Supplementary Information Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics Ellen Kuang 1, Matthew Marney 2, Daniel Cuevas 3, Robert A. Edwards 2,3,4 and Erica M. Forsberg 1,2,3,* 1 Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA; [email protected] (E.K.), [email protected] (E.M.F.) 2 Department of Biomedical Informatics, San Diego State University, San Diego, CA 92182, USA; [email protected] (M.M.); [email protected] (R.A.E.) 3 Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; [email protected] (D.C.) 4 Department of Biology, San Diego State University, San Diego, CA 92182, USA * Correspondence: [email protected]; Tel.: +1-619-594-5806 2. Results The output of MS_FBA generates both graphical visualizations (Figure S1) and a feature table containing the potential matches between the untargeted metabolomics data and the flux balance analysis metabolite list (Table S1 and S2). These show the molecule name, m/z value, retention time, peak group (e.g. same retention time window), the difference between the expected and observed M+1 isotope ratio, whether this is considered to be an isotope match (e.g. the isotope must be within 5% of the expected ratio) and the predicted adduct. These are illustrated below for the C. sedlakii data in both positive mode reverse phase (Table S1) and negative mode HILIC (Table S2). Figure S1. (a) This graphical output from MS_FBA shows all 1097 significant features from the XCMS Online results for the reverse phase positive mode run. The red dots show the intensity difference between the late (L) and mid (M) sample points, and the blue shows the intensity difference between stationary (S) to late (L). (b) This graph shows all features that were not matched to the compounds from the predicted compound list. Metabolites 2020, 10, x; doi: FOR PEER REVIEW www.mdpi.com/journal/metabolites Metabolites 2020, 10, x FOR PEER REVIEW 2 of 25 Table S1. Features matched to PyFBA predicted metabolites in the reverse phase run with data acquisition in positive mode. Compound m/z Retention Peak Isotope Isotope Adduct Time Group Difference Match (min) (%) D-glutamic acid 148.060 2.027 2 -0.242 TRUE [M+H]+ L-glutamic acid 148.060 2.027 2 -0.242 TRUE [M+H]+ O-acetyl-L-serine 148.060 2.027 2 -0.242 TRUE [M+H]+ D-glyceric acid 148.060 2.027 2 4.885 FALSE [M+C2H3N+H]+ L-pyroglutamic acid 130.050 2.019 2 -0.291 TRUE [M+H]+ 3-hydroxy-L-1-pyrroline-5- 130.050 2.019 2 -0.291 TRUE [M+H]+ carboxylate D-glutamic acid 130.050 2.019 2 -0.425 TRUE [M-H2O+H]+ L-glutamic acid 130.050 2.019 2 -0.425 TRUE [M-H2O+H]+ O-acetyl-L-serine 130.050 2.019 2 -0.425 TRUE [M-H2O+H]+ 3-oxopropanoic acid 130.050 2.019 2 4.836 FALSE [M+C2H3N+H]+ Pyruvic acid 130.050 2.019 2 4.836 FALSE [M+C2H3N+H]+ L-threonine 102.055 2.024 2 -0.419 TRUE [M-H2O+H]+ L-homoserine 102.055 2.024 2 -0.419 TRUE [M-H2O+H]+ Acetic acid 102.055 2.024 2 4.842 FALSE [M+C2H3N+H]+ Glycolaldehyde 102.055 2.024 2 4.842 FALSE [M+C2H3N+H]+ D-glutamic acid 295.114 2.027 2 -0.336 TRUE [2M+H]+ L-glutamic acid 295.114 2.027 2 -0.336 TRUE [2M+H]+ O-acetyl-L-serine 295.114 2.027 2 -0.336 TRUE [2M+H]+ L-proline 116.071 2.017 2 0.398 TRUE [M+H]+ Propionic acid 116.071 2.017 2 5.525 FALSE [M+C2H3N+H]+ (S)-lactaldehyde 116.071 2.017 2 5.525 FALSE [M+C2H3N+H]+ Lactaldehyde 116.071 2.017 2 5.525 FALSE [M+C2H3N+H]+ L-Arabino-1,4-lactone 131.034 2.023 2 1.228 FALSE [M-H2O+H]+ Diadenosine tetraphosphate 248.036 2.061 2 -3.550 FALSE [M+2H]+ Raffinose 527.159 2.002 2 0.710 TRUE [M+Na]+ Maltotriose 527.159 2.002 2 0.710 TRUE [M+Na]+ Metabolites 2020, 10, x FOR PEER REVIEW 3 of 25 6-O-(alpha-D- 527.159 2.002 2 0.710 TRUE [M+Na]+ galactopyranosyl)-6-O-(alpha- D-galactopyranosyl)-D- glucopyranose L-aspartic acid 175.071 2.056 2 -2.347 FALSE [M+C2H3N+H]+ Urocanic acid 175.071 2.056 2 -7.218 FALSE [M+2H2O+H]+ D-glyceric acid 170.042 2.000 2 -0.898 TRUE [M+C2H3N+Na]+ D-glutamic acid 170.042 2.000 2 -6.025 FALSE [M+Na]+ L-glutamic acid 170.042 2.000 2 -6.025 FALSE [M+Na]+ O-acetyl-L-serine 170.042 2.000 2 -6.025 FALSE [M+Na]+ Maltotetraose 689.212 2.045 2 -27.201 FALSE [M+Na]+ Stachyose 689.212 2.045 2 -27.201 FALSE [M+Na]+ Melibiose 343.124 2.048 2 -13.620 FALSE [M+H]+ Sucrose 343.124 2.048 2 -13.620 FALSE [M+H]+ Alpha-lactose 343.124 2.048 2 -13.620 FALSE [M+H]+ Trehalose 343.124 2.048 2 -13.620 FALSE [M+H]+ 5,6-Dimethylbenzimidazole 179.049 3.367 5 -1.853 FALSE [M+C2H3N+H]+ Salicin 309.094 3.366 5 -14.513 FALSE [M+Na]+ dUMP 309.050 3.391 5 -10.900 FALSE [M+H]+ Gamma-glutamylcysteine 233.059 3.366 5 -0.798 TRUE [M-H2O+H]+ Aspartyl phosphate 255.039 3.403 5 -2.472 FALSE [M+C2H3N+H]+ 3-oxo-O-phosphono-L- 255.039 3.403 5 -2.472 FALSE [M+C2H3N+H]+ homoserine 1-Stearoyl-sn-glycero-3- 480.308 20.648 9 5.190 FALSE [M+C2H3N+H]+ phosphate N1-acetylspermidine 188.176 1.569 11 -1.864 FALSE [M+H]+ N8-acetylspermidine 188.176 1.569 11 -1.864 FALSE [M+H]+ l-histidinol phosphate 245.054 1.623 11 -7.866 FALSE [M+H+Na]+ L-beta-lysine 191.077 1.542 11 -7.444 FALSE [M+2Na-H]+ L-lysine 191.077 1.542 11 -7.444 FALSE [M+2Na-H]+ Deoxy-TDP 358.039 7.243 12 0.144 TRUE [M+C2H3N+Na]+ 5'-phosphoribosylformyl- 358.039 7.243 12 -10.224 FALSE [M+2Na-H]+ Metabolites 2020, 10, x FOR PEER REVIEW 4 of 25 glycinamidine 1-stearoyl-sn-glycero-3- 480.308 21.147 15 4.816 FALSE [M+C2H3N+H]+ phosphate 1-stearoyl-sn-glycero-3- 502.290 21.147 15 5.318 FALSE [M+C2H3N+Na]+ phosphate N-acetylneuraminic acid 348.070 4.336 16 -0.413 TRUE [M+K]+ Adenine 136.062 4.331 16 -2.196 FALSE [M+H]+ dUMP 350.075 4.335 16 -8.337 FALSE [M+C2H3N+H]+ Pyridoxine phosphate 232.036 4.338 16 -9.436 FALSE [M-H2O+H]+ SEPHCHC 367.044 4.332 16 -15.646 FALSE [M+K]+ Cytidine-5'-diphosphate 404.028 4.327 16 -11.406 FALSE [M+H]+ Adenine 136.062 2.230 19 -1.270 TRUE [M+H]+ Betaine 118.086 2.219 19 0.033 TRUE [M+H]+ L-valine 118.086 2.219 19 0.033 TRUE [M+H]+ 1,2-propanediol 118.086 2.219 19 5.160 FALSE [M+C2H3N+H]+ L-aspartic acid 134.045 2.229 19 -4.910 FALSE [M+H]+ Palmitic acid 257.248 2.197 19 -0.434 TRUE [M+H]+ Glyoxylic acid 116.034 2.207 19 0.278 TRUE [M+C2H3N+H]+ L-aspartic acid 116.034 2.207 19 -4.983 FALSE [M-H2O+H]+ Maltohexaose 991.335 2.235 19 -4.719 FALSE [M+H]+ Butyric acid 130.087 1.944 20 -1.913 FALSE [M+C2H3N+H]+ Pyridoxamine 210.124 1.946 20 -7.017 FALSE [M+C2H3N+H]+ Cytidine 244.093 1.942 20 -11.155 FALSE [M+H]+ Gamma-glutamyl-beta-cyano- 244.093 1.942 20 -11.155 FALSE [M+H]+ alanine Melibiose 365.106 1.943 20 0.102 TRUE [M+Na]+ Sucrose 365.106 1.943 20 0.102 TRUE [M+Na]+ Alpha-lactose 365.106 1.943 20 0.102 TRUE [M+Na]+ Trehalose 365.106 1.943 20 0.102 TRUE [M+Na]+ Methanesulfonic acid 192.983 1.940 20 -4.070 FALSE [2M+H]+ Guanine 152.057 2.432 21 -1.686 FALSE [M+H]+ Metabolites 2020, 10, x FOR PEER REVIEW 5 of 25 Butyric acid 112.051 2.441 21 0.100 TRUE [M+H+Na]+ Cytosine 112.051 2.441 21 -0.934 TRUE [M+H]+ 5'-Cytidylic acid 324.059 2.438 21 0.181 TRUE [M+H]+ Cytidine 3'-monophosphate 324.059 2.438 21 0.181 TRUE [M+H]+ L-pyroglutamic acid 166.072 2.455 21 0.823 TRUE [M+2H2O+H]+ 3-hydroxy-L-1-pyrroline-5- 166.072 2.455 21 0.823 TRUE [M+2H2O+H]+ carboxylate Nicotinamide 123.055 3.874 27 -0.675 TRUE [M+H]+ Nicotinamide dinucleotide 664.116 3.867 27 1.863 FALSE [M+H]+ ADP-D-ribose 542.068 3.867 27 -0.945 TRUE [M-H2O+H]+ Phosphoribosyl-AMP 542.068 3.867 27 -0.945 TRUE [M-H2O+H]+ N-succinyl-L-glutamate 5- 232.083 3.874 27 2.199 FALSE [M+H]+ semialdehyde UDP-glucuronic acid 622.066 3.868 27 -15.300 FALSE [M+C2H3N+H]+ 2'-deoxyuridine 252.073 3.936 27 -10.775 FALSE [M+H+Na]+ 3-oxopropanoic acid 130.050 4.697 30 -0.825 TRUE [M+C2H3N+H]+ Pyruvic acid 130.050 4.697 30 -0.825 TRUE [M+C2H3N+H]+ L-pyroglutamic acid 130.050 4.697 30 -5.952 FALSE [M+H]+ 3-hydroxy-L-1-pyrroline-5- 130.050 4.697 30 -5.952 FALSE [M+H]+ carboxylate D-glutamic acid 130.050 4.697 30 -6.086 FALSE [M-H2O+H]+ L-glutamic acid 130.050 4.697 30 -6.086 FALSE [M-H2O+H]+ O-acetyl-L-serine 130.050 4.697 30 -6.086 FALSE [M-H2O+H]+ Sulfoacetic acid 177.007 2.106 34 -3.052 FALSE [M+2H2O+H]+ Urocanic acid 177.007 2.106 34 -7.363 FALSE [M+K]+ Maltotetraose 667.229 2.122 34 0.558 TRUE [M+H]+ Stachyose 667.229 2.122 34 0.558 TRUE [M+H]+ Glycerol 115.037 2.101 34 -3.446 FALSE [M+Na]+ Thiamine pyrophosphate 425.045 2.139 34 -15.698 FALSE [M+H]+ L-allysine 187.108 2.150 34 -4.515 FALSE [M+C2H3N+H]+ 6-amino-2-oxohexanoic acid 187.108 2.150 34 -4.515 FALSE [M+C2H3N+H]+ Metabolites 2020, 10, x FOR PEER REVIEW 6 of 25 L-Arabino-1,4-lactone 297.083 23.204 37 15.056 FALSE [2M+H]+ Folic acid 464.131 23.201 37 -23.550 FALSE [M+Na]+ Cifostodine 306.049 3.282 38 -0.498 TRUE [M+H]+ 5'-Cytidylic acid 306.049 3.282 38 -0.631 TRUE [M-H2O+H]+ Cytidine 3'-monophosphate 306.049 3.282 38 -0.631 TRUE [M-H2O+H]+ Butyric acid 112.051 3.289 38 0.100 TRUE [M+H+Na]+ Cytosine 112.051 3.289 38 -0.934 TRUE [M+H]+ Butyraldehyde 145.122 16.690 40 -8.889 FALSE [2M+H]+ Uroporphyrinogen III 427.265 17.918 42 10.303 FALSE [M+Na]+ Uroporphyrinogen I 427.265 17.918 42 10.303 FALSE [M+Na]+ 2',3'-cyclic UMP 329.016 17.886 42 -10.889 FALSE [M+Na]+ 2',3'-cyclic UMP 307.034 17.672 43 -0.367 TRUE [M+H]+ Pseudouridine 5'-phosphate 307.034 17.672 43 -0.501 TRUE [M-H2O+H]+ 3'-uridylic acid 307.034 17.672 43 -0.501 TRUE [M-H2O+H]+ Uridine 5'-monophosphate 307.034 17.672 43 -0.501 TRUE [M-H2O+H]+ Anthranilic acid 120.044 10.241 45 -8.147 FALSE [M-H2O+H]+ 4-aminobenzoic acid 120.044 10.241 45 -8.147 FALSE [M-H2O+H]+ L-arabino-1,4-lactone 149.045 10.247 45 -5.671 FALSE [M+H]+ sn-Glycerol 3-phosphate 173.021 10.163 45