Fig. 1

Nod2 genotype influences microbiota resilience after antibiotic exposure in adult mice. a Experimental strategy. Starting at 8 weeks of age, littermate WT and Nod2^−/− mice received either water or antibiotic (Abx) treatment for 7 days followed by 2 weeks of water to allow for microbial recovery. Arrows indicate time points of stool collection for sequencing. b Species richness at day 0, 7, and 21 as measured by the Chao1 rarefaction index. c Principal coordinates plot of Bray–Curtis dissimilarity for each time point. Each dot represents one mouse. (ANOSIM, WT+Abx d0 vs. 7: R = 0.6778, p = 0.001; Nod2^−/−+Abx d0 vs. 7: R = 0.7922, p = 0.001; WT+Abx d0 vs. 21: R = 0.1494, p = 0.013; Nod2^−/−+Abx d0 vs. 21: R = 0.2144, p = 0.001). d Changes in bacterial composition, at the Family level, over time in antibiotic-treated WT and Nod2^−/− littermates. e Taxonomic differences identified by LEfSe before and after antibiotic treatment (day 0 vs. 21) in WT (left) and Nod2^−/− (right) littermates. Taxa reduced on day 21 compared to day 0 have negative LDA scores; and taxa enriched on day 21 have positive LDA scores. Taxa that are different between antibiotic-treated WT and Nod2^−/− mice are indicated (asterisk). f Heat map of significant bacterial taxa using Euclidean distance and centroid linkage clustering module (blue: low abundance; yellow: high abundance). Values were generated using the median of each group at each time point. Data are presented as mean ± SD (b), or mean (d). *p < 0.05, **p < 0.01, ***p < 0.001; by paired Student’s t-test (b), ANOSIM (c), or Kruskal–Wallis (d). (WT n = 7, Nod2^−/− n = 7, WT+Abx n = 11, Nod2^−/−+Abx n = 13. Data are from three independent experiments.)