#METABOLOMICS WORKBENCH engelmab_20221206_025541 DATATRACK_ID:3631 STUDY_ID:ST002394 ANALYSIS_ID:AN003900 PROJECT_ID:PR001541 VERSION 1 CREATED_ON December 7, 2022, 7:25 am #PROJECT PR:PROJECT_TITLE Short-chain fatty acid (SCFA) analysis of DSS-treated murine intestinal PR:PROJECT_TITLE microbiota using continuous cultivation in bioreactors PR:PROJECT_SUMMARY We cultivated murine faecal microbiota in six replicate continuous bioreactors. PR:PROJECT_SUMMARY Three bioreactors were supplemented with 1% DSS and compared to the untreated PR:PROJECT_SUMMARY control bioreactors. PR:INSTITUTE Helmholtz Centre for Environmental Research PR:DEPARTMENT Molecular Systems Biology PR:LAST_NAME Engelmann PR:FIRST_NAME Beatrice PR:ADDRESS Permoserstraße 15, Leipzipg, Saxony, 03418, Germany PR:EMAIL beatrice.engelmann@ufz.de PR:PHONE 00493412351099 #STUDY ST:STUDY_TITLE Short-chain fatty acid (SCFA) analysis of DSS-treated murine intestinal ST:STUDY_TITLE microbiota using continuous cultivation in bioreactors ST:STUDY_SUMMARY We cultivated murine faecal microbiota in six replicate continuous bioreactors. ST:STUDY_SUMMARY Three bioreactors were supplemented with 1% DSS and compared to the untreated ST:STUDY_SUMMARY control bioreactors. ST:INSTITUTE Helmholtz Centre for Environmental Research ST:DEPARTMENT Molecular Systems Biology ST:LAST_NAME Engelmann ST:FIRST_NAME Beatrice ST:ADDRESS Permoserstraße 15, Leipzipg, Saxony, 03418, Germany ST:EMAIL beatrice.engelmann@ufz.de ST:PHONE 00493412351099 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - A_d11 Day:11 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d12 Day:12 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d13 Day:13 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d14 Day:14 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d15 Day:15 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d18 Day:18 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d19 Day:19 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - A_d20 Day:20 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d11 Day:11 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d12 Day:12 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d13 Day:13 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d14 Day:14 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d15 Day:15 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d18 Day:18 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d19 Day:19 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - B_d20 Day:20 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d11 Day:11 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d12 Day:12 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d13 Day:13 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d14 Day:14 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d15 Day:15 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d18 Day:18 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d19 Day:19 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - C_d20 Day:20 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d11 Day:11 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d12 Day:12 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d13 Day:13 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d14 Day:14 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d15 Day:15 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d18 Day:18 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d19 Day:19 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - D_d20 Day:20 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d11 Day:11 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d12 Day:12 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d13 Day:13 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d14 Day:14 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d15 Day:15 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d18 Day:18 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d19 Day:19 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - E_d20 Day:20 | Treatment:control RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d11 Day:11 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d12 Day:12 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d13 Day:13 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d14 Day:14 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d15 Day:15 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d18 Day:18 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d19 Day:19 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff SUBJECT_SAMPLE_FACTORS - F_d20 Day:20 | Treatment:1%DSS RAW_FILE_NAME=20191111_Jannike_A_B_C_D_E_F_11-20_Whg_Ret.wiff #COLLECTION CO:COLLECTION_SUMMARY Samples were taken at day 1 and as a multiple of 24 h during the control phase CO:COLLECTION_SUMMARY (day 12-14) and the early (day 15) and late treatment phase (day 18 to day 20) CO:COLLECTION_SUMMARY from the bioreactors under unaerobic conditions. CO:SAMPLE_TYPE Feces #TREATMENT TR:TREATMENT_SUMMARY Faecal pellets were isolated from the colon under aseptic conditions. Directly TR:TREATMENT_SUMMARY after collection, faecal pellets were stored at anaerobic conditions. The murine TR:TREATMENT_SUMMARY microbiota was cultivated in the chemostats from day 1 to day 13. At day 14, the TR:TREATMENT_SUMMARY bioreactors B, D and F were spiked with 1% DSS. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY In brief, 20 µl of each sample was mixed with ACN to a final concentration of SP:SAMPLEPREP_SUMMARY 50 %. SCFAs were derivatized with 200 mM 3-nitrophenylhydrazine and 120 mM SP:SAMPLEPREP_SUMMARY N-(3-dimethylaminopropyl)-N‘-ethylcarbodiimide hydrochloride in pyridine and SP:SAMPLEPREP_SUMMARY then diluted in 10 % ACN. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 RS CH:COLUMN_NAME Waters Acquity BEH C18 (100 x 2mm, 1.7um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME ABI Sciex 5500 QTrap MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS For identification and quantitation, a scheduled MRM method was used, with MS:MS_COMMENTS specific transitions for every SCFA. Data acquisition and peak integration were MS:MS_COMMENTS performed in Analyst® software (Version 1.6.2). Calculation of concentration MS:MS_COMMENTS was done using external calibration curves and statistics were performed using MS:MS_COMMENTS the R software programme. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS µM MS_METABOLITE_DATA_START Samples A_d11 A_d12 A_d13 A_d14 A_d15 A_d18 A_d19 A_d20 B_d11 B_d12 B_d13 B_d14 B_d15 B_d18 B_d19 B_d20 C_d11 C_d12 C_d13 C_d14 C_d15 C_d18 C_d19 C_d20 D_d11 D_d12 D_d13 D_d14 D_d15 D_d18 D_d19 D_d20 E_d11 E_d12 E_d13 E_d14 E_d15 E_d18 E_d19 E_d20 F_d11 F_d12 F_d13 F_d14 F_d15 F_d18 F_d19 F_d20 Factors Day:11 | Treatment:control Day:12 | Treatment:control Day:13 | Treatment:control Day:14 | Treatment:control Day:15 | Treatment:control Day:18 | Treatment:control Day:19 | Treatment:control Day:20 | Treatment:control Day:11 | Treatment:1%DSS Day:12 | Treatment:1%DSS Day:13 | Treatment:1%DSS Day:14 | Treatment:1%DSS Day:15 | Treatment:1%DSS Day:18 | Treatment:1%DSS Day:19 | Treatment:1%DSS Day:20 | Treatment:1%DSS Day:11 | Treatment:control Day:12 | Treatment:control Day:13 | Treatment:control Day:14 | Treatment:control Day:15 | Treatment:control Day:18 | Treatment:control Day:19 | Treatment:control Day:20 | Treatment:control Day:11 | Treatment:1%DSS Day:12 | Treatment:1%DSS Day:13 | Treatment:1%DSS Day:14 | Treatment:1%DSS Day:15 | Treatment:1%DSS Day:18 | Treatment:1%DSS Day:19 | Treatment:1%DSS Day:20 | Treatment:1%DSS Day:11 | Treatment:control Day:12 | Treatment:control Day:13 | Treatment:control Day:14 | Treatment:control Day:15 | Treatment:control Day:18 | Treatment:control Day:19 | Treatment:control Day:20 | Treatment:control Day:11 | Treatment:1%DSS Day:12 | Treatment:1%DSS Day:13 | Treatment:1%DSS Day:14 | Treatment:1%DSS Day:15 | Treatment:1%DSS Day:18 | Treatment:1%DSS Day:19 | Treatment:1%DSS Day:20 | Treatment:1%DSS 2Methylbutyrate 1.580062703 0.989202942 0.760094055 1.278603642 1.278603642 2.086513927 2.026222115 1.881521765 1.580062703 0.916852767 0.434518268 0.470693356 0.386284819 1.242428554 1.326837092 0.892736042 4.305252623 1.218311829 1.230370192 1.121844929 0.543043531 1.145961654 1.375070541 1.471537441 3.521459062 1.314778729 0.350109731 0.108942482 0.325993006 1.121844929 1.145961654 0.760094055 0.97714458 0.953027855 0.63951043 0.88067768 0.711860605 1.145961654 1.350953816 1.435362354 49.76527915 72.31441698 68.09399011 80.15235259 76.53484384 78.70534909 78.94651634 61.46189075 Isobutyrate 24.65597523 24.09682402 22.13979479 22.698946 24.37639963 25.91406545 26.75279226 24.37639963 24.09682402 23.39788501 19.62361435 17.94616073 18.08594853 22.00000699 20.74191677 20.32255336 27.87109468 27.73130688 32.06472874 24.37639963 21.72043139 24.09682402 25.91406545 24.23661182 29.4087605 27.87109468 24.51618743 21.44085578 21.30106798 24.23661182 28.70982149 23.95703622 21.58064358 24.09682402 25.77427765 25.91406545 25.35491424 28.84960929 29.2689727 27.31194347 69.94722312 91.19496904 91.89390805 116.4965612 114.6793198 109.0878077 108.9480199 75.678523 IsoCaproate 0.358135486 0.360048593 0.478661208 0.601100036 0.685276731 0.834499053 0.765627212 0.687189838 0.348569953 0.342830633 0.405963154 0.520749555 0.513097128 0.629796637 0.675711197 0.570490329 0.689102944 0.733104398 1.012417976 0.733104398 0.706320905 0.763714105 0.83067284 0.698668478 0.666145664 0.685276731 0.612578677 0.668058771 0.742669932 0.738843718 0.868934974 0.643188384 0.687189838 0.614491783 0.648927704 0.681450517 0.736930612 0.845977693 0.821107306 0.723538865 0.606839356 0.65084081 0.539880622 0.692929158 0.641275277 0.692929158 0.708234011 0.358135486 Butyrate 9340.205587 9521.739091 9657.889219 9612.505843 9839.422723 7797.1708 7978.704305 7570.25392 8387.154689 8840.98845 7116.420159 8251.004561 8024.087681 6662.586399 5618.768749 7751.787424 8296.387937 8614.07157 9294.822211 9612.505843 7615.637296 10111.72298 9113.288706 9067.90533 9294.822211 6934.886655 5664.152125 6662.586399 8251.004561 5845.685629 8251.004561 8024.087681 10247.87311 6844.119903 7978.704305 9113.288706 9022.521954 8205.621185 8024.087681 7524.870544 10928.62375 11563.99101 8069.471057 9022.521954 8886.371826 8523.304817 7161.803535 3558.363475 Acetate 20122.09997 19093.82234 21264.63068 21264.63068 21378.88375 18065.5447 18179.79777 16466.00171 19322.32848 20236.35304 18179.79777 19093.82234 20350.60611 15551.97715 12352.89117 17837.03856 15551.97715 17837.03856 19322.32848 21721.64296 16808.76093 21607.38989 19093.82234 19208.07541 17837.03856 15666.23022 12809.90346 18294.05084 22521.41445 15894.73636 21835.89603 20350.60611 20236.35304 16123.2425 19893.59383 22635.66752 22064.40217 22178.65524 22521.41445 20464.85918 22064.40217 23092.67981 17951.29163 21607.38989 21950.1491 22864.17366 19550.83462 9667.944016 Caproate 2.059462306 1.889109831 1.656811002 1.966542774 1.734243945 1.935569597 2.198841603 2.22981478 2.756358793 2.105922071 0.990887691 1.424512172 0.851508394 1.145753577 1.316106052 1.517431704 3.313875983 3.159010097 3.778473642 2.942197857 3.066090566 2.338220901 2.524059964 1.021860868 1.920083008 2.601492907 1.90459642 1.827163476 1.749730533 1.67229759 1.439998761 0.866994982 2.276274546 1.409025584 2.059462306 1.935569597 1.532918293 1.610351236 1.641324413 1.625837824 1.192213343 1.176726755 0.975401103 1.486458527 1.037347457 1.037347457 0.866994982 -0.759096822 Valerate 34.62576802 33.25866063 25.64191942 25.05601625 31.30565006 40.68010078 44.00021874 44.78142296 33.8445638 32.08685429 23.10300568 17.75175673 14.58787962 29.74324161 29.74324161 31.89155323 44.19551979 51.03105677 49.85925043 28.18083315 23.4936078 26.6184247 31.69625217 35.79757436 64.31152862 60.99141066 45.36732613 31.50095112 24.07951097 21.34529617 28.37613421 27.39962893 5.701681542 19.39228561 26.03252153 24.66541414 24.66541414 28.96203738 30.91504795 33.64926274 52.59346523 56.49948636 47.51563776 53.37466945 46.53913247 50.05455149 50.05455149 31.110349 Isovalerate 16.29526148 18.45403961 18.40007016 15.91747531 15.26984187 12.4634303 11.59991905 9.117324195 12.84121647 12.67930811 11.06022451 10.14274381 9.980835447 11.00625506 10.19671326 9.225263101 11.00625506 10.95228561 14.0825139 10.08877435 9.926865994 11.00625506 10.46656053 9.279232554 11.43801069 10.79037725 10.08877435 10.41259107 12.19358303 14.40633062 16.5111393 14.67617788 10.73640779 9.009385288 11.11419397 12.13961358 13.32694155 17.75243672 18.40007016 17.26671164 97.68119704 133.3010362 123.0468401 139.2376761 130.6025635 128.98348 125.7453128 80.95066652 Propionate 4742.98 3863.76 3503.05 4821.88 6005.45 7313.01 7989.33 7910.43 4990.96 4731.71 3345.24 1519.17 2883.09 4889.52 4292.1 6478.88 7651.17 6399.97 3593.23 4607.71 1947.51 4517.54 5013.51 7290.46 8936.18 7031.21 4675.35 3525.6 2792.91 3176.16 5092.41 5250.22 723.37 3965.21 3818.67 4269.55 3965.21 5103.68 6118.17 6749.4 7763.89 9759.04 8462.76 8710.74 8598.02 11382.22 10356.46 5317.85 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Kegg-number 2Methylbutyrate C18319 Isobutyrate C02632 IsoCaproate C21399 Butyrate C00246 Acetate C00033 Caproate C01585 Valerate C00803 Isovalerate C08262 Propionate C00163 METABOLITES_END #END