{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002518","ANALYSIS_ID":"AN004148","VERSION":"1","CREATED_ON":"02-08-2024"}, "PROJECT":{"PROJECT_TITLE":"Systems biology illuminates the alternative metabolic niche of the human gut bacterium Eggerthella lenta","PROJECT_TYPE":"Untargeted LC-MS","PROJECT_SUMMARY":"Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.","INSTITUTE":"University of California, San Francisco","DEPARTMENT":"Microbiology and Immunology","LABORATORY":"Peter Turnbaugh","LAST_NAME":"Noecker","FIRST_NAME":"Cecilia","ADDRESS":"513 Parnassus Ave HSW1501, San Francisco, CA 94143","EMAIL":"cecilia.noecker@ucsf.edu","PHONE":"415-502-3264","FUNDING_SOURCE":"This work was supported by the National Institutes of Health (2R01HL122593; 1R01AT011117; 1R01DK114034 to P.J.T., F32GM140808 to C.N.). P.J.T. is a Chan Zuckerberg Biohub Investigator and held an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund.","PUBLICATIONS":"https://doi.org/10.1101/2022.09.19.508335","DOI":"http://dx.doi.org/10.21228/M89B04"}, "STUDY":{"STUDY_TITLE":"Time course 3: Growth of Eggerthella lenta in defined media with some samples receiving 13C6 stable isotope labeled arginine","STUDY_TYPE":"Untargeted LC-MS","STUDY_SUMMARY":"This dataset contains untargeted metabolomics analysis of supernatants from Eggerthella lenta DSM 2243 grown in defined EDM1 media. One set of samples grew in EDM1 containing 13C6 stable isotope labeled arginine.","INSTITUTE":"University of California, San Francisco","LAST_NAME":"Noecker","FIRST_NAME":"Cecilia","ADDRESS":"513 Parnassus Ave HSW1501, San Francisco, CA 94143","EMAIL":"cecilia.noecker@ucsf.edu","PHONE":"415-502-3264","SUBMIT_DATE":"2023-03-22"}, "SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Eggerthella lenta","TAXONOMY_ID":"84112","GENOTYPE_STRAIN":"DSM 2243"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"MSA0029", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"HR_2243_TP0_2","F_ID":"F29","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0029.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0029.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0029.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0029.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0043", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"HR_2243_TP0_1","F_ID":"F43","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0043.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0043.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0043.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0043.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0050", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"HR_2243_TP0_3","F_ID":"F50","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0050.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0050.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0050.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0050.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0004", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"HR_2243_TP1_3","F_ID":"F4","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0004.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0004.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0004.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0049", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"HR_2243_TP1_1","F_ID":"F49","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0049.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0049.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0049.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0049.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0056", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"HR_2243_TP1_2","F_ID":"F56","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0056.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0056.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0056.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0056.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0031", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"HR_2243_TP2_1","F_ID":"F31","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0031.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0031.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0031.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0031.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0032", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"HR_2243_TP2_3","F_ID":"F32","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0032.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0032.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0032.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0032.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0064", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"HR_2243_TP2_2","F_ID":"F64","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0064.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0064.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0064.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0064.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0007", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"HR_2243_TP3_1","F_ID":"F7","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0007.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0007.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0007.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0014", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"HR_2243_TP3_2","F_ID":"F14","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0014.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0014.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0014.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0014.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0025", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"HR_2243_TP3_3","F_ID":"F25","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0025.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0025.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0025.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0025.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0044", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"HR_2243_TP4_3","F_ID":"F44","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0044.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0044.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0044.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0044.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0053", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"HR_2243_TP4_2","F_ID":"F53","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0053.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0053.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0053.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0053.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0060", "Factors":{"Strain":"2243","ArgGroup":"HR","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"HR_2243_TP4_1","F_ID":"F60","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0060.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0060.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0060.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0060.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0013", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"R_2243_TP0_1","F_ID":"F13","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0013.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0013.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0013.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0054", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"R_2243_TP0_3","F_ID":"F54","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0054.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0054.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0054.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0054.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0055", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"R_2243_TP0_2","F_ID":"F55","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0055.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0055.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0055.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0055.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0018", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"R_2243_TP1_3","F_ID":"F18","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0018.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0018.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0018.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0018.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0033", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"R_2243_TP1_2","F_ID":"F33","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0033.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0033.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0033.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0033.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0048", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"R_2243_TP1_1","F_ID":"F48","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0048.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0048.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0048.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0048.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0017", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"R_2243_TP2_2","F_ID":"F17","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0017.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0017.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0017.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0017.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0026", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"R_2243_TP2_3","F_ID":"F26","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0026.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0026.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0026.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0026.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0042", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"R_2243_TP2_1","F_ID":"F42","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0042.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0042.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0042.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0042.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0008", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"R_2243_TP3_1","F_ID":"F8","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0008.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0008.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0008.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0009", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"R_2243_TP3_3","F_ID":"F9","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0009.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0009.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0009.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0039", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"R_2243_TP3_2","F_ID":"F39","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0039.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0039.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0039.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0039.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0001", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_2243_TP4_2","F_ID":"F1","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0001.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0001.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0001.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0002", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_2243_TP4_1","F_ID":"F2","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0002.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0002.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0002.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0034", "Factors":{"Strain":"2243","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_2243_TP4_3","F_ID":"F34","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0034.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0034.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0034.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0034.mzML"} }, { "Subject ID":"-", "Sample ID":"BK1", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK1.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK1.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK1.mzML","RAW_FILE_NAME":"M00182_20220405Pos_BK1.mzML"} }, { "Subject ID":"-", "Sample ID":"BK2", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK2.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK2.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK2.mzML","RAW_FILE_NAME":"-"} }, { "Subject ID":"-", "Sample ID":"BK3", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK3.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK3.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK3.mzML","RAW_FILE_NAME":"M00182_20220405Pos_BK3.mzML"} }, { "Subject ID":"-", "Sample ID":"BK4", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK4.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK4.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK4.mzML","RAW_FILE_NAME":"M00182_20220405Pos_BK4.mzML"} }, { "Subject ID":"-", "Sample ID":"BK5", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK5.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK5.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK5.mzML","RAW_FILE_NAME":"M00182_20220405Pos_BK5.mzML"} }, { "Subject ID":"-", "Sample ID":"BK6", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK6.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK6.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK6.mzML","RAW_FILE_NAME":"M00182_20220405Pos_BK6.mzML"} }, { "Subject ID":"-", "Sample ID":"BK7", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_BK7.raw","RAW_FILE_NAME":"M00182_20220405Pos_BK7.raw","RAW_FILE_NAME":"M00182_20220405Neg_BK7.mzML","RAW_FILE_NAME":"M00182_20220405Pos_BK7.mzML"} }, { "Subject ID":"-", "Sample ID":"QC1", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC1.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC1.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC1.mzML","RAW_FILE_NAME":"M00182_20220405Pos_QC1.mzML"} }, { "Subject ID":"-", "Sample ID":"QC2", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC2.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC2.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC2.mzML","RAW_FILE_NAME":"M00182_20220405Pos_QC2.mzML"} }, { "Subject ID":"-", "Sample ID":"QC3", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC3.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC3.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC3.mzML","RAW_FILE_NAME":"M00182_20220405Pos_QC3.mzML"} }, { "Subject ID":"-", "Sample ID":"QC4", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC4.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC4.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC4.mzML","RAW_FILE_NAME":"M00182_20220405Pos_QC4.mzML"} }, { "Subject ID":"-", "Sample ID":"QC5", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC5.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC5.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC5.mzML","RAW_FILE_NAME":"M00182_20220405Pos_QC5.mzML"} }, { "Subject ID":"-", "Sample ID":"QC6", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC6.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC6.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC6.mzML","RAW_FILE_NAME":"M00182_20220405Pos_QC6.mzML"} }, { "Subject ID":"-", "Sample ID":"QC7", "Factors":{"Strain":"-","ArgGroup":"-","TimePoint":"-","Time":"-"}, "Additional sample data":{"Sample":"-","F_ID":"-","RAW_FILE_NAME":"M00182_20220405Neg_QC7.raw","RAW_FILE_NAME":"M00182_20220405Pos_QC7.raw","RAW_FILE_NAME":"M00182_20220405Neg_QC7.mzML","RAW_FILE_NAME":"-"} }, { "Subject ID":"-", "Sample ID":"MSA0028", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"HR_c_TP0_2","F_ID":"F28","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0028.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0028.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0028.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0028.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0059", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"HR_c_TP0_3","F_ID":"F59","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0059.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0059.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0059.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0059.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0062", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"HR_c_TP0_1","F_ID":"F62","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0062.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0062.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0062.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0062.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0012", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"HR_c_TP1_3","F_ID":"F12","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0012.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0012.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0012.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0012.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0024", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"HR_c_TP1_1","F_ID":"F24","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0024.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0024.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0024.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0024.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0046", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"HR_c_TP1_2","F_ID":"F46","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0046.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0046.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0046.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0046.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0030", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"HR_c_TP2_2","F_ID":"F30","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0030.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0030.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0030.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0030.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0038", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"HR_c_TP2_3","F_ID":"F38","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0038.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0038.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0038.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0038.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0057", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"HR_c_TP2_1","F_ID":"F57","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0057.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0057.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0057.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0057.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0016", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"HR_c_TP3_1","F_ID":"F16","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0016.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0016.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0016.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0016.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0027", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"HR_c_TP3_3","F_ID":"F27","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0027.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0027.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0027.mzML","RAW_FILE_NAME":"-"} }, { "Subject ID":"-", "Sample ID":"MSA0035", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"HR_c_TP3_2","F_ID":"F35","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0035.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0035.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0035.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0035.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0015", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"HR_c_TP4_3","F_ID":"F15","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0015.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0015.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0015.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0015.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0036", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"HR_c_TP4_1","F_ID":"F36","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0036.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0036.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0036.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0036.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0047", "Factors":{"Strain":"c","ArgGroup":"HR","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"HR_c_TP4_2","F_ID":"F47","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0047.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0047.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0047.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0047.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0045", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"R_c_TP0_3","F_ID":"F45","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0045.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0045.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0045.mzML","RAW_FILE_NAME":"-"} }, { "Subject ID":"-", "Sample ID":"MSA0052", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"R_c_TP0_2","F_ID":"F52","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0052.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0052.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0052.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0052.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0061", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP0","Time":"0"}, "Additional sample data":{"Sample":"R_c_TP0_1","F_ID":"F61","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0061.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0061.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0061.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0061.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0010", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"R_c_TP1_1","F_ID":"F10","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0010.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0010.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0010.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0010.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0021", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"R_c_TP1_3","F_ID":"F21","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0021.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0021.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0021.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0021.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0041", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP1","Time":"20"}, "Additional sample data":{"Sample":"R_c_TP1_2","F_ID":"F41","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0041.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0041.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0041.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0041.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0019", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"R_c_TP2_3","F_ID":"F19","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0019.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0019.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0019.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0019.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0022", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"R_c_TP2_2","F_ID":"F22","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0022.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0022.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0022.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0022.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0023", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP2","Time":"32"}, "Additional sample data":{"Sample":"R_c_TP2_1","F_ID":"F23","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0023.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0023.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0023.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0023.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0006", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"R_c_TP3_1","F_ID":"F6","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0006.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0006.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0006.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0020", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"R_c_TP3_3","F_ID":"F20","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0020.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0020.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0020.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0020.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0058", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP3","Time":"44"}, "Additional sample data":{"Sample":"R_c_TP3_2","F_ID":"F58","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0058.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0058.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0058.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0058.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0003", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_2_extra4","F_ID":"F3","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0003.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0003.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0003.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0005", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_1","F_ID":"F5","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0005.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0005.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0005.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0011", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_2_extra1","F_ID":"F11","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0011.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0011.raw","RAW_FILE_NAME":"-","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0011.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0037", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_2_extra2","F_ID":"F37","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0037.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0037.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0037.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0037.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0040", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_2_extra3","F_ID":"F40","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0040.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0040.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0040.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0040.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0051", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_2","F_ID":"F51","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0051.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0051.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0051.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0051.mzML"} }, { "Subject ID":"-", "Sample ID":"MSA0063", "Factors":{"Strain":"c","ArgGroup":"R","TimePoint":"TP4","Time":"56"}, "Additional sample data":{"Sample":"R_c_TP4_3","F_ID":"F63","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0063.raw","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0063.raw","RAW_FILE_NAME":"M00182_20220405_Neg_1_MSA0063.mzML","RAW_FILE_NAME":"M00182_20220405_Pos_1_MSA0063.mzML"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Time course experiments were conducted in tubes in the anaerobic chamber in a 37°C incubator. For all metabolomics experiments, three independent culture replicates were included for each condition, with an equal number of uninoculated control tubes. Starter cultures and inocula were prepared as described above for growth assays. 5mLs of defined media was added to VWR glass culture tubes (53283-800) with screw caps. The PBS-washed inoculum was added to culture tubes to obtain an approximate starting OD600 of 0.001. A preliminary growth assay was conducted to define time points spanning the exponential growth phase in the tested conditions. At each time point, OD600 measurements of all inoculated tubes were first measured using a Hach DR1900 spectrophotometer, with a paired control tube to normalize for the background. 100 μL from each tube were then transferred into a 96-well microplate, which was sealed and removed from the anaerobic chamber. Plates were centrifuged at 1,928 rcf at 4°C for 8 minutes, after which supernatants were collected into fresh polypropylene tubes or plates, sealed, and flash-frozen in liquid nitrogen. Two time course experiments were carried out with stable isotope-labeled substrates. Experimental groups included conditions in which sodium arginine in the defined media was replaced with 13C6 labeled arginine HCl, along with a matched experimental group with the same concentration of unlabeled substrate.","SAMPLE_TYPE":"Bacterial culture supernatant","COLLECTION_FREQUENCY":"at time points specified in study design table over 56 hours (full growth phase)","STORAGE_CONDITIONS":"-80℃"}, "TREATMENT":{"TREATMENT_SUMMARY":"For growth and metabolomics experiments, glycerol stocks of the 3 E. lenta strains were first streaked on BHI+ agar plates and incubated at 37°C for 2-3 days. Individual colonies were inoculated into 3-4 mL liquid BHI+ and incubated at 37°C for 40-48 hours, or until approximately early stationary phase. Culture optical density (600 nm wavelength absorbance, OD600) was measured using a Hach DR1900 spectrophotometer. 1 mL samples of BHI starter cultures were then centrifuged at 1,568 rcf for 4 minutes in a microcentrifuge (ThermoScientific mySpin 12) in the anaerobic chamber and resuspended in 1 mL sterile phosphate-buffered saline (PBS). The resulting suspension was vortexed and diluted to an approximate OD600 of 0.1, and used as inoculum into defined experimental conditions. Varying media conditions were prepared separately and all allowed to fully reduce in the anaerobic chamber prior to inoculation."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Bacterial culture supernatant and sterile media, used in culture, were thawed on wet ice. Once thawed, samples were homogenized by inversion five times. Extracellular culture supernatant samples were prepared as follows: 20 μL of culture supernatant were extracted using 80 μL of a chilled extraction solvent at −20°C (1:1 acetonitrile:methanol, 5% water containing stable isotope-labeled internal standards). Samples were homogenized via pipette action, incubated for 1 hour at −20°C, centrifuged at 4°C at 6000 rcf for 5 min. The supernatant was transferred to a new plate and immediately sealed and kept at 4°C prior to prompt analysis via LC-MS/MS."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Samples, sterile media, pools, and blanks were promptly added to a Thermo Vanquish Autosampler at 4°C in a Vanquish UHPLC (Thermo Fisher Scientific, Waltham, MA). Chromatographic separation was performed using an ACQUITY Bridged Ethylene Hybrid (BEH) Amide column 2.1 x 150 mm, 1.7-micron particle size, (Waters Corp. Milford, MA), using chromatographic conditions published elsewhere (HILIC method described in the Supplementary Methods of doi.org/10.1038/s41586-021-03707-9).","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)","COLUMN_TEMPERATURE":"40","FLOW_GRADIENT":"The gradient profile was held at 100% B for 2 minutes, from 100% B to 70% B in 5 minutes, holding at 70% B for 0.7 minute, from 70% B to 40% B for 1.3 minutes, holding at 40% B for 0.5 minutes, from 40% B to 30% B for 0.75 minutes, before returning to 100% B for 2.5 minutes and holding at 100% B for 4 minutes.","FLOW_RATE":"400 μL per minute","SOLVENT_A":"100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3","SOLVENT_B":"95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate","CHROMATOGRAPHY_TYPE":"HILIC"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. In SIRM samples, deuterated internal standards were replaced with CUDA and Val-Tyr-Val to enable untargeted enrichment analysis. LC-MS/MS analysis conditions for SIRM metabolomics were identical to those used for standard untargeted metabolomics. Intra- and extracellular untargeted data generated from SIRM experiments was analyzed separately using Compound Discoverer version 3.3 (Thermo Scientific, Bremen, Germany). Samples treated with labeled compounds were always paired with matched samples treated with unlabeled compounds in order to correct for naturally occurring isotope abundances. Unlabeled samples were used for compound detection and formula assignment via isotope pattern-based prediction, spectral library matches, or mass lists matches. The isotope patterns and formulas from the sample files then served as a reference for the detection of potential isotopologues per compound in the labeled sample type. A specification of the full Compound Discoverer workflow is available at https://github.com/turnbaughlab/2022_Noecker_ElentaMetabolism.","ION_MODE":"NEGATIVE"} }