Table 1. PERMANOVA decomposition of β-diversity as measured by UniFrac.

	Term	df	SS∧	F#	R 2	p-value
Weighted UniFrac	cage	5	0.3537	3.843	0.0728	0.0004
	diet	1	2.2813	123.94	0.46954	<1.00×10−4
	time point	2	0.5435	14.762	0.11185	<1.00×10−4
	drug	1	0.1156	6.278	0.02378	0.0028
	Residuals	85	1.5646	0.32202
	Total	94	4.8586
Unweighted UniFrac	cage	5	1.279	1.944	0.07742	<1.00×10−4
	diet	1	2.7293	20.7412	0.16519	<1.00×10−4
	time point	2	1.096	4.1644	0.06634	<1.00×10−4
	drug	1	0.2325	1.767	0.01407	0.021
	Residuals	85	11.1849	0.67698
	Total	94	16.5217

*df, degrees of freedom; ^∧ SS, Sum of squares; ^# F, pseudo-F-statistic.