Table 2.

Classification of rumen methanogen 16S rRNA sequence reads to taxa from Holstein, Jersey, Holstein-Jersey crossbreed dairy cows at 3, 93, 183, and 273 days in milk

DIMb	3			93			183			273			SE	Significancea
Breed	H	J	X	H	J	X	H	J	X	H	J	X		B	DIM	B x DIM
Methanobrevibacter	99.30	96.15	99.42	98.08	99.02	99.10	97.28	98.25	94.81	99.23	98.39	98.87	0.99	NS	†	NS
Mbr c woesei	2.12	2.47	1.58	1.03	1.10	1.12	0.59	0.86	0.69	1.06	0.94	1.03	0.22	NS	***	NS
Mbr. smithii	28.55	28.09	35.72	27.12	29.75	36.21	32.72	30.72	31.90	27.25	32.57	35.91	3.64	†	NS	NS
Mbr. gottschalkii	0.04	0.02	0.05	0.80	0.11	0.28	0.25	0.14	0.21	0.80	0.19	0.30	0.17	NS	*	NS
Mbr. millerae	10.99	8.39	8.0	5.17	7.04	7.80	7.45	8.55	6.08	5.02	8.72	7.45	1.15	NS	*	*
Mbr. thaueri	30.70	26.70	30.32	24.51	35.03	19.43	28.03	32.34	26.93	35.30	37.09	36.36	3.51	NS	*	***
SGMT Clade	70.29	63.15	74.49	57.45	71.93	63.71	68.45	71.74	65.13	68.37	78.56	80.02	5.81	NS	NS	NS
Mbr. ruminantium	26.18	29.82	22.88	38.73	25.31	33.45	27.43	24.92	28.38	29.01	18.41	17.24	5.41	NS	†	NS
Mbr. olleyae	0.36	0.37	0.19	0.48	0.35	0.46	0.47	0.35	0.33	0.44	0.23	0.29	0.08	NS	NS	NS
RO Clade	26.54	30.02	23.07	39.21	25.66	33.92	27.91	25.29	28.71	29.45	18.64	17.53	5.50	NS	†	NS
Methanosphaera	0.41	0.43	0.42	1.01	0.41	0.74	0.50	0.38	0.64	0.46	0.41	0.28	0.10	†	**	*
Methanoplasmatales	0.15	2.02	0.07	0.49	0.15	0.03	0.90	0.31	1.93	0.22	0.41	0.45	0.45	NS	NS	*
Methanosarcinales	0.08	1.33	0.08	0.35	0.37	0.12	1.16	0.99	2.27	0.01	0.55	0.19	0.51	NS	**	NS

^a P-value of the effects due to breed (Holstein, Jersey, and Holstein-Jersey crossbreed) and their interaction and comparison to time period (3, 93, 183, and 273 DIM)

^bDays in milk (DIM), H = Holstein (n = 7), J = Jersey (n = 8), X = Holstein-Jersey crossbreed (n = 7), Breed (B), ^c Mbr = Methanobrevibacter

*** P < 0.001; ** P < 0.01; * P < 0.05; † 0.05 ≤ P ≤ 0.10; no significance (NS) P > 0.10