Fig. 3

HDC was also elevated in CD, correlated with differential species and contributed significantly to patient stratification. a, Species that were correlated with HDCs in the group of healthy controls and untreated patients (Baseline + Control, Spearman correlation, p-value < 0.001). Also plotted are the correlation coefficients between HDCs and species abundances in patients at three time-points after they were treated (Week1, Week4 and Week8). Correlation coefficients were color-coded according to their significance levels. b, Ranking of feature importance in the HDC + All-species model. The models were trained by using HDC values and relative abundances of all species as input; only the data of the healthy controls and untreated patients were used. The importance scores were reported by the Random forest models. The features were ranked according to the median importance scores from 100 repeated results of cross-validation analysis (see Methods). Dif: species whose abundances are significantly different between untreated CD and controls (see Methods); Both: differential species that was also correlated with HDC; HDC: host DNA contents; Other: species that were neither HDC-related nor differential