Abundances of identifiable BAs in HMP2 cohort. BA levels were not universally decreased in dysbiotic CD patients, indicating that decreased levels of LCA, 3-oxoLCA, and isoLCA were not due to lower levels of all BAs in these cohorts. Boxplots show median and lower/upper quartiles with outliers outside of boxplot ‘whiskers’ (indicating the inner fences of the data). n=47 for dysbiotic CD, n = 169 for non-dysbiotic CD, n=12 for dysbiotic UC, n=110 for non-dysbiotic UC and n=122 for non-IBD. The percentage of zeros in each condition are added as x-axis tick labels. See Table S6 for full results.