Mice with CGD from 2 different animal facilities have distinct intestinal microbiome signatures. (A) Comparison of the α-diversity, as measured by the Shannon diversity index, for the WT (n = 5), gp91^phox–/– (n = 5), and p47^phox–/– (n = 4) mice from IRCM and the WT (n = 4), gp91^phox–/– (n = 5), and p47^phox–/– (n = 6) mice from the NIH at baseline. (B) PCoA of β-diversity as measured by Jaccard distances. (C) Relative abundance of phyla present in the stool from mice at baseline. EdgeR was used for the identification of specific taxonomic markers for the comparison between IRCM gp91^phox–/– mice and the NIH gp91^phox–/– mice (D), IRCM p47^phox–/– mice and the NIH p47^phox–/– mice (E), and gp91^phox–/– and p47^phox–/– mice from IRCM (F) showing the log₁₀ fold changes and Kruskal-Wallis cutoffs. P ≤ .05. ∗P < .05; ∗∗P < .01; ∗∗∗P < .001; ∗∗∗∗P < .0001.