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Additional file 1: Figure S1. ROC analysis of cross-validated scores from OPLS-DA models. (A) NMR analysis of urine; Tcv1 and Tcv2 represent the first and second PLS component when 2 PLS components were applied to separate 3 classes; (B) LC-MS analysis of urine; (C) bile acid analysis of urine; (D) NMR analysis of serum; (E) NMR analysis of feces. Figure S2. Relative metabolite levels in urine from cohorts 1 (A) and 2 (B), plasma from cohorts 3 (C) and 2 (D), and feces from cohort 1 (E). Metabolite levels are indicated by relative peak heights from the median fold normalized spectra of urine and feces and non-normalized serum spectra. Error bars are presented in SEM. a.u. stands for arbitrary unit. Figure S3. OPLS-DA cross-validated scores plots of urinary 1H NMR spectra of the RYGB and LGB patients from cohort 3 at pre-op (Q2Y=0.49; R2X=12.35%; R2Y=89.6%; p = 0.006), and 6-month post-op (Q2Y=0.44; R2X=30.66%; R2Y=95.2%; p = 0.038). The metabolites that significantly contributed to the classification of different time points are shown in Fig. 2C. Figure S4. OPLS-DA cross-validated scores plots of urinary reverse-phase liquid chromatography-mass spectrometry profiles of the bariatric patients from cohort 1 in ESI positive mode (Q2Y=0.46; R2X=24.8%; R2Y=73.4%; CVANOVA p = 2.9 x 10-14) and ESI negative mode (Q2Y=0.52; R2X=14%; R2Y=76.6%; CVANOVA p = 6.2 x 10-17). The identified metabolites that significantly contributed to the classification between pre-op (black) and 2-6 months post-op (green) are listed in the table. Positive correlation (r) represents higher relative concentrations of these metabolites at the post-op compared to pre-op. p[1] is loadings from the OPLS-DA models. Coefficient of variation (CV) was calculated based on the quality control (QC) samples to evaluate the analytical variation of the features. Figure S5. OPLS-DA cross-validated scores plots of urinary bile acid profiles of the RYGB patients from cohort 1 at pre-op (black), 2-6 months (green) and 1-2 years (orange) post-op (A. Q2Y=0.21; R2X=16.9%; R2Y=48.9%; CVANOVA p = 5.8x10-9). Bar plots of relative intensities of urinary bile acids identified from cohort 2 RYGB patients at pre-op (black) and 6 months post-op (green). Wilcoxon matched pairs signed rank test was used. ** 0.001< p

Additional file 1: Figure S1. ROC analysis of cross-validated scores from OPLS-DA models. (A) NMR analysis of urine; Tcv1 and Tcv2 represent the first and second PLS component when 2 PLS components were applied to separate 3 classes; (B) LC-MS analysis of urine; (C) bile acid analysis of urine; (D) NMR analysis of serum; (E) NMR analysis of feces. Figure S2. Relative metabolite levels in urine from cohorts 1 (A) and 2 (B), plasma from cohorts 3 (C) and 2 (D), and feces from cohort 1 (E). Metabolite levels are indicated by relative peak heights from the median fold normalized spectra of urine and feces and non-normalized serum spectra. Error bars are presented in SEM. a.u. stands for arbitrary unit. Figure S3. OPLS-DA cross-validated scores plots of urinary 1H NMR spectra of the RYGB and LGB patients from cohort 3 at pre-op (Q2Y=0.49; R2X=12.35%; R2Y=89.6%; p = 0.006), and 6-month post-op (Q2Y=0.44; R2X=30.66%; R2Y=95.2%; p = 0.038). The metabolites that significantly contributed to the classification of different time points are shown in Fig. 2C. Figure S4. OPLS-DA cross-validated scores plots of urinary reverse-phase liquid chromatography-mass spectrometry profiles of the bariatric patients from cohort 1 in ESI positive mode (Q2Y=0.46; R2X=24.8%; R2Y=73.4%; CVANOVA p = 2.9 x 10-14) and ESI negative mode (Q2Y=0.52; R2X=14%; R2Y=76.6%; CVANOVA p = 6.2 x 10-17). The identified metabolites that significantly contributed to the classification between pre-op (black) and 2-6 months post-op (green) are listed in the table. Positive correlation (r) represents higher relative concentrations of these metabolites at the post-op compared to pre-op. p[1] is loadings from the OPLS-DA models. Coefficient of variation (CV) was calculated based on the quality control (QC) samples to evaluate the analytical variation of the features. Figure S5. OPLS-DA cross-validated scores plots of urinary bile acid profiles of the RYGB patients from cohort 1 at pre-op (black), 2-6 months (green) and 1-2 years (orange) post-op (A. Q2Y=0.21; R2X=16.9%; R2Y=48.9%; CVANOVA p = 5.8x10-9). Bar plots of relative intensities of urinary bile acids identified from cohort 2 RYGB patients at pre-op (black) and 6 months post-op (green). Wilcoxon matched pairs signed rank test was used. ** 0.001< p