{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001436","ANALYSIS_ID":"AN002400","VERSION":"1","CREATED_ON":"July 30, 2020, 5:12 pm"},

"PROJECT":{"PROJECT_TITLE":"Gut microbiota mediates the interplay between immunity and glucose metabolism","PROJECT_TYPE":"preclinical studies","PROJECT_SUMMARY":"Diabetes, obesity and metabolic disease have reached epidemic proportions. Much research on these diseases has focused on tissues such as adipose, liver, muscle and pancreas. The role of the gut in glucose metabolism is relatively unstudied; however, it can also have a significant effect on systemic glucose control. Residing in the gut is a complex community of microbes, termed microbiota, which are important contributors to immunity and metabolism, frequently mediating cross-talks between these two functions. Changes in the gut microbiota of type 2 diabetes (T2D) patients are directly linked to metabolic dysregulation in the disease. Therefore, the goal of the project is to identify and test microbes and microbial factors involved in regulation of glucose metabolism. For this, microbiota perturbation by western diet followed by global analyses of gut microbiome and host transcriptome combined with causal inference analysis is employed. Newly inferred probiotics are tested in mice fed with western diet followed by metabolomics analysis. This research provides a mechanistic explanation of how probiotics helps disclose mechanisms of T2D as well as will identify protective microbial factors for development of therapy of diabetes.","INSTITUTE":"Oregon State University","DEPARTMENT":"Pharmaceutical Sciences","LABORATORY":"Morgun and Shulzhenko","LAST_NAME":"Andriy","FIRST_NAME":"Morgun","ADDRESS":"203 Pharmacy Bldg, Corvallis, OR 97331","EMAIL":"andriy.morgun@oregonstate.edu","PHONE":"1 541 737 8047","FUNDING_SOURCE":"NIH R01 DK103761"},

"STUDY":{"STUDY_TITLE":"Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet induced diabetes","STUDY_TYPE":"Supplementation of mice with probiotic bacteria","STUDY_SUMMARY":"For WD + Microbes 1 and WD + Microbes 3 experiments, C57BL/6 mice were fed western diet or western diet supplemented with Lactobacillus gasseri or Lactobacillus johnsonii for 8 weeks and serum was collected from each mice. For Pooled_1 (control group, western diet only), and Pooled_2 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For Pooled_3 (western diet + Lactobacillus johnsonii) group, serum from 4 mice was pooled. For Pooled_7 (control group, western diet only), Pooled_8 (western diet + Lactobacillus gasseri) and Pooled_9 (western diet + Lactobacillus johnsonii) groups, serum from 6 mice each was pooled. For WD + Microbes 6 experiment, C57BL/6 mice were fed western diet for 8 weeks. Then, one group (n = 5) of mice was supplemented with Lactobacillus gasseri for 12 weeks along with continuation of western diet and serum was collected. For Pooled_10 (control group, western diet only) and Pooled_11 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For GF + WD + LG experiment, C57BL/6 germ free mice were fed western diet or western diet supplemented with Lactobacillus gasseri for 2 weeks. For Pooled_12 (control, western diet only) and Pooled_13 (western diet + Lactobacillus gasseri) groups, serum from 2 mice each was pooled.","INSTITUTE":"Oregon State University","DEPARTMENT":"Pharmaceutical Sciences","LABORATORY":"Morgun and Shulzhenko","LAST_NAME":"Morgun","FIRST_NAME":"Andriy","ADDRESS":"203 Pharmacy Bldg","EMAIL":"andriy.morgun@oregonstate.edu","PHONE":"1 541 737 8047","NUM_GROUPS":"7"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57Bl/6","AGE_OR_AGE_RANGE":"10-20 weeks","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Sample_01",
"Factors":{"Treatment":"Western diet"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_01.d","RAW_FILE_NAME":"Sample-neg_01.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_02",
"Factors":{"Treatment":"Western diet + Lactobacillus gasseri"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_02.d","RAW_FILE_NAME":"Sample-neg_02.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_03",
"Factors":{"Treatment":"Western diet + Lactobacillus johnsonii"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_03.d","RAW_FILE_NAME":"Sample-neg_03.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_07",
"Factors":{"Treatment":"Western diet"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_07.d","RAW_FILE_NAME":"Sample-neg_07.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_08",
"Factors":{"Treatment":"Western diet + Lactobacillus gasseri"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_08.d","RAW_FILE_NAME":"Sample-neg_08.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_09",
"Factors":{"Treatment":"Western diet + Lactobacillus johnsonii"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_09.d","RAW_FILE_NAME":"Sample-neg_09.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_10",
"Factors":{"Treatment":"Western diet"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_10.d","RAW_FILE_NAME":"Sample-neg_10.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_11",
"Factors":{"Treatment":"Western diet + Lactobacillus gasseri"},
"Additional sample data":{"Genotype":"Wild-type, Specific pathogen free","RAW_FILE_NAME":"Sample-pos_11.d","RAW_FILE_NAME":"Sample-neg_11.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_12",
"Factors":{"Treatment":"Western diet"},
"Additional sample data":{"Genotype":"Wild-type, Germ free","RAW_FILE_NAME":"Sample-pos_12.d","RAW_FILE_NAME":"Sample-neg_12.d"}
},
{
"Subject ID":"-",
"Sample ID":"Sample_13",
"Factors":{"Treatment":"Western diet + Lactobacillus gasseri"},
"Additional sample data":{"Genotype":"Wild-type, Germ free","RAW_FILE_NAME":"Sample-pos_13.d","RAW_FILE_NAME":"Sample-neg_13.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After the end of the experiment, whole blood was collected in BD Microtainer Serum Separator Tube and allowed to clot by leaving undistubred at room temperature for 30 minutes. Then the tubes were centrifuged at 2000 x g for 10 minutes in 4°C and the supernatant was immediately transferred into a polypropylene tube and stored at -80°C until further analysis.","SAMPLE_TYPE":"Blood (serum)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Western diet fed mice were supplemented with Lactobacillus gasseri or Lactobacillus johnsonii. For control groups, equal volume of vehicle (PBS) was gavaged. Supplementation was done for 2 to 8 weeks."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites were extracted with 4 volumes of cold methanol/acetonitrile (1:1, v/v). To precipitate proteins, the samples were incubated for 1h at -20°C. After the samples were centrifuged at 4°C for 15 min at 13,000 rpm, the supernatant was collected and evaporated to dryness in a vacuum concentrator. The dry extracts were then reconstituted in 90 μL of acetonitrile/H2O (1:1, v/v) containing 10 ng/mL CUDA (12-[[(cyclohexylamino)carbonyl] amino]-dodecanoic acid)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Poroshell EC-C18 (100 x 3.0 mm, 2.7 um)","FLOW_RATE":"0.4 ml/min","COLUMN_TEMPERATURE":"40"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QToF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"None","MS_RESULTS_FILE":"ST001436_AN002400_Results.txt UNITS:AUC Has m/z:Yes Has RT:Yes RT units:Minutes"}

}