Table 1.

Primer sets used in the real time PCR analysis of ruminal microbiota^a.

Target taxon	Primer set	Primer sequence 5′–3′	References
Total archaea	Arch f	GYGCAGCAGGCGCGAAA	Zeitz et al., 2012
	Arch r	GGACTACCSGGGTATCTAAT
Total fungi	Denfun f	GAGGAAGTAAAAGTCGTAACAAGGTTTC	Denman and McSweeney, 2006
	Denfun r	CAAATTCACAAAGGGTAGGATGATT
Total protozoa	PSSU-316f	GCTTTCGWTGGTAGTGTATT	Sylvester et al., 2004
	PSSU-316f	CTTGCCCTCYAATCGTWCT
Total bacteria	Denbac f	CGGCAACGAGCGCAACCC	Denman and McSweeney, 2006
	Denbac r	CCATTGTAGCACGTGTGTAGCC
mcrA geneb	qmcrA F	TTCGGTGGATCDCARAGRGC	Denman et al., 2007
	qmcra R	GBARGTCGWAWCCGTAGAATCC
Fibrobacter	Fisu f	GGRCGGGATTGAATGTAC	Zeitz et al., 2012
succinogenes	Fisu r	AATCCGCTTGAATCTCCG
Ruminococcus	Ra1281 f	CCCTAAAAGCAGTCTTAGTTCG	Koike and Kobayashi, 2001
albus	Ra1439 r	CCTCCTTGCGGTTAGAACA
Ruminococcus	Rflav f	TGTCCCAGTTCAGATTGCAG	Zeitz et al., 2012
flavefaciens	Rflav r	GGCGTCCTCATTGCTGTTAG

^aqPCR was run at an annealing temperature of 60°C for all primers.

^bmcrA gene: methyl-coenzyme M reductase alpha subunit gene.