Host factors associated with the IBD microbiome. A complex network of host factors associated with the IBD microbiome (all associations FDR <0.05); only taxa with at least four significant associations are included in the network; green and purple edges indicate positive and negative associations, respectively; the width of an edge indicates the strength of the association. The effects of these factors on individual taxa are highly overlapping. The analysis identified covariates representing each type of host factor, consistent with previous results . Biopsy location and medication history had the strongest and most comprehensive effects on microbiome profile; the effect of NOD2 was moderate in comparison. Cohort membership (not shown) also affected microbiome profile. These results demonstrate the need for study designs and analysis methodologies that control carefully for numerous host genetic and environmental factors when performing microbiome-based biomarker discovery. Abx, antibiotics within 1 month; Imm, immunosuppressants within 1 month; L2, no ileal involvement; PPI, biopsy from pre-pouch ileum.