Fig. 2: Differential bacterial species and dysbiosis of metabolic pathways in patients with UC and CD compared with controls.
From: Noninvasive, microbiome-based diagnosis of inflammatory bowel disease
a,b, Top bacterial species associated with UC (a) and CD (b). Left, lollipop plot showing the coefficient of each species, with disease calculated by MaAsLin2 including adjustment for age and gender. Middle, the phylum of each species is indicated. Right, bar plot demonstrating the proportion of each species present in UC, CD and control groups. c,d, Relative abundance of ten bacterial species biomarkers in UC (n = 205) and controls (n = 118) (c), and of nine bacterial species biomarkers in CD (n = 174) and controls (n = 118) (d) as determined by metagenomics. Data shown as median (center line), 25th and 75th percentiles (box limits) and 5th and 95th percentiles (whiskers). P values were calculated using two-sided Wilcoxon rank-sum test. e,f, Performance of model with ten UC and nine CD bacterial species biomarkers for classification of patients with UC (e) and CD (f) compaerd with controls in discovery cohort. Shaded areas of ROC curves represent the 95% CI of AUC for the test set. g, SHAP values of the ten UC bacterial species biomarkers for each sample. h, SHAP values of the nine CD bacterial species biomarkers for each sample. Each point represents the SHAP value of each biomarker for each sample; the distribution of points indicates the impact of each biomarker on model output. Colors represent relative abundance of the biomarkers (yellow, high; purple, low). i, Correlation between functional dysbiosis scores and probability of disease generated by models based on ten UC and nine CD bacterial species biomarkers. Shaded area corresponds to 95% CI for the regression fit. Correlation coefficient and two-sided P values are given by Spearman correlation. Coeff., coefficient; pos. pred., positive prediction; neg. pred., negative prediction.
