Table 2.
Primer sequences and parameters
| Target | Primer sequences (5′→3′) | Products size, bp | T a a, °C | Reference |
|---|---|---|---|---|
| Total bacterial | Fb: CGGCAACGAGCGCAACCC | 130 | 60.0 | Denman and Mcsweeney (2006) |
| Rc: CCATTGTAGCACGTGTGTAGCC | ||||
| Total fungi | F: GCACTTCATTGTGTGTACTG | 120 | 60.0 | Denman and Mcsweeney (2006) |
| R: GGATGAAACTCGTTGACTTC | ||||
| Total protozoa | F: GCTTTCGWTGGTAGTGTATT | 223 | 55.0 | Sylvester et al. (2004) |
| R: CTTGCCCTCYAATCGTWCT | ||||
| Ruminococcus albus | F: CCCTAAAAGCAGTCTTAGTTCG | 176 | 55.0 | Koike and Kobayashi (2001) |
| R: CCTCCTTGCGGTTAGAACA | ||||
| Ruminococcus flavefaciens | F: CGAACGGAGATAATTTGAGTTTACTTAGG | 132 | 60.0 | Denman and Mcsweeney (2006) |
| R: CGGTCTCTGTATGTTATGAGGTATTACC | ||||
| Fibrobacter succinogenes | F: GTTCGGAATTACTGGGCGTAAA | 121 | 60.0 | Denman and Mcsweeney (2006) |
| R: CGCCTGCCCCTGAACTATC | ||||
| Butyrivibrio fibrisolvens | F: TCTGGAAACGGATGGTA | 295 | 55.0 | Koike and Kobayashi (2001) |
| R: CCTTTAAGACAGGAGTTTACAA | ||||
| Streptococcus bovis | F: TTCCTAGAGATAGGAAGTTTCTTCGG | 127 | 60.0 | Stevenson and Weimer (2007) |
| R: ATGATGGCAACTAACAATAGGGGT | ||||
| Prevotella ruminicola | F: GGTTATCTTGAGTGAGTT | 485 | 53.0 | Tajima et al. (2001) |
| R: CTGATGGCAACTAAAGAA | ||||
| Ruminobacter amylophilus | F: CAACCAGTCGCATTCAGA | 642 | 57.0 | Tajima et al. (2001) |
| R: CACTACTCATGGCAACAT |
a T a = optimal PCR annealing temperature.
bF = forward.
cR = reverse.