TABLE 4.

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

Genus	P01
	CO	95% CI (UL–LL)	FO	95% CI (UL–LL)	P-val
Bacteroidales BS11 gut group	0.02	(0.014–0.041)	1.51	(0.875–2.592)	<0.0001
Bacteroidales RF16 group	0.00	(0.002–0.004)	0.86	(0.584–1.277)	<0.0001
Bacteroidales S24-7 group	0.25	(0.161–0.392)	1.48	(0.945–2.308)	<0.0001
Prevotella 1	0.78	(0.321–1.893)	39.31	(16.199–95.412)	<0.0001
Prevotella 7	18.38	(7.415–45.541)	0.35	(0.142–0.874)	<0.0001
Prevotellaceae UCG-001	0.87	(0.443–1.701)	0.86	(0.440–1.686)	0.9852
Prevotellaceae UCG-003	0.00	(0.003–0.006)	1.17	(0.758–1.808)	<0.0001
Rikenellaceae RC9 gut group	0.23	(0.162–0.319)	1.66	(1.185–2.331)	<0.0001
Fibrobacter	0.01	(0.005–0.036)	0.40	(0.152–1.053)	<0.0001
Christensenellaceae R-7 group	0.09	(0.056–0.142)	2.94	(1.836–4.697)	<0.0001
Butyrivibrio 2	0.01	(0.006–0.012)	0.41	(0.277–0.595)	<0.0001
Lachnospiraceae NK3A20 group	5.95	(3.206–11.04)	1.96	(1.054–3.630)	0.0150
Pseudobutyrivibrio	0.19	(0.114–0.302)	0.73	(0.451–1.196)	0.0004
Roseburia	6.59	(3.899–11.127)	0.67	(0.398–1.136)	<0.0001
[Eubacterium] coprostanoligenes group	0.30	(0.220–0.408)	0.94	(0.690–1.281)	<0.0001
Ruminiclostridium 9	0.00	(0.003–0.008)	2.71	(1.555–4.712)	<0.0001
Ruminococcaceae NK4A214 group	0.07	(0.043–0.107)	1.89	(1.204–2.970)	<0.0001
Ruminococcaceae UCG-014	1.27	(0.813–1.981)	0.97	(0.624–1.520)	0.3932
Ruminococcus 1	0.55	(0.308–0.985)	2.10	(1.176–3.767)	0.0027
Saccharofermentans	0.00	(0.002–0.006)	0.74	(0.410–1.321)	<0.0001
Erysipelotrichaceae UCG-002	3.78	(0.824–17.337)	0.09	(0.020–0.421)	0.0017
Kandleria	0.00	(0.001–0.008)	1.82	(0.785–4.195)	<0.0001
Succiniclasticum	2.21	(1.634–2.981)	0.95	(0.705–1.286)	0.0005
Selenomonas 1	0.01	(0.007–0.020)	0.89	(0.537–1.470)	<0.0001
Mollicutes RF9	0.28	(0.160–0.490)	0.80	(0.459–1.411)	0.0114
	P02
	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
Bacteroidales BS11 gut group	2.59	(1.858–3.613)	3.28	(2.351–4.572)	1.72	(1.232–2.395)	4.9	(3.546–6.896)	0.309	0.000	0.692
Bacteroidales RF16 group	0.88	(0.526–1.488)	0.90	(0.538–1.522)	0.63	(0.376–1.064)	1.3	(0.752–2.129)	0.950	0.063	0.981
Bacteroidales S24-7 group	1.07	(0.716–1.597)	1.33	(0.892–1.989)	0.87	(0.582–1.298)	1.6	(1.098–2.447)	0.429	0.030	0.651
Prevotella 1	35.27	(30.002–41.453)	35.13	(29.884–41.291)	37.82	(32.174–44.455)	32.8	(27.867–38.504)	0.972	0.205	0.620
Prevotella 7	0.06	(0.034–0.093)	0.06	(0.039–0.106)	0.11	(0.069–0.189)	0.0	(0.019–0.053)	0.706	0.001	0.990
Prevotellaceae UCG-001	2.85	(1.997–4.065)	2.16	(1.512–3.078)	2.92	(2.045–4.162)	2.1	(1.477–3.007)	0.262	0.192	0.224
Prevotellaceae UCG-003	1.82	(1.312–2.511)	2.60	(1.883–3.602)	1.46	(1.053–2.014)	3.2	(2.347–4.491)	0.116	0.002	0.305
Rikenellaceae RC9 gut group	4.27	(3.432–5.324)	4.62	(3.707–5.751)	3.62	(2.904–4.505)	5.5	(4.381–6.796)	0.610	0.012	0.254
Fibrobacter	0.57	(0.377–0.851)	0.53	(0.351–0.792)	0.22	(0.144–0.324)	1.4	(0.921–2.080)	0.798	<0.0001	0.512
Christensenellaceae R-7 group	6.55	(5.607–7.656)	7.67	(6.562–8.961)	5.74	(4.913–6.709)	8.8	(7.489–10.225)	0.152	0.001	0.090
Butyrivibrio 2	0.92	(0.624–1.357)	0.93	(0.634–1.377)	1.41	(0.955–2.077)	0.6	(0.414–0.900)	0.955	0.005	0.636
Lachnospiraceae NK3A20 group	1.86	(1.449–2.382)	2.17	(1.696–2.789)	2.26	(1.763–2.897)	1.8	(1.395–2.293)	0.361	0.180	0.341
Pseudobutyrivibrio	1.13	(0.835–1.530)	1.05	(0.778–1.425)	1.61	(1.187–2.173)	0.7	(0.548–1.003)	0.734	0.001	0.454
Roseburia	0.34	(0.225–0.502)	0.27	(0.180–0.403)	0.72	(0.479–1.069)	0.1	(0.085–0.189)	0.431	<0.0001	0.561
[Eubacterium] coprostanoligenes group	1.07	(0.897–1.284)	1.16	(0.973–1.393)	1.00	(0.839–1.201)	1.2	(1.040–1.490)	0.511	0.093	0.036
Ruminiclostridium 9	0.59	(0.336–1.022)	0.62	(0.356–1.083)	1.34	(0.767–2.333)	0.3	(0.156–0.474)	0.881	0.000	0.672
Ruminococcaceae NK4A214 group	1.93	(1.559–2.382)	2.09	(1.691–2.585)	2.41	(1.949–2.979)	1.7	(1.352–2.067)	0.577	0.019	0.946
Ruminococcaceae UCG-014	1.35	(1.048–1.727)	1.15	(0.896–1.476)	1.21	(0.939–1.547)	1.3	(1.000–1.647)	0.364	0.715	0.925
Ruminococcus 1	1.14	(0.943–1.371)	0.99	(0.822–1.194)	0.90	(0.750–1.090)	1.2	(1.033–1.502)	0.290	0.020	0.448
Saccharofermentans	0.78	(0.635–0.962)	0.68	(0.548–0.831)	0.59	(0.478–0.723)	0.9	(0.730–1.105)	0.309	0.007	0.136
Erysipelotrichaceae UCG-002	0.01	(0.005–0.018)	0.01	(0.007–0.024)	0.02	(0.012–0.040)	0.0	(0.003–0.011)	0.565	0.006	0.377
Kandleria	0.09	(0.039–0.196)	0.04	(0.017–0.082)	0.42	(0.189–0.943)	0.0	(0.003–0.017)	0.127	<0.0001	0.079
Succiniclasticum	1.27	(0.959–1.682)	1.54	(1.159–2.034)	1.09	(0.824–1.445)	1.8	(1.350–2.367)	0.331	0.017	0.165
Selenomonas 1	0.00	(0.003–0.006)	0.01	(0.004–0.008)	0.01	(0.007–0.012)	0.0	(0.002–0.004)	0.269	<0.0001	0.228
Mollicutes RF9	0.01	(0.012–0.019)	0.01	(0.010–0.015)	0.01	(0.010–0.016)	0.0	(0.011–0.018)	0.213	0.607	0.782
	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
Bacteroidales BS11 gut group	3.66	(3.085–4.331)	3.77	(3.180–4.465)	3.71	(3.130–4.395)	3.71	(3.133–4.400)	0.795	0.993	0.198
Bacteroidales RF16 group	0.89	(0.644–1.218)	0.73	(0.532–1.006)	0.82	(0.594–1.123)	0.79	(0.577–1.091)	0.385	0.894	0.026
Bacteroidales S24-7 group	3.70	(3.034–4.510)	3.40	(2.789–4.146)	3.58	(2.937–4.366)	3.51	(2.881–4.282)	0.538	0.888	0.173
Prevotella 1	33.59	(29.770–37.902)	32.74	(29.019–36.945)	32.68	(28.966–36.879)	33.65	(29.824–37.971)	0.758	0.725	0.839
Prevotella 7	0.06	(0.040–0.093)	0.08	(0.052–0.120)	0.08	(0.050–0.116)	0.06	(0.042–0.097)	0.383	0.526	0.823
Prevotellaceae UCG-001	2.60	(2.148–3.141)	2.56	(2.116–3.093)	2.45	(2.028–2.965	2.71	(2.241–3.276)	0.907	0.447	0.154
Prevotellaceae UCG-003	2.64	(2.146–3.252)	2.42	(1.965–2.978)	2.63	(2.132–3.232)	2.43	(1.978–2.997)	0.539	0.599	0.598
Rikenellaceae RC9 gut group	3.71	(3.260–4.225)	3.69	(3.240–4.195)	3.64	(3.197–4.140)	3.76	(3.306–4.281)	0.937	0.706	0.754
Fibrobacter	1.01	(0.732–1.398)	1.10	(0.795–1.518)	1.04	(0.749–1.431)	1.07	(0.776–1.483)	0.712	0.873	0.686
Christensenellaceae R-7 group	7.26	(6.358–8.301)	9.17	(8.025–10.479)	8.74	(7.647–9.985)	7.62	(6.672–8.712)	0.018	0.147	0.404
Butyrivibrio 2	0.61	(0.466–0.796)	0.62	(0.471–0.804)	0.67	(0.509–0.869)	0.56	(0.431–0.736)	0.645	0.370	0.645
Lachnospiraceae NK3A20 group	0.69	(0.572–0.836)	0.86	(0.710–1.037)	0.73	(0.608–0.888)	0.81	(0.668–0.976)	0.109	0.472	0.607
Pseudobutyrivibrio	1.02	(0.826–1.271)	0.92	(0.738–1.136)	1.06	(0.852–1.311)	0.89	(0.715–1.101)	0.450	0.247	0.034
Roseburia	0.34	(0.283–0.418)	0.27	(0.222–0.327)	0.29	(0.237–0.349)	0.32	(0.266–0.392)	0.078	0.385	0.059
[Eubacterium] coprostanoligenes group	1.23	(1.009–1.494)	1.23	(1.013–1.501)	1.15	(0.943–1.397)	1.32	(1.084–1.605)	0.972	0.310	0.386
Ruminiclostridium 9	0.12	(0.066–0.204)	0.13	(0.071–0.220)	0.13	(0.075–0.234)	0.11	(0.062–0.192)	0.840	0.608	0.133
Ruminococcaceae NK4A214 group	2.87	(2.502–3.298)	2.98	(2.594–3.418)	3.07	(2.671–3.520)	2.79	(2.430–3.203)	0.705	0.325	0.810
Ruminococcaceae UCG-014	0.67	(0.531–0.843)	0.61	(0.481–0.763)	0.62	(0.492–0.781)	0.65	(0.519–0.824)	0.530	0.738	0.901
Ruminococcus 1	1.97	(1.519–2.552)	1.75	(1.352–2.271)	1.64	(1.263–2.121)	2.11	(1.626–2.731)	0.515	0.166	0.053
Saccharofermentans	1.02	(0.887–1.167)	1.00	(0.871–1.147)	0.97	(0.846–1.113)	1.05	(0.914–1.202)	0.851	0.419	0.117
Erysipelotrichaceae UCG-002	0.00	(0.002–0.007)	0.00	(0.001–0.003)	0.01	(0.002–0.005)	0.00	(0.001–0.005)	0.061	0.794	0.336
Kandleria	0.12	(0.044–0.345)	0.10	(0.035–0.277)	0.11	(0.040–0.311)	0.11	(0.039–0.307)	0.757	0.986	0.122
Succiniclasticum	2.66	(2.152–3.297)	2.18	(1.761–2.698)	2.20	(1.776–2.721)	2.64	(2.133–3.269)	0.181	0.219	0.053
Selenomonas 1	0.85	(0.545–1.335)	0.71	(0.451–1.106)	0.71	(0.456–1.118)	0.84	(0.539–1.321)	0.543	0.590	0.133
Mollicutes RF9	1.46	(1.182–1.793)	1.33	(1.077–1.633)	1.36	(1.106–1.677)	1.42	(1.152–1.746)	0.517	0.776	0.870

^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 35 bacterial genera with a relative abundance > 0.50% 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.