Table 3. Summary of beta diversity analysis.

A non-parametric ANOSIM (Analysis of Similarity) method was applied to dataset presented in Fig 3D (PBS or adoptive T cell transfer in Rag2^-/- or DKO mice, from day 0 to day 13). Among single variables, only the genotype of the T cell recipient mice was significantly different based on a UniFrac beta diversity metric. In multivariate analysis, genotype was the single contributor to differences in beta diversity. Each row is a comparison of microbial diversity done with one or more factors, indicated by the labels. Beta diversity was calculated using Analysis of Similarity (ANOSIM) and significance was considered reached when both a and b were true as follows: a) p-value < 0.05 and b) R value > 0.3.

Genotype	Treatment	Time	R	p value	Significance beta diversity
Genotype			0.967	0.001	Yes
	Treatment		0.0259	0.028	No
		Time	-0.0173	0.768	No
Genotype	Treatment		0.65	0.001	Yes
Genotype		Time	0.503	0.001	Yes
	Treatment	Time	-0.023	0.801	No