Fig. 3
Dysbiosis index identifies a subset of symptomatic patients with altered microbial communities. a Classification of healthy and symptomatic patients as dysbiotic or healthy-like based on the CLOUD test, which evaluates each sample by its distance to healthy controls’ microbiome distribution. b The log-transformed CLOUD statistic for samples (or dysbiosis index (DI)) from healthy controls (n = 38, red) and symptomatic patients (n = 126, blue). Tukey boxplots show the median with IQR and 1.5 IQR whiskers. c Heatmap of significantly different genus-level taxa from healthy control and symptomatic patients that contribute significantly to the DI identified using Boruta feature selection from the random forest model40. Samples classified as dysbiotic or healthy-like are indicated at the top by orange and green, respectively. Pearson correlation of DI with alpha diversity based on d phylogenetic diversity (p < 0.0001, r = −0.47, Pearson correlation), e observed OTUs (p < 0.0001, r = −0.4, Pearson correlation), f Shannon index (p < 0.0001, r = −0.36, Pearson correlation)
