{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003361","ANALYSIS_ID":"AN005503","PROJECT_ID":"PR002087","VERSION":"1","CREATED_ON":"August 1, 2024, 5:02 pm"},

"PROJECT":{"PROJECT_TITLE":"Bile acid–induced gut mitochondrial dysfunction promotes Enterobacteriaceae colonization and associates with dysbiosis in Crohn''s disease","PROJECT_SUMMARY":"Members of the Enterobacteriaceae family of bacteria are often overrepresented in inflammatory bowel disease (IBD). Bile acids (BAs) are cholesterol derivatives that are known to affect the growth of potentially pathogenic commensals (pathobionts), including those from the Enterobacteriaceae family. Furthermore, BAs are often increased in the colonic lumen of IBD patients, including patients with Crohn’s disease (CD). Here, we investigated whether bile acids influence gut colonization by Enterobacteriaceae.","INSTITUTE":"University of British Columbia","LAST_NAME":"Finlay","FIRST_NAME":"Brett","ADDRESS":"office: MSL 333 lab: MSL 363","EMAIL":"bfinlay@interchange.ubc.ca","PHONE":"604-822-2210","FUNDING_SOURCE":"Canadian Institutes of Health Research (CIHR) [FDN-159935] and Genome Canada/Genome BC (264PRO)"},

"STUDY":{"STUDY_TITLE":"Bile acid–induced gut mitochondrial dysfunction promotes Enterobacteriaceae colonization and associates with dysbiosis in Crohn''s disease","STUDY_SUMMARY":"Here, we investigated whether bile acids influence gut colonization by Enterobacteriaceae. In an external human dataset, we found association between mucosal Enterobacteriaceae and the expression of mitochondrial damage–related genes. In a murine model, increased intestinal BA availability enhanced colonization by E. coli in an oxygen-dependent manner. Overall, this study establishes BAs as a potential bridge that facilitates interactions between commensals and the host epithelium, laying the essential foundation for future investigations into various intestinal diseases.","INSTITUTE":"University of British Columbia","LAST_NAME":"Finlay","FIRST_NAME":"Brett","ADDRESS":"office: MSL 333 lab: MSL 363","EMAIL":"bfinlay@msl.ubc.ca","PHONE":"604-822-2210"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"A1",
"Factors":{"Time point":"Day 0","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/6","RAW_FILE_NAME(Raw file name)":"A1_5-2-2024_Y-A1_18341"}
},
{
"Subject ID":"-",
"Sample ID":"A2",
"Factors":{"Time point":"Day 0","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/7","RAW_FILE_NAME(Raw file name)":"A2_5-1-2024_Y-A2_18308"}
},
{
"Subject ID":"-",
"Sample ID":"A3",
"Factors":{"Time point":"Day 0","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/8","RAW_FILE_NAME(Raw file name)":"A3_5-2-2024_Y-A3_18337"}
},
{
"Subject ID":"-",
"Sample ID":"A4",
"Factors":{"Time point":"Day 0","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/9","RAW_FILE_NAME(Raw file name)":"A4_5-2-2024_Y-A4_18354"}
},
{
"Subject ID":"-",
"Sample ID":"A5",
"Factors":{"Time point":"Day 0","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/10","RAW_FILE_NAME(Raw file name)":"A5_5-1-2024_Y-A5_18300"}
},
{
"Subject ID":"-",
"Sample ID":"A6",
"Factors":{"Time point":"Day 0","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/11","RAW_FILE_NAME(Raw file name)":"A6_5-1-2024_Y-A6_18317"}
},
{
"Subject ID":"-",
"Sample ID":"A7",
"Factors":{"Time point":"Day 0","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/12","RAW_FILE_NAME(Raw file name)":"A7_5-1-2024_Y-A7_18315"}
},
{
"Subject ID":"-",
"Sample ID":"A8",
"Factors":{"Time point":"Day 0","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/13","RAW_FILE_NAME(Raw file name)":"A8_5-1-2024_Y-A8_18325"}
},
{
"Subject ID":"-",
"Sample ID":"A9",
"Factors":{"Time point":"Day 0","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/14","RAW_FILE_NAME(Raw file name)":"A9_5-1-2024_Y-A9_18327"}
},
{
"Subject ID":"-",
"Sample ID":"A10",
"Factors":{"Time point":"Day 0","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/15","RAW_FILE_NAME(Raw file name)":"A10_5-2-2024_Y-B1_18345"}
},
{
"Subject ID":"-",
"Sample ID":"A11",
"Factors":{"Time point":"Day 0","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/16","RAW_FILE_NAME(Raw file name)":"A11_5-1-2024_Y-B2_18304"}
},
{
"Subject ID":"-",
"Sample ID":"A12",
"Factors":{"Time point":"Day 0","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/17","RAW_FILE_NAME(Raw file name)":"A12_5-2-2024_Y-B3_18331"}
},
{
"Subject ID":"-",
"Sample ID":"C1",
"Factors":{"Time point":"Day 14","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/18","RAW_FILE_NAME(Raw file name)":"C1_5-1-2024_Y-B4_18326"}
},
{
"Subject ID":"-",
"Sample ID":"C2",
"Factors":{"Time point":"Day 14","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/19","RAW_FILE_NAME(Raw file name)":"C2_5-2-2024_Y-B5_18336"}
},
{
"Subject ID":"-",
"Sample ID":"C3",
"Factors":{"Time point":"Day 14","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/20","RAW_FILE_NAME(Raw file name)":"C3_5-2-2024_Y-B6_18353"}
},
{
"Subject ID":"-",
"Sample ID":"C4",
"Factors":{"Time point":"Day 14","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/21","RAW_FILE_NAME(Raw file name)":"C4_5-1-2024_Y-B7_18318"}
},
{
"Subject ID":"-",
"Sample ID":"C5",
"Factors":{"Time point":"Day 14","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/22","RAW_FILE_NAME(Raw file name)":"C5_5-2-2024_Y-B8_18344"}
},
{
"Subject ID":"-",
"Sample ID":"C6",
"Factors":{"Time point":"Day 14","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/23","RAW_FILE_NAME(Raw file name)":"C6_5-2-2024_Y-B9_18342"}
},
{
"Subject ID":"-",
"Sample ID":"C7",
"Factors":{"Time point":"Day 14","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/24","RAW_FILE_NAME(Raw file name)":"C7_5-2-2024_Y-C1_18330"}
},
{
"Subject ID":"-",
"Sample ID":"C8",
"Factors":{"Time point":"Day 14","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/25","RAW_FILE_NAME(Raw file name)":"C8_5-2-2024_Y-C2_18348"}
},
{
"Subject ID":"-",
"Sample ID":"C9",
"Factors":{"Time point":"Day 14","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/26","RAW_FILE_NAME(Raw file name)":"C9_5-1-2024_Y-C3_18309"}
},
{
"Subject ID":"-",
"Sample ID":"C10",
"Factors":{"Time point":"Day 14","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/27","RAW_FILE_NAME(Raw file name)":"C10_5-1-2024_Y-C4_18313"}
},
{
"Subject ID":"-",
"Sample ID":"C11",
"Factors":{"Time point":"Day 14","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/28","RAW_FILE_NAME(Raw file name)":"C11_5-1-2024_Y-C5_18306"}
},
{
"Subject ID":"-",
"Sample ID":"C12",
"Factors":{"Time point":"Day 14","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/29","RAW_FILE_NAME(Raw file name)":"C12_5-1-2024_Y-C6_18302"}
},
{
"Subject ID":"-",
"Sample ID":"D1",
"Factors":{"Time point":"Day 21","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/30","RAW_FILE_NAME(Raw file name)":"D1_5-2-2024_Y-C7_18350"}
},
{
"Subject ID":"-",
"Sample ID":"D2",
"Factors":{"Time point":"Day 21","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/31","RAW_FILE_NAME(Raw file name)":"D2_5-2-2024_Y-C8_18332"}
},
{
"Subject ID":"-",
"Sample ID":"D3",
"Factors":{"Time point":"Day 21","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/32","RAW_FILE_NAME(Raw file name)":"D3_5-2-2024_Y-C9_18340"}
},
{
"Subject ID":"-",
"Sample ID":"D4",
"Factors":{"Time point":"Day 21","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/33","RAW_FILE_NAME(Raw file name)":"D4_5-2-2024_Y-D1_18333"}
},
{
"Subject ID":"-",
"Sample ID":"D5",
"Factors":{"Time point":"Day 21","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/34","RAW_FILE_NAME(Raw file name)":"D5_5-2-2024_Y-D2_18352"}
},
{
"Subject ID":"-",
"Sample ID":"D6",
"Factors":{"Time point":"Day 21","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/35","RAW_FILE_NAME(Raw file name)":"D6_5-2-2024_Y-D3_18329"}
},
{
"Subject ID":"-",
"Sample ID":"D7",
"Factors":{"Time point":"Day 21","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/36","RAW_FILE_NAME(Raw file name)":"D7_5-1-2024_Y-D4_18303"}
},
{
"Subject ID":"-",
"Sample ID":"D8",
"Factors":{"Time point":"Day 21","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/37","RAW_FILE_NAME(Raw file name)":"D8_5-1-2024_Y-D5_18314"}
},
{
"Subject ID":"-",
"Sample ID":"D9",
"Factors":{"Time point":"Day 21","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/38","RAW_FILE_NAME(Raw file name)":"D9_5-1-2024_Y-D6_18320"}
},
{
"Subject ID":"-",
"Sample ID":"D10",
"Factors":{"Time point":"Day 21","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/39","RAW_FILE_NAME(Raw file name)":"D10_5-2-2024_Y-D7_18349"}
},
{
"Subject ID":"-",
"Sample ID":"D11",
"Factors":{"Time point":"Day 21","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/40","RAW_FILE_NAME(Raw file name)":"D11_5-1-2024_Y-D8_18319"}
},
{
"Subject ID":"-",
"Sample ID":"D12",
"Factors":{"Time point":"Day 21","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/41","RAW_FILE_NAME(Raw file name)":"D12_5-1-2024_Y-D9_18324"}
},
{
"Subject ID":"-",
"Sample ID":"E1",
"Factors":{"Time point":"Day 28","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/42","RAW_FILE_NAME(Raw file name)":"E1_5-1-2024_Y-E1_18307"}
},
{
"Subject ID":"-",
"Sample ID":"E2",
"Factors":{"Time point":"Day 28","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/43","RAW_FILE_NAME(Raw file name)":"E2_5-1-2024_Y-E2_18301"}
},
{
"Subject ID":"-",
"Sample ID":"E3",
"Factors":{"Time point":"Day 28","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/44","RAW_FILE_NAME(Raw file name)":"E3_5-1-2024_Y-E3_18316"}
},
{
"Subject ID":"-",
"Sample ID":"E4",
"Factors":{"Time point":"Day 28","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/45","RAW_FILE_NAME(Raw file name)":"E4_5-1-2024_Y-E4_18305"}
},
{
"Subject ID":"-",
"Sample ID":"E5",
"Factors":{"Time point":"Day 28","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/46","RAW_FILE_NAME(Raw file name)":"E5_5-1-2024_Y-E5_18312"}
},
{
"Subject ID":"-",
"Sample ID":"E6",
"Factors":{"Time point":"Day 28","Treatment":"Con","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/47","RAW_FILE_NAME(Raw file name)":"E6_5-2-2024_Y-E6_18339"}
},
{
"Subject ID":"-",
"Sample ID":"E7",
"Factors":{"Time point":"Day 28","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/48","RAW_FILE_NAME(Raw file name)":"E7_5-2-2024_Y-E7_18343"}
},
{
"Subject ID":"-",
"Sample ID":"E8",
"Factors":{"Time point":"Day 28","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/49","RAW_FILE_NAME(Raw file name)":"E8_5-2-2024_Y-E8_18338"}
},
{
"Subject ID":"-",
"Sample ID":"E9",
"Factors":{"Time point":"Day 28","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/50","RAW_FILE_NAME(Raw file name)":"E9_5-2-2024_Y-E9_18355"}
},
{
"Subject ID":"-",
"Sample ID":"E10",
"Factors":{"Time point":"Day 28","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/51","RAW_FILE_NAME(Raw file name)":"E10_5-1-2024_Y-F1_18328"}
},
{
"Subject ID":"-",
"Sample ID":"E11",
"Factors":{"Time point":"Day 28","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/52","RAW_FILE_NAME(Raw file name)":"E11_5-2-2024_Y-F2_18351"}
},
{
"Subject ID":"-",
"Sample ID":"E12",
"Factors":{"Time point":"Day 28","Treatment":"Chol","Sample source":"Feces"},
"Additional sample data":{"Genotype":"C57BL/53","RAW_FILE_NAME(Raw file name)":"E12_5-1-2024_Y-F3_18321"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Feces were collected aseptically from 4-8 wks old mice. Briefly, mice were placed in an empty autoclaved cage without bedding. Mice were then allowed to defecate normally and the first two fecal pellets were collected using sterile forceps, followed by snap freezing in liquid nitrogen. For processing, feces were homogenized in 100% methanol (50 mg/mL) and spun (13,500 rpm, 10 mins) to collect BA-containing supernatant.","SAMPLE_TYPE":"Feces"},

"TREATMENT":{"TREATMENT_SUMMARY":"Female C57BL/6 mice (4 weeks old; The Jackson Laboratory) were randomized and then, reared and maintained on control (Con) or 2% cholestyramine diets (Chol; D18062501I and D22112802I, respectively; Research Diets Inc.) until the end of the experiment. Fecal BA levels were quantified using mass spectrometer as described below. BA levels at the end of 4 weeks on diet were normalized to baseline BA levels (day 0) and represented as absolute intensity."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Murine feces were homogenized in 100% methanol (50 mg/mL) and spun (13,500 rpm, 10 mins) to collect BA-containing supernatant. Extracted samples were resuspended using 100% methanol before LC-MS analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"A longer ACQUITY UPLC CSH C18 analytical column (130Å, 1.7 µm, 2.1 mm X 150 mm, Waters) was used to achieve chromatographic separation, with a multistep elution gradient.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters ACQUITY UPLC CSH C18 (150 x 2.1mm,1.7um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"100% acetonitrile; 0.1% formic","FLOW_GRADIENT":"0 min 30% B, 2.5 min 30% B, 10 min 55% B, 11 min 99%B, 13min 99% B, 13.5 min 30% B, 17 min 30% B","FLOW_RATE":"0.35 mL/min","COLUMN_TEMPERATURE":"65"},

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

"MS":{"INSTRUMENT_NAME":"Bruker Impact II","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"To ensure strict quality control and evaluate the performance of the instrument, 20 µL aliquots were taken from each individual sample and combined to form a quality control sample (QC). This QC sample was then injected after every five samples, which helped in assessing the stability of the instrument and the coefficient of variation (CV) associated with the detected ions. Raw data processing was performed using Progenesis QI™ software (V3.0.7600.27622) incorporating METLIN™ plugin V1.0.7642.33805 (NonLinear Dynamics, Newcastle Upon Tyne, UK). This included peak picking, alignment, normalization and integration. Statistical analysis was performed using peak area."},

"MS_METABOLITE_DATA":{
"Units":"Relative abundance",

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}

}