TABLE 5.

Effect of dietary treatments^a on the abundant archaea species^b during the three measurement phases^c.

Species	P01
	CO	95% CI (UL–LL)	FO	95% CI (UL–LL)	P-val
Methanomassiliicoccales Group 10 sp.	0.15	(0.053–0.451)	0.61	(0.210–1.789)	0.073
Methanobrevibacter.boviskoreani.clade	64.03	(47.111–87.013)	0.05	(0.036–0.067)	<0.001
Methanobrevibacter.gottschalkii.clade	2.53	(1.332–4.812)	57.40	(30.195–109.124)	<0.001
Methanobrevibacter.ruminantium.clade	0.81	(0.272–2.416)	24.36	(8.177–72.556)	<0.001
Methanosphaera sp. A4	8.58	(4.322–17.029)	0.05	(0.027–0.106)	<0.001
Methanosphaera sp. Group 5	4.35	(2.719–6.954)	1.73	(1.084–2.772)	0.009
Methanosphaera sp. ISO3_F5	0.07	(0.032–0.144)	4.35	(2.062–9.194)	<0.001
	P02
Species	CO	95% CI (UL–LL)	FO	95% CI (UL–LL)	HQ	95% CI (UL–LL)	LQ	95% CI (UL–LL)	P-T1	P-T2	P-int
Methanomassiliicoccales Group 10 sp.	1.69	(0.889–3.201)	1.48	(0.777–2.799)	0.56	(0.297–1.070)	4.41	(2.325–8.372)	0.761	<0.001	0.966
Methanobrevibacter boviskoreani.clade	0.06	(0.023–0.149)	0.03	(0.012–0.075)	0.04	(0.014–0.088)	0.05	(0.020–0.128)	0.294	0.564	0.586
Methanobrevibacter gottschalkii.clade	58.91	(51.408–67.507)	65.36	(57.035–74.896)	58.16	(50.750–66.643)	66.21	(57.775–75.867)	0.274	0.176	0.787
Methanobrevibacter.ruminantium.clade	10.25	(5.966–17.622)	10.35	(6.020–17.782)	10.61	(6.172–18.229)	10.00	(5.820–17.191)	0.981	0.875	0.847
Methanosphaera sp. A4	0.08	(0.034–0.184)	0.06	(0.024–0.133)	0.13	(0.055–0.299)	0.04	(0.015–0.082)	0.577	0.036	0.327
Methanosphaera sp. Group 5	9.03	(5.219–15.626)	5.76	(3.327–9.960)	14.94	(8.636–25.853)	3.48	(2.011–6.020)	0.240	<0.001	0.373
Methanosphaera sp. ISO3_F5	3.34	(1.885–5.9226)	3.36	(1.894–5.948)	6.13	(3.460–10.870)	1.83	(1.032–3.241)	0.991	0.005	0.323
Species	P03
	CO	95% CI (UL–LL)	FO	95% CI (UL–LL)	HQ	95% CI (UL–LL)	LQ	95% CI (UL–LL)	P-T1	P-T2	P-int
Methanomassiliicoccales Group 10 sp.	4.65	(3.189–6.787)	4.60	(3.154–6.712)	3.55	(2.433–5.179)	6.03	(4.133–8.797)	0.966	0.052	0.882
Methanobrevibacter.boviskoreani.clade	0.04	(0.025–0.066)	0.03	(0.021–0.056)	0.05	(0.030–0.080)	0.03	(0.018–0.046)	0.628	0.113	0.016
Methanobrevibacter.gottschalkii.clade	64.56	(60.961–68.375)	64.22	(60.635–68.008)	62.89	(59.380–66.602)	65.93	(62.249–69.819)	0.892	0.239	0.937
Methanobrevibacter.ruminantium.clade	11.94	(9.892–14.405)	11.99	(9.933–14.464)	15.35	(12.719–18.521)	9.32	(7.725–11.250)	0.975	<0.001	0.833
Methanosphaera sp. A4	0.04	(0.009–0.133)	0.04	(0.009–0.130)	0.04	(0.010–0.143)	0.03	(0.009–0.121)	0.982	0.860	0.674
Methanosphaera sp. Group 5	3.01	(2.116–4.283)	2.44	(1.717–3.476)	2.40	(1.689–3.420)	3.06	(2.151–4.354)	0.393	0.324	0.200
Methanosphaera sp. ISO3_F5	6.92	(5.061–9.453)	10.27	(7.517–14.042)	8.93	(6.531–12.200)	7.96	(5.825–10.881)	0.077	0.595	0.668

^aDietary treatments corresponded to phase 1 (P01) concentrate (CO) vs. pasture (FO) diets and phase 2 (P02) high-quality (HQ) vs. low-quality (LQ) pastures, with measurements in P01 (9 weeks), P02 (19 weeks), and phase 3 (P03; 41 weeks) when all calves were offered a common pasture diet.

^bMeasured effect corresponded to the seven archaeal species with a relative abundance > 1.00% across rumen samples.

^cDietary treatments in each phase were evaluated as follows: a one-way ANOVA in P01 to analyze FO vs. CO diets and a 2 × 2 factorial ANOVA in P02 and P03 to evaluate FO vs. CO and HQ vs. LQ dietary treatment effects and their interactions.