{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001606","ANALYSIS_ID":"AN002639","VERSION":"1","CREATED_ON":"November 24, 2020, 12:34 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolic interactions between gut microbiota and the mammalian host","PROJECT_SUMMARY":"Untargeted metabolomics performed on various host compartments under different colonization states in gnotobiotic mice.","INSTITUTE":"Stanford University","LABORATORY":"Dodd","LAST_NAME":"Pruss","FIRST_NAME":"Kali","ADDRESS":"300 Pasteur Drive, Lane 235","EMAIL":"kmpruss@stanford.edu","PHONE":"6507212961"},

"STUDY":{"STUDY_TITLE":"Aromatic amino acid metabolism by the anaerobic gut bacterium Clostridium sporogenes","STUDY_SUMMARY":"Germ-free mice were mono-colonized with wild-type Clostridium sporogenes or its isogenic phenyllactate dehydratase (fldC) mutant. Feces, cecal contents, serum, and urine were collected for untargeted GC-TOF analysis.","INSTITUTE":"Stanford University","LABORATORY":"Dodd","LAST_NAME":"Pruss","FIRST_NAME":"Kali","ADDRESS":"300 Pasteur Drive, Lane 235","EMAIL":"kmpruss@stanford.edu","PHONE":"6507212961"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_WT-1_014",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa18_2"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_WT-2_015",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa06_2"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_WT-3_016",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa30_3"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_WT-4_017",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa38_3"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_WT-5_018",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa12_2"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_fldC-1_034",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa36_3"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_fldC-2_035",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa26_1"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_fldC-3_036",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa04_2"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_fldC-4_037",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa05_2"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Cecal Contents_fldC-5_038",
"Factors":{"host_compartment":"Cecal Contents","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa27_1"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_WT-1_009",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa35_3"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_WT-2_010",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa25_1"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_WT-3_011",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa24_1"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_WT-4_012",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa29_1"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_WT-5_013",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa22_1"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_fldC-1_029",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa39_3"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_fldC-2_030",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa17_2"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_fldC-3_031",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa37_3"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_fldC-4_032",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa14_2"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Feces_fldC-5_033",
"Factors":{"host_compartment":"Feces","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa32_3"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_WT-1_001",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa11_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_WT-2_002",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa23_1"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_WT-3_003",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa16_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_WT-4_004",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa09_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_WT-5_005",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa19_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_fldC-1_019",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa03_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_fldC-2_020",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa34_3"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_fldC-3_021",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa02_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_fldC-4_022",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa01_2"}
},
{
"Subject ID":"-",
"Sample ID":"3 - Serum_fldC-5_023",
"Factors":{"host_compartment":"Serum","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa31_3"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_WT-1_006",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa10_2"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_WT-4_007",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa40_3"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_WT-5_008",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa21_1"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_fldC-1_024",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa20_1"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_fldC-2_025",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa13_2"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_fldC-3_026",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa28_1"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_fldC-4_027",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa33_3"}
},
{
"Subject ID":"-",
"Sample ID":"4 - Urine_fldC-5_028",
"Factors":{"host_compartment":"Urine","bacterial_genotype":"fldC"},
"Additional sample data":{"RAW_FILE_NAME":"170306bOEsa08_2"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Feces, cecal contents, and urine were collected under sterile conditions and snap-frozen in liquid nitrogen prior to storage at -80. Whole blood was collected via cardiac puncture and centrifuged at room temperature for 10 minutes at 2,500 x g in serum separator tubes prior to storage at -80C.","SAMPLE_TYPE":"Feces;Urine;Serum","STORAGE_VIALS":"-80"},

"TREATMENT":{"TREATMENT_SUMMARY":"Swiss-webster germ-free mice were maintained in sterile gnotobiotic isolators for the duration of the experiment. Mice were mono-colonized with either strain (WT or fldC mutant) of Clostridium sporogenes and tissues collected four weeks thereafter."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Bacteria were grown anaerobically from glycerol stocks maintained at -80C and gavaged to individual mice in 200 µl volumes."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Injector conditions: Agilent 6890 GC is equipped with a Gerstel automatic liner exchange system (ALEX) that includes a multipurpose sample (MPS2) dual rail, and a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany) with temperature program as follows: 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume is 0.5 μl with 10 μl/s injection speed on a splitless injector with purge time of 25 seconds. Liner (Gerstel #011711-010-00) is changed after every 10 samples, (using the Maestro1 Gerstel software vs. 1.1.4.18). Before and after each injection, the 10 μl injection syringe is washed three times with 10 μl ethyl acetate. Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min.","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890 GC","COLUMN_NAME":"Restekâ„¢ Rtxâ„¢-5Sil (30m x 0.25mm, 0.25µm)","CHROMATOGRAPHY_COMMENTS":"0 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film))"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Leco Pegasus IV TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da. Data processing: Peaks reported are normalized to average mtic for each treatment. The algorithm used was developed to replace missing values, assuming each study investigates a specific organ. When very different organs (like in this study) are tested, a compound that is found in one organ but not in others would still be yielding data through noise replacements, or sometimes by adjacent compounds. We therefore report % of positive detections for all compounds in each organ.","MS_RESULTS_FILE":"ST001606_AN002639_Results.txt UNITS:peak area Has m/z:No Has RT:No RT units:No RT data"},

"MS_METABOLITE_DATA":{
"Units":"peak area",

"Data":[{"Metabolite":"zymosterol","1 - Cecal Contents_WT-1_014":"1396","1 - Cecal Contents_WT-2_015":"1258","1 - Cecal Contents_WT-3_016":"1197","1 - Cecal Contents_WT-4_017":"138","1 - Cecal Contents_WT-5_018":"1549","1 - Cecal Contents_fldC-1_034":"1292","1 - Cecal Contents_fldC-2_035":"1280","1 - Cecal Contents_fldC-3_036":"1072","1 - Cecal Contents_fldC-4_037":"1470","1 - Cecal Contents_fldC-5_038":"1473","2 - Feces_WT-1_009":"735","2 - Feces_WT-2_010":"2105","2 - Feces_WT-3_011":"1413","2 - Feces_WT-4_012":"878","2 - Feces_WT-5_013":"922","2 - Feces_fldC-1_029":"598","2 - Feces_fldC-2_030":"1032","2 - Feces_fldC-3_031":"1433","2 - Feces_fldC-4_032":"1282","2 - Feces_fldC-5_033":"601","3 - Serum_WT-1_001":"219","3 - Serum_WT-2_002":"240","3 - Serum_WT-3_003":"135","3 - Serum_WT-4_004":"118","3 - Serum_WT-5_005":"150","3 - Serum_fldC-1_019":"161","3 - Serum_fldC-2_020":"193","3 - Serum_fldC-3_021":"156","3 - Serum_fldC-4_022":"282","3 - Serum_fldC-5_023":"216","4 - Urine_WT-1_006":"92","4 - Urine_WT-4_007":"333","4 - Urine_WT-5_008":"153","4 - Urine_fldC-1_024":"95","4 - Urine_fldC-2_025":"158","4 - Urine_fldC-3_026":"174","4 - Urine_fldC-4_027":"155","4 - Urine_fldC-5_028":"261"},{"Metabolite":"xylulose NIST","1 - Cecal Contents_WT-1_014":"1229","1 - Cecal Contents_WT-2_015":"1268","1 - Cecal Contents_WT-3_016":"1758","1 - Cecal Contents_WT-4_017":"1224","1 - Cecal Contents_WT-5_018":"1437","1 - Cecal Contents_fldC-1_034":"1480","1 - Cecal Contents_fldC-2_035":"1428","1 - Cecal Contents_fldC-3_036":"1442","1 - Cecal Contents_fldC-4_037":"1527","1 - Cecal Contents_fldC-5_038":"1570","2 - Feces_WT-1_009":"942","2 - Feces_WT-2_010":"212","2 - Feces_WT-3_011":"1110","2 - Feces_WT-4_012":"1289","2 - Feces_WT-5_013":"1096","2 - Feces_fldC-1_029":"1120","2 - Feces_fldC-2_030":"1274","2 - Feces_fldC-3_031":"1327","2 - Feces_fldC-4_032":"1687","2 - Feces_fldC-5_033":"1714","3 - Serum_WT-1_001":"573","3 - Serum_WT-2_002":"449","3 - Serum_WT-3_003":"480","3 - Serum_WT-4_004":"529","3 - Serum_WT-5_005":"684","3 - Serum_fldC-1_019":"524","3 - Serum_fldC-2_020":"487","3 - Serum_fldC-3_021":"380","3 - Serum_fldC-4_022":"324","3 - Serum_fldC-5_023":"446","4 - Urine_WT-1_006":"1748","4 - Urine_WT-4_007":"1332","4 - Urine_WT-5_008":"1446","4 - Urine_fldC-1_024":"1158","4 - Urine_fldC-2_025":"870","4 - Urine_fldC-3_026":"2206","4 - Urine_fldC-4_027":"722","4 - Urine_fldC-5_028":"1746"},{"Metabolite":"xylose","1 - Cecal Contents_WT-1_014":"6647","1 - Cecal Contents_WT-2_015":"6091","1 - Cecal Contents_WT-3_016":"7335","1 - Cecal Contents_WT-4_017":"5848","1 - Cecal Contents_WT-5_018":"6297","1 - Cecal Contents_fldC-1_034":"4643","1 - Cecal Contents_fldC-2_035":"3520","1 - Cecal Contents_fldC-3_036":"4951","1 - Cecal Contents_fldC-4_037":"6680","1 - Cecal Contents_fldC-5_038":"6928","2 - Feces_WT-1_009":"5518","2 - Feces_WT-2_010":"415","2 - Feces_WT-3_011":"7275","2 - Feces_WT-4_012":"4392","2 - Feces_WT-5_013":"5434","2 - Feces_fldC-1_029":"3926","2 - Feces_fldC-2_030":"2169","2 - Feces_fldC-3_031":"4824","2 - Feces_fldC-4_032":"7401","2 - Feces_fldC-5_033":"5905","3 - Serum_WT-1_001":"186","3 - Serum_WT-2_002":"207","3 - Serum_WT-3_003":"111","3 - Serum_WT-4_004":"176","3 - Serum_WT-5_005":"141","3 - Serum_fldC-1_019":"259","3 - Serum_fldC-2_020":"132","3 - Serum_fldC-3_021":"56","3 - Serum_fldC-4_022":"76","3 - Serum_fldC-5_023":"171","4 - Urine_WT-1_006":"1071","4 - Urine_WT-4_007":"1909","4 - Urine_WT-5_008":"1482","4 - Urine_fldC-1_024":"870","4 - Urine_fldC-2_025":"467","4 - Urine_fldC-3_026":"1835","4 - Urine_fldC-4_027":"1328","4 - Urine_fldC-5_028":"1234"},{"Metabolite":"xylonic acid","1 - Cecal Contents_WT-1_014":"957","1 - Cecal Contents_WT-2_015":"935","1 - Cecal Contents_WT-3_016":"1063","1 - Cecal Contents_WT-4_017":"663","1 - Cecal Contents_WT-5_018":"969","1 - Cecal Contents_fldC-1_034":"881","1 - Cecal Contents_fldC-2_035":"751","1 - Cecal Contents_fldC-3_036":"1105","1 - Cecal Contents_fldC-4_037":"1003","1 - Cecal Contents_fldC-5_038":"1010","2 - Feces_WT-1_009":"586","2 - Feces_WT-2_010":"544","2 - Feces_WT-3_011":"796","2 - Feces_WT-4_012":"524","2 - Feces_WT-5_013":"651","2 - Feces_fldC-1_029":"603","2 - Feces_fldC-2_030":"645","2 - Feces_fldC-3_031":"962","2 - Feces_fldC-4_032":"994","2 - Feces_fldC-5_033":"728","3 - Serum_WT-1_001":"149","3 - Serum_WT-2_002":"134","3 - Serum_WT-3_003":"151","3 - Serum_WT-4_004":"158","3 - Serum_WT-5_005":"153","3 - Serum_fldC-1_019":"122","3 - Serum_fldC-2_020":"124","3 - Serum_fldC-3_021":"112","3 - Serum_fldC-4_022":"182","3 - Serum_fldC-5_023":"60","4 - Urine_WT-1_006":"395","4 - Urine_WT-4_007":"501","4 - Urine_WT-5_008":"466","4 - Urine_fldC-1_024":"462","4 - Urine_fldC-2_025":"198","4 - Urine_fldC-3_026":"579","4 - Urine_fldC-4_027":"398","4 - Urine_fldC-5_028":"265"},{"Metabolite":"xylitol","1 - Cecal Contents_WT-1_014":"13759","1 - Cecal Contents_WT-2_015":"13790","1 - Cecal Contents_WT-3_016":"15269","1 - Cecal Contents_WT-4_017":"12553","1 - Cecal Contents_WT-5_018":"13747","1 - Cecal Contents_fldC-1_034":"11214","1 - Cecal Contents_fldC-2_035":"10143","1 - Cecal Contents_fldC-3_036":"12660","1 - Cecal Contents_fldC-4_037":"12861","1 - Cecal Contents_fldC-5_038":"14661","2 - Feces_WT-1_009":"11294","2 - Feces_WT-2_010":"9663","2 - Feces_WT-3_011":"12975","2 - Feces_WT-4_012":"13153","2 - Feces_WT-5_013":"11274","2 - Feces_fldC-1_029":"10305","2 - Feces_fldC-2_030":"13291","2 - Feces_fldC-3_031":"12033","2 - Feces_fldC-4_032":"14261","2 - Feces_fldC-5_033":"13058","3 - Serum_WT-1_001":"1203","3 - Serum_WT-2_002":"702","3 - Serum_WT-3_003":"821","3 - Serum_WT-4_004":"913","3 - Serum_WT-5_005":"655","3 - Serum_fldC-1_019":"592","3 - Serum_fldC-2_020":"712","3 - Serum_fldC-3_021":"549","3 - Serum_fldC-4_022":"525","3 - Serum_fldC-5_023":"644","4 - Urine_WT-1_006":"16646","4 - Urine_WT-4_007":"16411","4 - Urine_WT-5_008":"14247","4 - Urine_fldC-1_024":"16091","4 - Urine_fldC-2_025":"11993","4 - Urine_fldC-3_026":"20833","4 - Urine_fldC-4_027":"14941","4 - Urine_fldC-5_028":"17924"},{"Metabolite":"xanthurenic acid","1 - 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