Populations of Select Cultured and Uncultured Bacteria in the Rumen of Sheep and the Effect of Diets and Ruminal Fractions

Table 2

Primers and probe used for real-time PCR quantification of recognized rumen bacterial species, genera, or uncultured bacteria.

Primers	Sequences (5^′→3^′)	Target	Annealing temperature (°C)	Amplicon length (bp)	References
27f	AGA GTT TGA TCM TGG CTC AG	Bacteria	54	1,535	[19]
1525r	AAG GAG GTG WTC CAR CC
340f	TCC TAC GGG AGG CAG CAG T	Bacteria	60	467	[20]
806r	GGA CTA CCA GGG TAT CTA ATC CTG TT
TaqMan probe	6-FAM-5′-CGT ATT ACC GCG GCT		70
	GCT GGC AC-3′-TAMRA
Bac303f	GAA GGT CCC CCA CAT TG	Bacteroides and Prevotella	56	418	[21]
Bac708r	CAA TCG GAG TTC TTC GTG
ARC787F	ATT AGA TAC CCS BGT AGT CC	Archaea	60	273	[22]
ARC1059R	GCC ATG CAC CWC CTC T
Ra1281f	CCC TAA AAG CAG TCT TAG TTC G	R. albus	55	175	[23]
Ra1439r	CCT CCT TGC GGT TAG AAC A
Fs-f	GGT ATG GGA TGA GCT TGC	F. succinogenes	63	446	[24]
Fs-r	GCC TGC CCC TGA ACT ATC
530f	GTG CCA GCM GCC GCG G	Butyrivibrio	65	371	[19] and this study
Buty-900r	TGC GGC ACY GAC TCC CTA TG
Sel-Mit-f	TGC TAA TAC CGA ATG TTG	S. ruminantium and M. multacida	53	513	[24]
Sel-Mit-r	TCC TGC ACT CAA GAA AGA
Ram-f	CAA CCA GTC GCA TTC AGA	Ruminobacter amylophilus	57	642	[24]
Ram-r	CAC TAC TCA TGG CAA CAT
Rf154f-K	TCT GGA AAC GGA TGG TA	R. flavefaciens	55	295	[23]
Rf425r-K	CCT TTA AGA CAG GAG TTT ACA A