Extended Data Fig. 3: Lymphopenic status of NOD1^−/− and ΔCARD NOD1 mice is not associated with gut microbiota composition.

a, Representative contour plots of thymus and spleen from CD45.1/2⁺ mice treated ad libitum with drinking water containing VANM antibiotic cocktail for 4 weeks before and 8 weeks after being irradiated and reconstituted with an equal number of BM cells from CD45.1⁺ ΔCARD NOD1 and CD45.2⁺ WT mice (n = 5). Statistical differences were determined by one-way ANOVA (Tukey’s multiple comparisons). ***P < 0.001. b, c, Three week old NOD1^−/− (b) and ΔCARD NOD1 (c) were co-housed with age and gender matched WT animals for six weeks at which time the cellularity of different lymphoid organs was determined. (a-c) Each symbol depicts values obtained for an individual mice (n = 5). Bars represent the mean ± s.e.m of values from one representative out of two independent experiments performed. Statistical differences were determined by two-sided Mann-Whitney test.*P < 0.05, **P < 0.01, ***P < 0.001. d, Survival kinetics of co-housed WT (n = 9) and ΔCARD NOD1 (n = 12) mice infected i.p. with T. gondii ME-49 cysts. Significance was determined by Log-rank (Mantel-Cox) test.**P < 0.01. e, Stacked bar plot showing taxonomic relative abundance of fecal microbial communities at the family level in stool samples collected from WT (n = 9) and ΔCARD NOD1 (n = 11) mice before and after co-housing.

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