Additional file 2 of Roux-en-Y gastric bypass-induced bacterial perturbation contributes to altered host-bacterial co-metabolic phenotype
Creators: name: Li, Jia V.
name: Ashrafian, Hutan
name: Sarafian, Magali
name: Homola, Daniel
name: Rushton, Laura
name: Barker, Grace
name: Cabrera, Paula Momo
name: Lewis, Matthew R.
name: Darzi, Ara
name: Lin, Edward
name: Gletsu-Miller, Nana Adwoa
name: Atkin, Stephen L.
name: Sathyapalan, Thozhukat
name: Gooderham, Nigel J.
name: Nicholson, Jeremy K.
name: Marchesi, Julian R.
name: Athanasiou, Thanos
name: Holmes, Elaine
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Cancer
subject: Computational Biology

description: 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&lt; p &lt;0.01. Data were presented as mean±SEM. The bile acids and their retention time (min) and m/z were given in the titles. Figure S6. Relative intensities of urinary bile acids from sleeve gastrectomy (SG) and laparoscopic gastric banding (LGB) patients from cohort 1 at pre-op (black), 2-6 months (green) and 1-2 years post-op (orange). Kruskal-Wallis test was used, and Dunn’s test was used for adjusting multiple comparisons. The adjusted p values: ****, p &lt; 0.0001, ***, p &lt; 0.001, ** p &lt; 0.01, * p &lt; 0.05. Data were presented as mean±SEM. The bile acids and their retention time (min) and m/z were given in the titles. Figure S7. OPLS-DA cross-validated scores plots of serum 1H NMR CPMG spectra of the RYGB patients from cohort 3 between pre-op and 3 (A, Q2Y=0.69; R2X=35.1%; R2Y=98.2% p = 0.002), 6 (B, Q2Y=0.63; R2X=40.4%; R2Y=97.9% p = 0.002), 9 (C, Q2Y=0.80; R2X=37.9%; R2Y=98.6% p = 0.002) or 12-month (D, Q2Y=0.68; R2X=45.5%; R2Y=98.3% p = 0.008) post-op. OPLS-DA cross-validated scores plots of serum 1H NMR CPMG spectra of the RYGB patients between pre-op and 6-month post-op of cohort 2 (E, Q2Y=0.56; R2X=37.7%; R2Y=87.7% p = 0.002) or combined cohorts 2 and 3 (F, Q2Y=0.25; R2X=31.4%; R2Y=72.9% p = 0.002). Figure S8. Partial 1H NMR spectra of faecal batch culture media supplemented with tyrosine or tryptophan at 0 (black), 7 (blue), 24 (red) and 48 (pink) hours. Triplicates were carried out and the median spectra at each time point are shown. The top and middle panels are from healthy and RYGB donors, respectively. The bottom panel is from one of the RYGB donors. X axis is chemical shift in ppm and Y axis is peak intensities. Figure S9. Partial 1H NMR spectra of bacterial isolate culture in a defined simple media supplemented with phenylalanine (top panel), tryptophan (middle panel) or choline (bottom panel). Triplicates were carried out and all media spectra are shown. Black: control media; blue: B. uniformis; red: K. oxytoca, pink: E. cloacae; green: E. coli; light blue: B. vulgatus. X axis is chemical shift in ppm and Y axis is peak intensities. Table S1. Summary of exemplar human clinical studies investigating the metabolic effects of bariatric surgery to date. Table S2. Summary of the number of patients and body mass index (BMI) at each time based on types of bariatric surgery. Values are shown as mean±SD. Kruskal-Wallis ANOVA test was used to test the significance of BMI changes across the time points in cohorts 1 and 3, while Friedman test was used for cohort 2 for paired analysis.