{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001263","ANALYSIS_ID":"AN002097","VERSION":"1","CREATED_ON":"October 8, 2019, 1:27 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic Profiling of Oxalate-Degrading Probiotic Lactobacillus acidophilus and Lactobacillus gasseri","PROJECT_TYPE":"Metabolomic/Lipidomic Profiling","PROJECT_SUMMARY":"Metabolomic and lipidomic profiling of Lactobacillus acidophilus and Lactobacillus gasseri","INSTITUTE":"University of Florida","DEPARTMENT":"Pathology, Immunology and Laboratory Medicine","LABORATORY":"Timothy J. Garrett, PhD","LAST_NAME":"Chamberlain","FIRST_NAME":"Casey","ADDRESS":"UF Dept of Pathology PO Box 100275 Gainesville, FL 32610","EMAIL":"chamberlainc@ufl.edu","PHONE":"3522735720","FUNDING_SOURCE":"NIH"},

"STUDY":{"STUDY_TITLE":"Metabolomic Profiling of Oxalate-Degrading Probiotic Lactobacillus acidophilus and Lactobacillus gasseri","STUDY_TYPE":"Metabolomic/Lipidomic Profiling","STUDY_SUMMARY":"Metabolomic and lipidomic profiling of Lactobacillus acidophilus and Lactobacillus gasseri to identify unique differences in their biochemistry that could potentially influence their ability to serve as probiotic agents for oxalate diseases.","INSTITUTE":"University of Florida","DEPARTMENT":"Pathology, Immunology and Laboratory Medicine","LABORATORY":"Timothy J. Garrett, PhD","LAST_NAME":"Chamberlain","FIRST_NAME":"Casey","ADDRESS":"UF Dept of Pathology PO Box 100275 Gainesville, FL 32610","EMAIL":"chamberlainc@ufl.edu","PHONE":"3522735720","NUM_GROUPS":"2","TOTAL_SUBJECTS":"16","NUM_MALES":"N/A","NUM_FEMALES":"N/A"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Lactobacillus","TAXONOMY_ID":"1578","GENDER":"Not applicable","CELL_BIOSOURCE_OR_SUPPLIER":"American Type Culture Collection (ATCC)","CELL_STRAIN_DETAILS":"L. acidophilus (ATCC 4357), L. gasseri (ATCC 33323)"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_1",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_2",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_3",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_4",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_5",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_6",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_7",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. acidophilus_8",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_1",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_2",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_3",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_4",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_5",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_6",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_7",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
},
{
"Subject ID":"-",
"Sample ID":"L. gasseri_8",
"Factors":{"Factor":"data1"},
"Additional sample data":{"Concentration (mg/mL)":"75","Analyses":"Metabolomics, Lipidomics"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cultured in MRS media from frozen glycerol stocks for 24 hours. Harvested, washed, and resuspended in PBS-based buffer solution. Individual cultures treated as biological replicates.","SAMPLE_TYPE":"Bacterial cells","STORAGE_CONDITIONS":"-80℃","COLLECTION_TUBE_TEMP":"-80C"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment. Simply a metabolomic comparison between species."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Normalized to 75 mg/mL in PBS-based buffer solution. Metabolites extracted by protein precipitation using 8:1:1 acetonitrile:methanol:acetone. Lipids extracted using the Folch method with 4:2:1 chloroform:methanol:water."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Gradient elution was performed with 0.1% formic acid in water as solvent A and acetonitrile as solvent B, at a flow rate of 0.35 mL/min, as such: 0 - 3 min: 100% A, 3 - 13 min: 100% → 20% A, 13 - 16.5 min: 20% A, 16.5 - 20 min: 100% A at 0.6 mL/min (column flush & equilibration).","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)","FLOW_RATE":"0.35 mL/min","COLUMN_TEMPERATURE":"25","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"acetonitrile"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"See manuscript","MS_RESULTS_FILE":"ST001263_AN002097_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Minutes"}

}