{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001287","ANALYSIS_ID":"AN002148","VERSION":"1","CREATED_ON":"December 17, 2019, 12:59 pm"},

"PROJECT":{"PROJECT_TITLE":"Luminal succinate in UC-HMA (human microbiota-associated) mice.","PROJECT_TYPE":"MS analysis","PROJECT_SUMMARY":"Luminal succinate level in UC-HMA (UC patient derived microbiota colonized HMA) mice, C. difficile infection susceptible mice. Patients with ulcerative colitis (UC) are known to be at higher risk for Clostridium difficile (C. difficile) infection (CDI), and CDI in UC patients is recognized as a major clinical problem because it worsens UC outcome. In order to assess the role of gut dysbiosis, seen in UC patients, we have established a human microbiota-associated mouse model in which germ-free mice are colonized with gut microbiota from UC patients. Utilizing this model, we found that UC microbiota colonized HMA mice (UC-HMA mice) were susceptible to CDI. To address the mechanism by which UC-HMA mice are unable to acquire the colonization resistance against C. difficile, we analyzed the luminal metabolites in UC-HMA mice, especially in succinate which is a crucial metabolite doe the growth of C. difficile.","INSTITUTE":"University of Michigan","DEPARTMENT":"Internal Medicine-Gastroenterology","LABORATORY":"Kamada Lab","LAST_NAME":"Kamada","FIRST_NAME":"Nobuhiko","ADDRESS":"Ann Arbor, MI","EMAIL":"nkamada@umich.edu","PHONE":"734-763-2142"},

"STUDY":{"STUDY_TITLE":"Luminal succinate in UC-HMA (human microbiota-associated) mice.","STUDY_TYPE":"MS analysis","STUDY_SUMMARY":"Patients with ulcerative colitis (UC) are known to be at higher risk for Clostridium difficile (C. difficile) infection (CDI), and CDI in UC patients is recognized as a major clinical problem because it worsens UC outcome. In order to assess the role of gut dysbiosis, seen in UC patients, we have established a human microbiota-associated mouse model in which germ-free mice are colonized with gut microbiota from UC patients. Utilizing this model, we found that UC microbiota colonized HMA mice (UC-HMA mice) were susceptible to CDI. To address the mechanism by which UC-HMA mice are unable to acquire the colonization resistance against C. difficile, we analyzed the luminal metabolites in UC-HMA mice, especially in succinate which is a crucial metabolite doe the growth of C. difficile.","INSTITUTE":"University of Michigan","DEPARTMENT":"Biomedical Research Core Facilities","LABORATORY":"Metabolomics core","LAST_NAME":"Kachman","FIRST_NAME":"Maureen","ADDRESS":"Ann Arbor, MI","EMAIL":"mkachman@med.umich.edu","PHONE":"734-232-0842","NUM_GROUPS":"63","TOTAL_SUBJECTS":"3"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"UC-hGB"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"SU0024964",
"Sample ID":"S00034622",
"Factors":{"Replication":"#1","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_027.d"}
},
{
"Subject ID":"SU0024965",
"Sample ID":"S00034623",
"Factors":{"Replication":"#1","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_036.d"}
},
{
"Subject ID":"SU0024966",
"Sample ID":"S00034624",
"Factors":{"Replication":"#1","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_025.d"}
},
{
"Subject ID":"SU0024967",
"Sample ID":"S00034625",
"Factors":{"Replication":"#1","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_017.d"}
},
{
"Subject ID":"SU0024968",
"Sample ID":"S00034626",
"Factors":{"Replication":"#1","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_018.d"}
},
{
"Subject ID":"SU0024969",
"Sample ID":"S00034627",
"Factors":{"Replication":"#2","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_038.d"}
},
{
"Subject ID":"SU0024970",
"Sample ID":"S00034628",
"Factors":{"Replication":"#2","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_016.d"}
},
{
"Subject ID":"SU0024971",
"Sample ID":"S00034629",
"Factors":{"Replication":"#2","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_021.d"}
},
{
"Subject ID":"SU0024972",
"Sample ID":"S00034630",
"Factors":{"Replication":"#2","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_023.d"}
},
{
"Subject ID":"SU0024973",
"Sample ID":"S00034631",
"Factors":{"Replication":"#2","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_019.d"}
},
{
"Subject ID":"SU0024974",
"Sample ID":"S00034632",
"Factors":{"Replication":"#2","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_033.d"}
},
{
"Subject ID":"SU0024975",
"Sample ID":"S00034633",
"Factors":{"Replication":"#2","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_012.d"}
},
{
"Subject ID":"SU0024976",
"Sample ID":"S00034634",
"Factors":{"Replication":"#2","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_028.d"}
},
{
"Subject ID":"SU0024977",
"Sample ID":"S00034635",
"Factors":{"Replication":"#2","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_041.d"}
},
{
"Subject ID":"SU0024978",
"Sample ID":"S00034636",
"Factors":{"Replication":"#2","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_010.d"}
},
{
"Subject ID":"SU0024979",
"Sample ID":"S00034637",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_029.d"}
},
{
"Subject ID":"SU0024980",
"Sample ID":"S00034638",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_034.d"}
},
{
"Subject ID":"SU0024981",
"Sample ID":"S00034639",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_035.d"}
},
{
"Subject ID":"SU0024982",
"Sample ID":"S00034640",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_030.d"}
},
{
"Subject ID":"SU0024983",
"Sample ID":"S00034641",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_039.d"}
},
{
"Subject ID":"SU0024984",
"Sample ID":"S00034642",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_014.d"}
},
{
"Subject ID":"SU0024985",
"Sample ID":"S00034643",
"Factors":{"Replication":"#3","Treatment":"Ctrl"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_026.d"}
},
{
"Subject ID":"SU0024986",
"Sample ID":"S00034644",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_037.d"}
},
{
"Subject ID":"SU0024987",
"Sample ID":"S00034645",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_013.d"}
},
{
"Subject ID":"SU0024988",
"Sample ID":"S00034646",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_040.d"}
},
{
"Subject ID":"SU0024989",
"Sample ID":"S00034647",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_024.d"}
},
{
"Subject ID":"SU0024990",
"Sample ID":"S00034648",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_015.d"}
},
{
"Subject ID":"SU0024991",
"Sample ID":"S00034649",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_011.d"}
},
{
"Subject ID":"SU0024992",
"Sample ID":"S00034650",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_032.d"}
},
{
"Subject ID":"SU0024993",
"Sample ID":"S00034651",
"Factors":{"Replication":"#3","Treatment":"SuccinateConsumingBacteria"},
"Additional sample data":{"RAW_FILE_NAME":"2018-04-20_022.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mouse feces","SAMPLE_TYPE":"Feces"},

"TREATMENT":{"TREATMENT_SUMMARY":"None"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"2018-4-20_Succinate_fecal_EX00837.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent Q-TOF 6520","COLUMN_NAME":"Phenomenex Luna NH2, 1mm ID","METHODS_FILENAME":"002-HILIC-27min-1mm-flatInsert_-_A2B2.m.zip"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6520 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Agilent Quant V8 was used for data analysis"},

"MS_METABOLITE_DATA":{
"Units":"Peak area normalized",

"Data":[{"Metabolite":"STEARIC ACID","S00034622":"198345518","S00034623":"183116852","S00034624":"140240168","S00034625":"234455815","S00034626":"194128103","S00034627":"237120674","S00034628":"284712690","S00034629":"268690828","S00034630":"252873052","S00034631":"291647876","S00034632":"344062199","S00034633":"209840663","S00034634":"236940338","S00034635":"209316610","S00034636":"233439831","S00034637":"197776481","S00034638":"238284059","S00034639":"191918697","S00034640":"134382245","S00034641":"208358132","S00034642":"205445682","S00034643":"190292847","S00034644":"245961911","S00034645":"264987066","S00034646":"218492110","S00034647":"148169360","S00034648":"118875934","S00034649":"212548882","S00034650":"149897994","S00034651":"147915551"},{"Metabolite":"OLEIC ACID","S00034622":"418701428","S00034623":"398256327","S00034624":"319180059","S00034625":"491220037","S00034626":"383804209","S00034627":"387914108","S00034628":"478431158","S00034629":"406448667","S00034630":"414173010","S00034631":"490586951","S00034632":"511812654","S00034633":"358736311","S00034634":"436511837","S00034635":"332531035","S00034636":"364606093","S00034637":"381641164","S00034638":"365297528","S00034639":"374288684","S00034640":"271767250","S00034641":"390076896","S00034642":"356553000","S00034643":"324002517","S00034644":"360043595","S00034645":"389861078","S00034646":"328918318","S00034647":"247676740","S00034648":"203744089","S00034649":"349542612","S00034650":"258687565","S00034651":"303737177"},{"Metabolite":"PALMITIC ACID","S00034622":"249990853","S00034623":"247127596","S00034624":"188568482","S00034625":"284494675","S00034626":"264840551","S00034627":"274232757","S00034628":"317618255","S00034629":"299081913","S00034630":"277355753","S00034631":"317721355","S00034632":"346176035","S00034633":"258702849","S00034634":"278828017","S00034635":"234410515","S00034636":"272000064","S00034637":"244664916","S00034638":"298742857","S00034639":"251279409","S00034640":"170940373","S00034641":"281749592","S00034642":"251145284","S00034643":"245268919","S00034644":"285429133","S00034645":"283257804","S00034646":"272545336","S00034647":"194448935","S00034648":"153254839","S00034649":"244864095","S00034650":"193885493","S00034651":"196474608"},{"Metabolite":"TAURINE","S00034622":"9366535","S00034623":"7284149","S00034624":"11365623","S00034625":"8554694","S00034626":"8820796","S00034627":"6105660","S00034628":"7563650","S00034629":"8214745","S00034630":"7303694","S00034631":"6792147","S00034632":"13598546","S00034633":"13043335","S00034634":"15745267","S00034635":"9458928","S00034636":"5967214","S00034637":"31273646","S00034638":"13380590","S00034639":"17102684","S00034640":"20644912","S00034641":"17054478","S00034642":"32139491","S00034643":"10960365","S00034644":"12738879","S00034645":"10876095","S00034646":"17138947","S00034647":"9288535","S00034648":"5438632","S00034649":"9134353","S00034650":"10704306","S00034651":"10158336"},{"Metabolite":"MALATE","S00034622":"71621","S00034623":"76518","S00034624":"57217","S00034625":"32694","S00034626":"69128","S00034627":"55962","S00034628":"31547","S00034629":"34741","S00034630":"33612","S00034631":"53851","S00034632":"45494","S00034633":"70678","S00034634":"48456","S00034635":"72295","S00034636":"47410","S00034637":"55329","S00034638":"55902","S00034639":"58918","S00034640":"64819","S00034641":"43230","S00034642":"41131","S00034643":"37716","S00034644":"39638","S00034645":"21290","S00034646":"35763","S00034647":"64847","S00034648":"46028","S00034649":"43804","S00034650":"56267","S00034651":"57424"},{"Metabolite":"ALPHA-KETOGLUTARATE","S00034622":"323254","S00034623":"333042","S00034624":"656168","S00034625":"824512","S00034626":"729901","S00034627":"333971","S00034628":"419870","S00034629":"548742","S00034630":"681152","S00034631":"344366","S00034632":"660254","S00034633":"1318758","S00034634":"525151","S00034635":"329128","S00034636":"571147","S00034637":"1555984","S00034638":"469320","S00034639":"682421","S00034640":"1414988","S00034641":"594899","S00034642":"655473","S00034643":"546326","S00034644":"394782","S00034645":"583390","S00034646":"507155","S00034647":"1186406","S00034648":"586261","S00034649":"609644","S00034650":"979137","S00034651":"815542"},{"Metabolite":"CITRATE/ISOCITRATE","S00034622":"170722","S00034623":"273808","S00034624":"242034","S00034625":"172516","S00034626":"474121","S00034627":"148478","S00034628":"235951","S00034629":"278797","S00034630":"98090","S00034631":"280695","S00034632":"250816","S00034633":"171952","S00034634":"132093","S00034635":"422750","S00034636":"165452","S00034637":"181585","S00034638":"216723","S00034639":"420899","S00034640":"410023","S00034641":"274949","S00034642":"188647","S00034643":"212825","S00034644":"178447","S00034645":"292776","S00034646":"303479","S00034647":"263371","S00034648":"204196","S00034649":"280966","S00034650":"157187","S00034651":"176511"}],

"Metabolites":[{"Metabolite":"STEARIC ACID","quantified m/z":"283.264","retention index":"3.386","PubChem ID":"5281","KEGG ID":"","other_id":"HMDB0000827","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"QIQXTHQIDYTFRH-UHFFFAOYSA-N"},{"Metabolite":"OLEIC ACID","quantified m/z":"281.248","retention index":"3.469","PubChem ID":"445639","KEGG ID":"","other_id":"HMDB0000207","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"ZQPPMHVWECSIRJ-KTKRTIGZSA-N"},{"Metabolite":"PALMITIC ACID","quantified m/z":"255.233","retention index":"3.618","PubChem ID":"985","KEGG ID":"","other_id":"HMDB0000220","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"IPCSVZSSVZVIGE-UHFFFAOYSA-N"},{"Metabolite":"TAURINE","quantified m/z":"124.0068","retention index":"8.194","PubChem ID":"1123","KEGG ID":"","other_id":"HMDB0000251","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"XOAAWQZATWQOTB-UHFFFAOYSA-N"},{"Metabolite":"MALATE","quantified m/z":"133.0137","retention index":"14.5","PubChem ID":"525","KEGG ID":"","other_id":"HMDB0000744","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"BJEPYKJPYRNKOW-UHFFFAOYSA-N"},{"Metabolite":"ALPHA-KETOGLUTARATE","quantified m/z":"145.0137","retention index":"14.611","PubChem ID":"51","KEGG ID":"","other_id":"HMDB0000208","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"KPGXRSRHYNQIFN-UHFFFAOYSA-N"},{"Metabolite":"CITRATE/ISOCITRATE","quantified m/z":"191.0192","retention index":"15.4","PubChem ID":"311","KEGG ID":"","other_id":"HMDB0000094","other_id_type":"HMDB","id_confidence":"1","ri_type":"Time, min","inchi_key":"KRKNYBCHXYNGOX-UHFFFAOYSA-N"}]
}

}