The data were based on a matched cohort, including healthy lean (HL, n = 103), healthy overweight/obese (HO, n = 103) and overweight/obese with T2DM (OD, n = 103) groups. a Total BAs based on all (male and female, n = 309), male (n = 153) and female (n = 156) samples. b Fold changes of 23 BAs in HO and OD groups relative to the mean values of HL group. c Heatmaps of Spearman correlation coefficients of 6 BA species with representative metabolic markers. d–h Group differences of total and individual HCA species. i Heatmaps of Spearman correlation coefficients of total and individual HCA species with representative metabolic markers. Data are expressed as median with interquartile range (a, d–h), and mean with SE (b). In the bar plots (a, b, d–h), * and # indicate the statistical significance (p < 0.05) between two groups and among three groups, respectively, based on two-sided Kruskal–Wallis test. In the heatmaps (c, i), r value indicates Spearman correlation coefficient, and * indicates the statistical significance (p < 0.05) based on Spearman correlation.