Table 3.

Comparison of Ruminococcus flavefaciens percentage by real-time PCR and MG-RAST analysis for same samples processed by shotgun and amplicon sequencing

		Ruminococcus flavefaciens (% ± SD)
Sample		qPCR	Shotgun	Amplicon
50% roughage	GL	0.45 ± 0.002	0.18 ± 0.0009	0.35 ± 0.002
	DL	0.45 ± 0.002	0.10 ± 0.000	0.30 ± 0.0008
	GS	1.33 ± 0.006	0.50 ± 0.0008	0.98 ± 0.0005
	DS	0.58 ± 0.004	0.53 ± 0.0009	1.07 ± 0.008
75% roughage	GL	0.40 ± 0.002	0.20 ± 0.000	0.30 ± 0.000
	DL	0.48 ± 0.001	0.23 ± 0.0005	0.40 ± 0.000
	GS	0.55 ± 0.004	0.35 ± 0.001	1.00 ± 0.000
	DS	0.77 ± 0.004	0.38 ± 0.0005	1.00 ± 0.000
100% roughage	GL	0.20 ± 0.010	0.15 ± 0.0005	0.35 ± 0.001
	DL	0.25 ± 0.002	0.25 ± 0.0005	0.75 ± 0.001
	GS	0.24 ± 0.0008	0.30 ± 0.000	0.85 ± 0.008
	DS	0.63 ± 0.005	0.60 ± 0.0008	1.33 ± 0.005

GL = Green liquid, DL = Dry liquid, GS = Green solid, DS = Dry solid.