Permutation-based repeated measures ANCOVA results for each of the six phyla/subphyla bacterial categories (Clade).

Sequencing results for all three platforms were available for 157 samples (44 ileal CD, 53 colitis and 60 control non-IBD). The variables and first order interactions with P≤0.05 are listed above. To address multiple comparison issues, the Benjamini-Hochberg method was applied to adjust P-values to the false discovery rate (FDR). The variables and first order interactions with FDR ≤0.05 are bolded.