | BifF | TCGCGTCYGGTGTGAAAG | 56 | Rinttila et al. (2004) |
| BifR | CCACATCCAGCRTCCAC | |||
| Escherichia coli (340 bp) | E. coli Fw | GTTAATACCTTTGCTCATTGA | 59 | Malinen et al. (2003) |
| E. coli Rv | ACCAGGGTATCTAATCCTGTT | |||
| Faecalibacterium prausnitzii (140 bp) | Fprau 07 | CCATGAATTGCCTTCAAAACTGTT | 59 | Sokol et al. (2009) |
| Fprau 02 | GAGCCTCAGCGTCAGTTGGT | |||
| Enterococcus spp. (144 bp) | EnteroF | CCCTTATTGTTAGTTGCCATCATT | 59 | Rinttila et al. (2004) |
| EnteroR | ACTCGTTGTACTTCCCATTGT |