Crohn’s disease associated gut microbiomes are functionally distinct from microbiome associated with ulcerative colitis or healthy controls.

<p>Crohn’s disease (CD) associated gut microbiomes are functionally differentiated from their healthy (H) and ulcerative colitis (UC) associated counterparts in the MGS cohort. (A) Boxplots illustrate that CD gut microbiomes exhibit lower protein family richness than UC and H microbiomes (p < 0.05). (B) The average genome size of the organisms in CD microbiomes is larger than the corresponding average in UC patients or healthy controls (p = 0.1). (C) Principal components analysis (PCA) of protein family abundance profiles identifies differentiation in beta-diversity between CD (red) and non-CD populations (Ulcerative colitis, green; Healthy, blue) for the first two (upper panel) and first and third (lower panel) principal components. Here, PCA was conducted by scaling all KO abundances to have zero mean and unit variance, though similar structure is identified using different PCA parameters. Ellipses represent 95% confidence intervals as quantified by the ordiellipse function in the R package vegan [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004573#pcbi.1004573.ref045" target="_blank">45</a>]. A permutational multivariate analysis of variance (adonis) quantified the reported p-values for the null hypothesis that the PCA axes are not different by group based on 1e4 permutations. These trends are also observed in an independent analysis of the MetaHIT cohort (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004573#pcbi.1004573.s015" target="_blank">S11 Fig</a>).