Covariation of microbial community structure in IBD with treatment, environment, biometrics, and disease subtype. Fecal and biopsy samples from 228 IBD patients and healthy controls are plotted as squares (ileal CD) or circles (not ileal involved) and colored by disease status. Axes show the first two components of overall variation as determined by multiple factor analysis (see Materials and methods). Covariation in the presence of clinical factors (bold) and in microbial taxa (italic) is shown. Sample origin (biopsy versus stool) is the single most influential factor in determining microbial community structure, accompanied by host age, treatment types, and disease (particularly ileal CD).