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

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

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]
Total bacteria	1525r	AAG GAG GTG WTC CAR CC	55	1535	[41]
Total bacteria	Eub358f	TCC TAC GGG AGG CAG CAG T	60	448	[42]
Total bacteria	Eub806r	GGA CTA CCA GGG TAT CTA ATC CTG TT	60	448	[42]
	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]
Archaea	ARC1059r	GCC ATG CAC CWC CTC T	60	272	[16]
Protozoa	316f	GCT TTC GWT GGT AGT GTA TT	54	223	[43]
Protozoa	539r	CTT GCC CTC YAA TCG TWC T	54	223	[43]
Fibrobacter succinogenes	Fs219f	GGT ATG GGA TGA GCT TGC	63	446	[44]
Fibrobacter succinogenes	Fs654r	GCC TGC CCC TGA ACT ATC	63	446	[44]
Ruminococcus flavefaciens	Rf154f	TCT GGA AAC GGA TGG TA	55	295	[44]
Ruminococcus flavefaciens	Rf425r	CCT TTA AGA CAG GAG TTT ACA A	55	295	[44]
Ruminococcus albus	Ra1281f	CCC TAA AAG CAG TCT TAG TTC G	55	175	[44]
Ruminococcus albus	Ra1439r	CCT CCT TGC GGT TAG AAC A	55	175	[44]
Prevotella spp.	BAC303f	GAA GGT CCC CCA CAT TG	56	418	[45]
Prevotella spp.	BAC708r	CAA TCG GAG TTC TTC GTG	56	418	[45]
Clostridium aminophilum	C.amin-57 F	ACG GAA ATT ACA GAA GGA AG	57	560	[46]
Clostridium aminophilum	C.amin-616R	GTT TCC AAA GCA ATT CCA C	57	560	[46]
PCR-DGGE
Total bacteria	GC-A357f	CCC TAC GGG GCG CAG CAG	61 → 56 °C	194	[17]
Total bacteria	519r	GWA TTA CCG CGG CKG CTG	61 → 56 °C	194	[17]
Archaea	GC-RC344f	ACG GGG YGC AGC AGG CGC GA	61 → 56 °C	191	[18]
Archaea	519r	GWA TTA CCG CGG CKG CTG	61 → 56 °C	191	[18]

ISSN: 2049-1891