#METABOLOMICS WORKBENCH engelmab_20221128_052657 DATATRACK_ID:3601 STUDY_ID:ST002393 ANALYSIS_ID:AN003898 PROJECT_ID:PR001540 VERSION 1 CREATED_ON December 6, 2022, 12:12 am #PROJECT PR:PROJECT_TITLE Untargeted metabolomics analysis of DSS-treated murine intestinal microbiota PR:PROJECT_TITLE 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, 04318 Leipzig, Germany PR:EMAIL beatrice.engelmann@ufz.de PR:PHONE 00493411099 #STUDY ST:STUDY_TITLE Untargeted metabolomics analysis of DSS-treated murine intestinal microbiota ST:STUDY_TITLE cultivated in continuous 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, 04318 Leipzig, Germany ST:EMAIL beatrice.engelmann@ufz.de ST:PHONE +493411099 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #FACTORS #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_n Day:11 | Treatment:control RAW_FILE_NAME=A_d11_n.d SUBJECT_SAMPLE_FACTORS - A_d12_n Day:12 | Treatment:control RAW_FILE_NAME=A_d12_n.d SUBJECT_SAMPLE_FACTORS - A_d13_n Day:13 | Treatment:control RAW_FILE_NAME=A_d13_n.d SUBJECT_SAMPLE_FACTORS - A_d14_n Day:14 | Treatment:control RAW_FILE_NAME=A_d14_n.d SUBJECT_SAMPLE_FACTORS - A_d15_n Day:15 | Treatment:control RAW_FILE_NAME=A_d15_n.d SUBJECT_SAMPLE_FACTORS - A_d18_n Day:18 | Treatment:control RAW_FILE_NAME=A_d18_n.d SUBJECT_SAMPLE_FACTORS - A_d19_n Day:19 | Treatment:control RAW_FILE_NAME=A_d19_n.d SUBJECT_SAMPLE_FACTORS - A_d20_n Day:20 | Treatment:control RAW_FILE_NAME=A_d20_n.d SUBJECT_SAMPLE_FACTORS - A_d11_p Day:11 | Treatment:control RAW_FILE_NAME=A_d11_p.d SUBJECT_SAMPLE_FACTORS - A_d12_p Day:12 | Treatment:control RAW_FILE_NAME=A_d12_p.d SUBJECT_SAMPLE_FACTORS - A_d13_p Day:13 | Treatment:control RAW_FILE_NAME=A_d13_p.d SUBJECT_SAMPLE_FACTORS - A_d14_p Day:14 | Treatment:control RAW_FILE_NAME=A_d14_p.d SUBJECT_SAMPLE_FACTORS - A_d15_p Day:15 | Treatment:control RAW_FILE_NAME=A_d15_p.d SUBJECT_SAMPLE_FACTORS - A_d18_p Day:18 | Treatment:control RAW_FILE_NAME=A_d18_p.d SUBJECT_SAMPLE_FACTORS - A_d19_p Day:19 | Treatment:control RAW_FILE_NAME=A_d19_p.d SUBJECT_SAMPLE_FACTORS - A_d20_p Day:20 | Treatment:control RAW_FILE_NAME=A_d20_p.d SUBJECT_SAMPLE_FACTORS - B_d11_n Day:11 | Treatment:1%DSS RAW_FILE_NAME=B_d11_n.d SUBJECT_SAMPLE_FACTORS - B_d12_n Day:12 | Treatment:1%DSS RAW_FILE_NAME=B_d12_n.d SUBJECT_SAMPLE_FACTORS - B_d13_n Day:13 | Treatment:1%DSS RAW_FILE_NAME=B_d13_n.d SUBJECT_SAMPLE_FACTORS - B_d14_n Day:14 | Treatment:1%DSS RAW_FILE_NAME=B_d14_n.d SUBJECT_SAMPLE_FACTORS - B_d15_n Day:15 | Treatment:1%DSS RAW_FILE_NAME=B_d15_n.d SUBJECT_SAMPLE_FACTORS - B_d18_n Day:18 | Treatment:1%DSS RAW_FILE_NAME=B_d18_n.d SUBJECT_SAMPLE_FACTORS - B_d19_n Day:19 | Treatment:1%DSS RAW_FILE_NAME=B_d19_n.d SUBJECT_SAMPLE_FACTORS - B_d20_n Day:20 | Treatment:1%DSS RAW_FILE_NAME=B_d20_n.d SUBJECT_SAMPLE_FACTORS - B_d11_p Day:11 | Treatment:1%DSS RAW_FILE_NAME=B_d11_p.d SUBJECT_SAMPLE_FACTORS - B_d12_p Day:12 | Treatment:1%DSS RAW_FILE_NAME=B_d12_p.d SUBJECT_SAMPLE_FACTORS - B_d13_p Day:13 | Treatment:1%DSS RAW_FILE_NAME=B_d13_p.d SUBJECT_SAMPLE_FACTORS - B_d14_p Day:14 | Treatment:1%DSS RAW_FILE_NAME=B_d14_p.d SUBJECT_SAMPLE_FACTORS - B_d15_p Day:15 | Treatment:1%DSS RAW_FILE_NAME=B_d15_p.d SUBJECT_SAMPLE_FACTORS - B_d18_p Day:18 | Treatment:1%DSS RAW_FILE_NAME=B_d18_p.d SUBJECT_SAMPLE_FACTORS - B_d19_p Day:19 | Treatment:1%DSS RAW_FILE_NAME=B_d19_p.d SUBJECT_SAMPLE_FACTORS - B_d20_p Day:20 | Treatment:1%DSS RAW_FILE_NAME=B_d20_p.d SUBJECT_SAMPLE_FACTORS - C_d11_n Day:11 | Treatment:control RAW_FILE_NAME=C_d11_n.d SUBJECT_SAMPLE_FACTORS - C_d12_n Day:12 | Treatment:control RAW_FILE_NAME=C_d12_n.d SUBJECT_SAMPLE_FACTORS - C_d13_n Day:13 | Treatment:control RAW_FILE_NAME=C_d13_n.d SUBJECT_SAMPLE_FACTORS - C_d14_n Day:14 | Treatment:control RAW_FILE_NAME=C_d14_n.d SUBJECT_SAMPLE_FACTORS - C_d15_n Day:15 | Treatment:control RAW_FILE_NAME=C_d15_n.d SUBJECT_SAMPLE_FACTORS - C_d18_n Day:18 | Treatment:control RAW_FILE_NAME=C_d18_n.d SUBJECT_SAMPLE_FACTORS - C_d19_n Day:19 | Treatment:control RAW_FILE_NAME=C_d19_n.d SUBJECT_SAMPLE_FACTORS - C_d20_n Day:20 | Treatment:control RAW_FILE_NAME=C_d20_n.d SUBJECT_SAMPLE_FACTORS - C_d11_p Day:11 | Treatment:control RAW_FILE_NAME=C_d11_p.d SUBJECT_SAMPLE_FACTORS - C_d12_p Day:12 | Treatment:control RAW_FILE_NAME=C_d12_p.d SUBJECT_SAMPLE_FACTORS - C_d13_p Day:13 | Treatment:control RAW_FILE_NAME=C_d13_p.d SUBJECT_SAMPLE_FACTORS - C_d14_p Day:14 | Treatment:control RAW_FILE_NAME=C_d14_p.d SUBJECT_SAMPLE_FACTORS - C_d15_p Day:15 | Treatment:control RAW_FILE_NAME=C_d15_p.d SUBJECT_SAMPLE_FACTORS - C_d18_p Day:18 | Treatment:control RAW_FILE_NAME=C_d18_p.d SUBJECT_SAMPLE_FACTORS - C_d19_p Day:19 | Treatment:control RAW_FILE_NAME=C_d19_p.d SUBJECT_SAMPLE_FACTORS - C_d20_p Day:20 | Treatment:control RAW_FILE_NAME=C_d20_p.d SUBJECT_SAMPLE_FACTORS - D_d11_n Day:11 | Treatment:1%DSS RAW_FILE_NAME=D_d11_n.d SUBJECT_SAMPLE_FACTORS - D_d12_n Day:12 | Treatment:1%DSS RAW_FILE_NAME=D_d12_n.d SUBJECT_SAMPLE_FACTORS - D_d13_n Day:13 | Treatment:1%DSS RAW_FILE_NAME=D_d13_n.d SUBJECT_SAMPLE_FACTORS - D_d14_n Day:14 | Treatment:1%DSS RAW_FILE_NAME=D_d14_n.d SUBJECT_SAMPLE_FACTORS - D_d15_n Day:15 | Treatment:1%DSS RAW_FILE_NAME=D_d15_n.d SUBJECT_SAMPLE_FACTORS - D_d18_n Day:18 | Treatment:1%DSS RAW_FILE_NAME=D_d18_n.d SUBJECT_SAMPLE_FACTORS - D_d19_n Day:19 | Treatment:1%DSS RAW_FILE_NAME=D_d19_n.d SUBJECT_SAMPLE_FACTORS - D_d20_n Day:20 | Treatment:1%DSS RAW_FILE_NAME=D_d20_n.d SUBJECT_SAMPLE_FACTORS - D_d11_p Day:11 | Treatment:1%DSS RAW_FILE_NAME=D_d11_p.d SUBJECT_SAMPLE_FACTORS - D_d12_p Day:12 | Treatment:1%DSS RAW_FILE_NAME=D_d12_p.d SUBJECT_SAMPLE_FACTORS - D_d13_p Day:13 | Treatment:1%DSS RAW_FILE_NAME=D_d13_p.d SUBJECT_SAMPLE_FACTORS - D_d14_p Day:14 | Treatment:1%DSS RAW_FILE_NAME=D_d14_p.d SUBJECT_SAMPLE_FACTORS - D_d15_p Day:15 | Treatment:1%DSS RAW_FILE_NAME=D_d15_p.d SUBJECT_SAMPLE_FACTORS - D_d18_p Day:18 | Treatment:1%DSS RAW_FILE_NAME=D_d18_p.d SUBJECT_SAMPLE_FACTORS - D_d19_p Day:19 | Treatment:1%DSS RAW_FILE_NAME=D_d19_p.d SUBJECT_SAMPLE_FACTORS - D_d20_p Day:20 | Treatment:1%DSS RAW_FILE_NAME=D_d20_p.d SUBJECT_SAMPLE_FACTORS - E_d11_n Day:11 | Treatment:control RAW_FILE_NAME=E_d11_n.d SUBJECT_SAMPLE_FACTORS - E_d12_n Day:12 | Treatment:control RAW_FILE_NAME=E_d12_n.d SUBJECT_SAMPLE_FACTORS - E_d13_n Day:13 | Treatment:control RAW_FILE_NAME=E_d13_n.d SUBJECT_SAMPLE_FACTORS - E_d14_n Day:14 | Treatment:control RAW_FILE_NAME=E_d14_n.d SUBJECT_SAMPLE_FACTORS - E_d15_n Day:15 | Treatment:control RAW_FILE_NAME=E_d15_n.d SUBJECT_SAMPLE_FACTORS - E_d18_n Day:18 | Treatment:control RAW_FILE_NAME=E_d18_n.d SUBJECT_SAMPLE_FACTORS - E_d19_n Day:19 | Treatment:control RAW_FILE_NAME=E_d19_n.d SUBJECT_SAMPLE_FACTORS - E_d20_n Day:20 | Treatment:control RAW_FILE_NAME=E_d20_n.d SUBJECT_SAMPLE_FACTORS - E_d11_p Day:11 | Treatment:control RAW_FILE_NAME=E_d11_p.d SUBJECT_SAMPLE_FACTORS - E_d12_p Day:12 | Treatment:control RAW_FILE_NAME=E_d12_p.d SUBJECT_SAMPLE_FACTORS - E_d13_p Day:13 | Treatment:control RAW_FILE_NAME=E_d13_p.d SUBJECT_SAMPLE_FACTORS - E_d14_p Day:14 | Treatment:control RAW_FILE_NAME=E_d14_p.d SUBJECT_SAMPLE_FACTORS - E_d15_p Day:15 | Treatment:control RAW_FILE_NAME=E_d15_p.d SUBJECT_SAMPLE_FACTORS - E_d18_p Day:18 | Treatment:control RAW_FILE_NAME=E_d18_p.d SUBJECT_SAMPLE_FACTORS - E_d19_p Day:19 | Treatment:control RAW_FILE_NAME=E_d19_p.d SUBJECT_SAMPLE_FACTORS - E_d20_p Day:20 | Treatment:control RAW_FILE_NAME=E_d20_p.d SUBJECT_SAMPLE_FACTORS - F_d11_n Day:11 | Treatment:1%DSS RAW_FILE_NAME=F_d11_n.d SUBJECT_SAMPLE_FACTORS - F_d12_n Day:12 | Treatment:1%DSS RAW_FILE_NAME=F_d12_n.d SUBJECT_SAMPLE_FACTORS - F_d13_n Day:13 | Treatment:1%DSS RAW_FILE_NAME=F_d13_n.d SUBJECT_SAMPLE_FACTORS - F_d14_n Day:14 | Treatment:1%DSS RAW_FILE_NAME=F_d14_n.d SUBJECT_SAMPLE_FACTORS - F_d15_n Day:15 | Treatment:1%DSS RAW_FILE_NAME=F_d15_n.d SUBJECT_SAMPLE_FACTORS - F_d18_n Day:18 | Treatment:1%DSS RAW_FILE_NAME=F_d18_n.d SUBJECT_SAMPLE_FACTORS - F_d19_n Day:19 | Treatment:1%DSS RAW_FILE_NAME=F_d19_n.d SUBJECT_SAMPLE_FACTORS - F_d20_n Day:20 | Treatment:1%DSS RAW_FILE_NAME=F_d20_n.d SUBJECT_SAMPLE_FACTORS - F_d11_p Day:11 | Treatment:1%DSS RAW_FILE_NAME=F_d11_p.d SUBJECT_SAMPLE_FACTORS - F_d12_p Day:12 | Treatment:1%DSS RAW_FILE_NAME=F_d12_p.d SUBJECT_SAMPLE_FACTORS - F_d13_p Day:13 | Treatment:1%DSS RAW_FILE_NAME=F_d13_p.d SUBJECT_SAMPLE_FACTORS - F_d14_p Day:14 | Treatment:1%DSS RAW_FILE_NAME=F_d14_p.d SUBJECT_SAMPLE_FACTORS - F_d15_p Day:15 | Treatment:1%DSS RAW_FILE_NAME=F_d15_p.d SUBJECT_SAMPLE_FACTORS - F_d18_p Day:18 | Treatment:1%DSS RAW_FILE_NAME=F_d18_p.d SUBJECT_SAMPLE_FACTORS - F_d19_p Day:19 | Treatment:1%DSS RAW_FILE_NAME=F_d19_p.d SUBJECT_SAMPLE_FACTORS - F_d20_p Day:20 | Treatment:1%DSS RAW_FILE_NAME=F_d20_p.d #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, culture supernatants were thawed and 100 µL were mixed with 500 µL SP:SAMPLEPREP_SUMMARY methanol:acetonitrile (ACN):water (2:3:1) followed by vortex and sonication. SP:SAMPLEPREP_SUMMARY After centrifugation, 100 µL of the supernatant were dried in a SpeedVac™ SP:SAMPLEPREP_SUMMARY vacuum concentrator (Eppendorf, Hamburg, Germany). Prior to measurement, the SP:SAMPLEPREP_SUMMARY extract was resuspended in 100 µl 1 % ACN and 0.1 % formic acid in water. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um) CH:SOLVENT_A Water + 0.1% FA CH:SOLVENT_B ACN + 0.1% FA #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6540 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS All samples were acquired in positive and negative ionization mode. The QTOF was MS:MS_COMMENTS set up in centroid mode with a scan range of 60 – 1000 m/z. After each full MS:MS_COMMENTS scan, the five most intense ions (threshold 200 counts) were subjected to MS:MS_COMMENTS fragmentation. The obtained raw data (.d-files) were imported into the MS:MS_COMMENTS Progenesis QI® software (version2.1, Waters Corporation) for further analysis. MS:MS_RESULTS_FILE ST002393_AN003898_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END