Significant associations of microbial clade abundance and community ecology with IBD and treatment. (a) Taxonomic distribution of clades significant to disease and ileal involvement. Abundant clades not significantly associated with IBD are annotated in gray for context (top 90th percentile of at least 10% of samples and including 5+ genera). Node (non-associated clade) sizes are proportional to the log of the clade's average abundance. (b) Significance of association of sample ecology with disease (CD/UC, ileal/pancolonic), treatment (antibiotics, immunosuppression, mesalamine, steroids), and environment (smoking, stool/biopsy sample origin). Diversity (Simpson's index), evenness (Pielou's index), and richness (Chao1) were calculated for each community (see Materials and methods). False discovery rate q-values are -log10 transformed for visualization, such that values > 0.60 correspond to q < 0.25. Antibiotic treatment is strongly associated with reduced diversity, and stool samples with increased diversity relative to biopsies.