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Table 2 Primers used to quantify ruminal microbes (qPCR) and to profile bacterial and archaeal communities (DGGE)

From: Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations

Organisms Primers Sequences (5′ → 3′) Annealing temperature, °C Amplicon length, bp References
Real-time PCR
 Total bacteria 27f AGA GTT TGA TCM TGG CTC AG 55 1535 [41]
1525r AAG GAG GTG WTC CAR CC
 Total bacteria Eub358f TCC TAC GGG AGG CAG CAG T 60 448 [42]
Eub806r GGA CTA CCA GGG TAT CTA ATC CTG TT
  TaqMan probe 6-FAM-5′-CGT ATT ACC GCG GCT GCT GGC AC-3′-TAMRA 70   
 Archaea ARC787f ATT AGA TAC CCS BGT AGT CC 60 272 [16]
ARC1059r GCC ATG CAC CWC CTC T
 Protozoa 316f GCT TTC GWT GGT AGT GTA TT 54 223 [43]
539r CTT GCC CTC YAA TCG TWC T
 Fibrobacter succinogenes Fs219f GGT ATG GGA TGA GCT TGC 63 446 [44]
Fs654r GCC TGC CCC TGA ACT ATC
 Ruminococcus flavefaciens Rf154f TCT GGA AAC GGA TGG TA 55 295 [44]
Rf425r CCT TTA AGA CAG GAG TTT ACA A
 Ruminococcus albus Ra1281f CCC TAA AAG CAG TCT TAG TTC G 55 175 [44]
Ra1439r CCT CCT TGC GGT TAG AAC A
 Prevotella spp. BAC303f GAA GGT CCC CCA CAT TG 56 418 [45]
BAC708r CAA TCG GAG TTC TTC GTG
 Clostridium aminophilum C.amin-57 F ACG GAA ATT ACA GAA GGA AG 57 560 [46]
C.amin-616R GTT TCC AAA GCA ATT CCA C
PCR-DGGE
 Total bacteria GC-A357f CCC TAC GGG GCG CAG CAG 61 → 56 °C 194 [17]
519r GWA TTA CCG CGG CKG CTG
 Archaea GC-RC344f ACG GGG YGC AGC AGG CGC GA 61 → 56 °C 191 [18]
519r GWA TTA CCG CGG CKG CTG
  1. FAM: 6-carboxyfluorescein; TAMRA: 6-carboxytetramethylrhodamine