Fig. 2

Therapeutic diet ameliorates dysbiosis associated with chronic enteropathy and induces changes in the microbiome associated with remission. a Density of Pielou’s evenness index for DR animals at different time points in the study. b Weighted UniFrac distance to healthy controls for DR animals. c Volcano plot showing differentially abundant OTUs enriched in either DR dogs with active disease (day 0, red points) or in remission after diet therapy (day 14, blue points). Selected taxa (e.g., Escherichia-Shigella spp., Clostridium spp., and Blautia; OTUs with mean abundance > 5 counts) are labeled. The relative abundance of d E. coli and e C. perfringens in DR animals throughout the study and compared to healthy controls. f Density of Pielou’s evenness index in NDR animals. g Weighted UniFrac distance to healthy dogs for NDR animals. Diet therapy began at day 0, metronidazole administration at day 14, and prednisone at day 28 (see the “Methods”). h Bubble plot showing differentially abundant genera (fold change > 2 and P < 0.05) between day 14 versus day 0 for DR (left) and NDR (right) animals. Bubble size indicates absolute log fold change between day 14 and day 0, and color reflects direction of change. i, j The relative abundance of E. coli and C. perfringens in NDR animals throughout the study and compared to healthy controls. The distribution comparison of density (a, f) was performed by comparing quantiles via the Harrell-Davis estimator (FDR < 0.01). ns, not significant. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 using the two-sided Wilcoxon rank sum test for b and g or using the two-sided Wilcoxon signed-rank sum test for panels d, e, i, and j