Table 3.

Mean abundances of bacterial taxa present at >0.1% of total fecal sequences which were significantly different (P < 0.05) between pre- vs. post-weaned calves¹.

Phylum	Taxa2	Pre-weaning	Post-weaning	log2 FC	SE3	P-value4
Actinobacteria	g. Bifidobacterium	1.21	0.341	-2.54	0.417	<0.001
Bacteroidetes	g. CF231	0.186	0.399	1.39	0.368	<0.001
	g. Bacteroides	31.0	17.8	-1.17	0.139	<0.001
	o. Bacteroidales	1.98	3.55	0.92	0.230	<0.001
	g. Prevotella	1.15	3.29	1.28	0.274	<0.001
	f. S24-7	1.46	10.9	3.53	0.278	<0.001
Elusimicrobia	g. Elusimicrobium	0.026	0.192	1.64	0.453	0.001
Firmicutes	g. Lactobacillus	2.87	0.195	-3.63	0.355	<0.001
	f. Lactobacillaceae	0.320	0.039	-2.94	0.398	<0.001
	o. Lactobacillales	0.008	0.001	-5.01	0.892	<0.001
	f. Streptococcaceae	1.55	0.271	-3.62	0.326	<0.001
	g. Streptococcus	0.174	0.026	-4.22	0.364	<0.001
	f. Christensenellaceae	0.101	0.488	2.39	0.377	<0.001
	g. Clostridium	0.094	0.246	2.36	0.447	<0.001
	f. Clostridiaceae	0.230	0.659	1.46	0.220	<0.001
	g. Eubacterium	0.007	0.002	-2.43	0.981	0.032
	g. Blautia	9.82	2.49	-2.68	0.250	<0.001
	g. Butyrivibrio	0.077	0.222	1.40	0.312	<0.001
	g. Coprococcus	3.74	0.675	-2.72	0.281	<0.001
	g. Dorea	0.801	0.334	-1.40	0.320	<0.001
	f. Lachnospiraceae	2.90	5.58	0.37	0.134	0.015
	g. Roseburia	0.055	0.347	2.56	0.315	<0.001
	o. Clostridiales	0.602	3.11	1.99	0.212	<0.001
	g. rc4-4	0.075	0.272	2.09	0.366	<0.001
	f. Peptostreptococcaceae	0.177	0.085	-1.30	0.370	0.001
	g. Faecalibacterium	4.07	0.944	-2.48	0.331	<0.001
	g. Ruminococcus	3.04	10.4	1.50	0.186	<0.001
	g. Anaerovibrio	0.098	0.364	1.19	0.348	0.002
	f. Veillonellaceae	0.037	0.088	0.96	0.302	0.004
	g. Collinsella	0.236	0.024	-3.13	0.387	<0.001
	g. Eggerthella	0.027	0.006	-2.50	0.701	0.001
	o. Coriobacteriales	0.005	0.018	1.37	0.413	0.003
	f. [Coprobacillaceae]	2.91	0.810	-3.39	0.336	<0.001
	g. [Eubacterium]	0.141	0.103	-1.89	0.322	<0.001
	g. Bulleidia	0.014	0.032	1.11	0.463	0.038
	f. Erysipelotrichaceae	0.038	0.265	1.04	0.346	0.007
Proteobacteria	o. RF32	0.151	0.314	0.96	0.365	0.022
	o. NA	0.694	1.02	1.04	0.306	0.002
	g. Helicobacter	0.017	0.010	-2.16	0.660	0.003
	g. Succinivibrio	0.477	2.29	1.55	0.382	<0.001
Spirochaetes	g. Treponema	0.057	1.157	3.08	0.363	<0.001
Tenericutes	f. Anaeroplasmataceae	0.084	1.33	3.77	0.419	<0.001
	o. Anaeroplasmatales	0.169	1.09	4.00	0.405	<0.001
	c. Mollicutes	0.007	0.013	1.45	0.563	0.025

¹Bacterial taxa present in at least 50% of calves and represented at least 0.1% of the bacterial community in at least one calf. ²Sequences that could not be assigned to a genus are displayed using the highest taxonomic level (class, c.; order, o.; family, f.) they could be assigned to. ³FC, fold change; SE, standard error for the log₂ fold change estimate. ⁴P-values for treatment effect (weaning strategy) were never significant, and are thus, not presented. Fecal taxa present but not significantly different between pre- and post-weaned calves are presented in Supplementary Table 2.