Table 3.

Phylum-level taxonomic composition of the ileal bacterial communities.

Phylum	Day 42		Day 84			Weaning time		Age		W × A
	CON	EW	CON	EW	SEM	P-value	QFDR	P-value	QFDR	P-value	QFDR
Firmicutes	79.01	78.80	70.67	62.2	1.481	<0.001	<0.001	<0.001	<0.001	<0.001	<0.001
Actinobacteria	12.06	12.41	10.84	10.24	0.284	0.782	1.000	0.002	0.006	0.315	0.630
Bacteroidetes	1.28	4.32	2.03	5.10	0.441	<0.001	<0.001	0.242	0.485	0.979	1.000
Proteobacteria	0.62	1.36	2.22	4.51	0.315	<0.001	<0.001	<0.001	<0.001	<0.001	<0.001
Euryarchaeota	0.69	0.70	0.98	1.30	0.055	0.001	0.002	<0.001	<0.001	0.002	0.002
Lentisphaerae	0.47	0.55	0.53	0.56	0.036	0.180	0.721	0.807	1.000	0.373	0.745
Verrucomicrobia	0.52	0.33	0.08	0.25	0.042	0.781	1.000	<0.001	0.001	0.005	0.011
Tenericutes	0.01	0.09	0.69	0.57	0.069	0.775	1.000	<0.001	<0.001	0.156	0.313
Planctomycetes	0.02	0.04	0.11	0.22	0.068	0.042	0.054	<0.001	<0.001	0.046	0.551
Cyanobacteria	0.02	0.03	0.12	0.81	0.071	<0.001	<0.001	<0.001	<0.001	<0.001	<0.001
TM7	0.03	0.01	3.11	3.21	0.347	0.870	1.000	<0.001	<0.001	0.824	1.000
Chlamydiae	0	0	0.63	0	0.061	<0.001	<0.001	<0.001	<0.001	<0.001	<0.001
Other (<0.1%)	0.06	0.07	0.06	0.10	0.005	0.579	0.772	<0.001	<0.001	<0.001	<0.001
Unclassified	5.12	1.52	7.84	10.98	0.751	0.006	0.025	0.019	0.028	0.021	0.028

The CON group was weaned on day 56; the EW group was weaned on day 28.