Covariation of microbial community function in IBD with treatment, environment, biometrics, and disease subtype. Fecal and biopsy samples from 231 IBD patients and healthy controls are plotted as squares (iCD) or circles and colored by disease status. Axes show the first two components of overall variation as determined by multiple factor analysis (see Materials and methods). Clinical and environmental covariates are shown in bold, while individual microbial functions (Gene Ontology terms) are italicized. Covariation patterns are similar to those determined using microbial abundance (Figure 1).