{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002393","ANALYSIS_ID":"AN003899","VERSION":"1","CREATED_ON":"December 6, 2022, 12:12 am"}, "PROJECT":{"PROJECT_TITLE":"Untargeted metabolomics analysis of DSS-treated murine intestinal microbiota using continuous cultivation in bioreactors","PROJECT_SUMMARY":"We cultivated murine faecal microbiota in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared to the untreated control bioreactors.","INSTITUTE":"Helmholtz Centre for Environmental Research","DEPARTMENT":"Molecular Systems Biology","LAST_NAME":"Engelmann","FIRST_NAME":"Beatrice","ADDRESS":"Permoserstrasse 15, 04318 Leipzig, Germany","EMAIL":"beatrice.engelmann@ufz.de","PHONE":"00493411099"}, "STUDY":{"STUDY_TITLE":"Untargeted metabolomics analysis of DSS-treated murine intestinal microbiota cultivated in continuous bioreactors","STUDY_SUMMARY":"We cultivated murine faecal microbiota in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared to the untreated control bioreactors.","INSTITUTE":"Helmholtz Centre for Environmental Research","DEPARTMENT":"Molecular Systems Biology","LAST_NAME":"Engelmann","FIRST_NAME":"Beatrice","ADDRESS":"Permoserstrasse 15, 04318 Leipzig, Germany","EMAIL":"beatrice.engelmann@ufz.de","PHONE":"+493411099"}, "SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"A_d11_n", "Factors":{"Day":"11","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d11_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d12_n", "Factors":{"Day":"12","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d12_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d13_n", "Factors":{"Day":"13","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d13_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d14_n", "Factors":{"Day":"14","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d14_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d15_n", "Factors":{"Day":"15","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d15_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d18_n", "Factors":{"Day":"18","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d18_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d19_n", "Factors":{"Day":"19","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d19_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d20_n", "Factors":{"Day":"20","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d20_n.d"} }, { "Subject ID":"-", "Sample ID":"A_d11_p", "Factors":{"Day":"11","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d11_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d12_p", "Factors":{"Day":"12","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d12_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d13_p", "Factors":{"Day":"13","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d13_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d14_p", "Factors":{"Day":"14","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d14_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d15_p", "Factors":{"Day":"15","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d15_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d18_p", "Factors":{"Day":"18","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d18_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d19_p", "Factors":{"Day":"19","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d19_p.d"} }, { "Subject ID":"-", "Sample ID":"A_d20_p", "Factors":{"Day":"20","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"A_d20_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d11_n", "Factors":{"Day":"11","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d11_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d12_n", "Factors":{"Day":"12","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d12_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d13_n", "Factors":{"Day":"13","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d13_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d14_n", "Factors":{"Day":"14","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d14_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d15_n", "Factors":{"Day":"15","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d15_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d18_n", "Factors":{"Day":"18","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d18_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d19_n", "Factors":{"Day":"19","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d19_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d20_n", "Factors":{"Day":"20","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d20_n.d"} }, { "Subject ID":"-", "Sample ID":"B_d11_p", "Factors":{"Day":"11","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d11_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d12_p", "Factors":{"Day":"12","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d12_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d13_p", "Factors":{"Day":"13","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d13_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d14_p", "Factors":{"Day":"14","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d14_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d15_p", "Factors":{"Day":"15","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d15_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d18_p", "Factors":{"Day":"18","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d18_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d19_p", "Factors":{"Day":"19","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d19_p.d"} }, { "Subject ID":"-", "Sample ID":"B_d20_p", "Factors":{"Day":"20","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"B_d20_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d11_n", "Factors":{"Day":"11","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d11_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d12_n", "Factors":{"Day":"12","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d12_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d13_n", "Factors":{"Day":"13","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d13_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d14_n", "Factors":{"Day":"14","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d14_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d15_n", "Factors":{"Day":"15","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d15_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d18_n", "Factors":{"Day":"18","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d18_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d19_n", "Factors":{"Day":"19","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d19_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d20_n", "Factors":{"Day":"20","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d20_n.d"} }, { "Subject ID":"-", "Sample ID":"C_d11_p", "Factors":{"Day":"11","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d11_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d12_p", "Factors":{"Day":"12","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d12_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d13_p", "Factors":{"Day":"13","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d13_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d14_p", "Factors":{"Day":"14","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d14_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d15_p", "Factors":{"Day":"15","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d15_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d18_p", "Factors":{"Day":"18","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d18_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d19_p", "Factors":{"Day":"19","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d19_p.d"} }, { "Subject ID":"-", "Sample ID":"C_d20_p", "Factors":{"Day":"20","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"C_d20_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d11_n", "Factors":{"Day":"11","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d11_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d12_n", "Factors":{"Day":"12","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d12_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d13_n", "Factors":{"Day":"13","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d13_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d14_n", "Factors":{"Day":"14","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d14_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d15_n", "Factors":{"Day":"15","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d15_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d18_n", "Factors":{"Day":"18","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d18_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d19_n", "Factors":{"Day":"19","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d19_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d20_n", "Factors":{"Day":"20","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d20_n.d"} }, { "Subject ID":"-", "Sample ID":"D_d11_p", "Factors":{"Day":"11","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d11_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d12_p", "Factors":{"Day":"12","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d12_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d13_p", "Factors":{"Day":"13","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d13_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d14_p", "Factors":{"Day":"14","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d14_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d15_p", "Factors":{"Day":"15","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d15_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d18_p", "Factors":{"Day":"18","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d18_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d19_p", "Factors":{"Day":"19","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d19_p.d"} }, { "Subject ID":"-", "Sample ID":"D_d20_p", "Factors":{"Day":"20","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"D_d20_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d11_n", "Factors":{"Day":"11","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d11_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d12_n", "Factors":{"Day":"12","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d12_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d13_n", "Factors":{"Day":"13","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d13_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d14_n", "Factors":{"Day":"14","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d14_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d15_n", "Factors":{"Day":"15","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d15_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d18_n", "Factors":{"Day":"18","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d18_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d19_n", "Factors":{"Day":"19","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d19_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d20_n", "Factors":{"Day":"20","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d20_n.d"} }, { "Subject ID":"-", "Sample ID":"E_d11_p", "Factors":{"Day":"11","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d11_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d12_p", "Factors":{"Day":"12","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d12_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d13_p", "Factors":{"Day":"13","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d13_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d14_p", "Factors":{"Day":"14","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d14_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d15_p", "Factors":{"Day":"15","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d15_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d18_p", "Factors":{"Day":"18","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d18_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d19_p", "Factors":{"Day":"19","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d19_p.d"} }, { "Subject ID":"-", "Sample ID":"E_d20_p", "Factors":{"Day":"20","Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"E_d20_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d11_n", "Factors":{"Day":"11","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d11_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d12_n", "Factors":{"Day":"12","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d12_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d13_n", "Factors":{"Day":"13","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d13_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d14_n", "Factors":{"Day":"14","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d14_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d15_n", "Factors":{"Day":"15","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d15_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d18_n", "Factors":{"Day":"18","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d18_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d19_n", "Factors":{"Day":"19","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d19_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d20_n", "Factors":{"Day":"20","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d20_n.d"} }, { "Subject ID":"-", "Sample ID":"F_d11_p", "Factors":{"Day":"11","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d11_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d12_p", "Factors":{"Day":"12","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d12_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d13_p", "Factors":{"Day":"13","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d13_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d14_p", "Factors":{"Day":"14","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d14_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d15_p", "Factors":{"Day":"15","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d15_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d18_p", "Factors":{"Day":"18","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d18_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d19_p", "Factors":{"Day":"19","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d19_p.d"} }, { "Subject ID":"-", "Sample ID":"F_d20_p", "Factors":{"Day":"20","Treatment":"1%DSS"}, "Additional sample data":{"RAW_FILE_NAME":"F_d20_p.d"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Samples were taken at day 1 and as a multiple of 24 h during the control phase (day 12-14) and the early (day 15) and late treatment phase (day 18 to day 20) from the bioreactors under unaerobic conditions.","SAMPLE_TYPE":"Feces"}, "TREATMENT":{"TREATMENT_SUMMARY":"Faecal pellets were isolated from the colon under aseptic conditions. Directly after collection, faecal pellets were stored at anaerobic conditions. The murine microbiota was cultivated in the chemostats from day 1 to day 13. At day 14, the bioreactors B, D and F were spiked with 1% DSS."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"In brief, culture supernatants were thawed and 100 µL were mixed with 500 µL methanol:acetonitrile (ACN):water (2:3:1) followed by vortex and sonication. After centrifugation, 100 µL of the supernatant were dried in a SpeedVac™ vacuum concentrator (Eppendorf, Hamburg, Germany). Prior to measurement, the extract was resuspended in 100 µl 1 % ACN and 0.1 % formic acid in water."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1260","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","SOLVENT_A":"Water + 0.1% FA","SOLVENT_B":"ACN + 0.1% FA"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Agilent 6540 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 60 – 1000 m/z. After each full scan, the five most intense ions (threshold 200 counts) were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.1, Waters Corporation) for further analysis.","MS_RESULTS_FILE":"ST002393_AN003899_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes"} }