Fig. 2

Random forest model based on gut microbiota species and metabolites accurately and specifically predicts NAFLD-O. A Receiver operating characteristic (ROC) curves and confusion matrices evaluating the ability of random forest models to predict NAFLD. Each color represents the model performance using as features species and pathways (purple), or species and metabolites (red and blue). Blue indicates the model performance when being validated in an external US cohort. B Evaluation of model cross-study portability and prediction rate on NAFLD-L and other metabolic diseases. Models using species plus metabolites or species plus pathways as features were used. C Feature importance for the random forest model built with species and metabolites. The color indicates feature prediction as evaluated by Shapley values: blue for Control-NAFLD-O and red for NAFLD-O. D Abundance comparison between each disease and its control for the species selected in the model built with species and metabolites. ANCOM-II was used for statistical comparisons. Circle size corresponds to the mean difference, with a higher size/value indicating a stronger difference. Full circle: higher in control; empty circle: higher in disease. CLR: centered log ratio