Table 1. Difference in the microbial community between the two groups measured using permutational multivariate analysis of variances (PERMANOVA) on Bray–Curtis and Jaccard distance metrics using the Adonis function.

Comparison	Adonis Bray-Curtis			Adonis Jaccard
	R-square	P-value	PERMDISP (P-value)	R-square	P-value	PERMDISP (P-value)
Caecal contents vs dust	0.41	<0.001	0.54	0.32	<0.001	0.73
Caecal contents vs litter	0.61	<0.001	0.43	0.45	<0.001	0.56
Caecal vs ileal contents	0.58	<0.001	0.005	0.43	<0.001	0.005
Caecal contents vs excreta	0.32	<0.001	<0.001	0.25	<0.001	<0.001
Ileal contents vs dust	0.41	<0.001	0.09	0.31	<0.001	0.07
Ileal contents vs litter	0.38	<0.001	0.19	0.28	<0.001	0.18
Ileal contents vs excreta	0.06	0.02	0.06	0.05	0.02	0.04
Dust vs excreta	0.27	<0.001	<0.001	0.22	<0.001	<0.001
Dust vs litter	0.25	<0.001	0.81	0.21	<0.001	0.78
Litter vs excreta	0.31	<0.001	0.001	0.25	<0.001	0.73

PERMDISP = permutational multivariate dispersions test calculated using Bray-Curtis and Jaccard distance metrics. R-square is the proportion of the variance explained by the group. Bolded values signify statistical difference at a P<0.05 level.