Fig. 2
Lower diversity and altered composition of the cecal and sigmoid colon microbiota in CD patients with endoscopically quiescent disease compared to controls. A Alpha diversity metrics (Chao1, Shannon) are shown for the cecal and sigmoid MLI microbiome of CD and controls. Significance was determined by ANOVA adjusting for gender, age, and obesity. ***p<10−4. B PCoA plots based on Bray-Curtis dissimilarity. Color represents IBD status. p-values calculated by multivariate PERMANOVA adjusting for gender, age, and obesity. C Receiver operating characteristics (ROC) curve for random forest classifiers differentiating CD vs. control subjects based upon cecal and sigmoid MLI microbiota. Area under the curve (AUC) is shown for each site. The colored regions signify the 95% confidence intervals of the curves. D Taxonomic summary at the phylum level of the cecal and sigmoid colon MLI microbiome of CD and controls. *q<0.05, **q<0.005, ***q<10−4 in DESeq2 models adjusting for gender and obesity. E ASVs with a statistically significant difference in relative abundance between CD and controls in multivariate DESeq2 models adjusting for gender and obesity are shown separately for sigmoid and cecum