{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001219","ANALYSIS_ID":"AN002032","VERSION":"1","CREATED_ON":"July 19, 2019, 6:57 pm"},

"PROJECT":{"PROJECT_TITLE":"Vitamin D regulates the microbiota to induce RORgt/FoxP3+ regulatory T cells","PROJECT_SUMMARY":"The active form of vitamin D (1,25(OH)2D) suppresses experimental models of inflammatory bowel disease in part by regulating the microbiota. In this study, the role of vitamin D in the regulation of microbe induced RORgt/FoxP3+ T regulatory (reg) cells in the colon was determined. Vitamin D sufficient (D+) mice had significantly higher frequencies of FoxP3+ and RORgt/FoxP3+ T reg cells in the colon compared to vitamin D deficient (D-) mice. The higher frequency of RORgt/FoxP3+ T reg cells in D+ colon correlated with higher numbers of bacteria from the Clostridium XIVa and Bacteroides in D+ compared to D- cecum. D- mice with fewer RORgt/FoxP3+ T reg cells were significantly more susceptible to colitis than D+ mice. Transfer of the cecal bacteria from D+ or D- mice to germfree recipients phenocopied the higher numbers of RORgt/FoxP3+ cells and reduced susceptibility to colitis in D+ versus D- recipient mice. 1,25(OH)2D treatment of the D- mice beginning at 3 weeks of age did not completely recover RORgt/FoxP3+ T reg cells or the Bacteriodes, Bacteriodes thetaiotaomicron, and Clostridium XIVa numbers to D+ values. Early vitamin D status shapes the microbiota to optimize the population of colonic RORgt/FoxP3+ T reg cells important for resistance to colitis.","INSTITUTE":"The Pennsylvania State University (Penn State)","LAST_NAME":"Nichols","FIRST_NAME":"Robert","ADDRESS":"650 toftrees Ave apt 108, state college, PA, 16803","EMAIL":"rgn5011@psu.edu","PHONE":"7247662694"},

"STUDY":{"STUDY_TITLE":"Vitamin D regulates the microbiota to induce RORgt/FoxP3+ regulatory T cells","STUDY_SUMMARY":"The active form of vitamin D (1,25(OH)2D) suppresses experimental models of inflammatory bowel disease in part by regulating the microbiota. In this study, the role of vitamin D in the regulation of microbe induced RORgt/FoxP3+ T regulatory (reg) cells in the colon was determined. Vitamin D sufficient (D+) mice had significantly higher frequencies of FoxP3+ and RORgt/FoxP3+ T reg cells in the colon compared to vitamin D deficient (D-) mice. The higher frequency of RORgt/FoxP3+ T reg cells in D+ colon correlated with higher numbers of bacteria from the Clostridium XIVa and Bacteroides in D+ compared to D- cecum. D- mice with fewer RORgt/FoxP3+ T reg cells were significantly more susceptible to colitis than D+ mice. Transfer of the cecal bacteria from D+ or D- mice to germfree recipients phenocopied the higher numbers of RORgt/FoxP3+ cells and reduced susceptibility to colitis in D+ versus D- recipient mice. 1,25(OH)2D treatment of the D- mice beginning at 3 weeks of age did not completely recover RORgt/FoxP3+ T reg cells or the Bacteriodes, Bacteriodes thetaiotaomicron, and Clostridium XIVa numbers to D+ values. Early vitamin D status shapes the microbiota to optimize the population of colonic RORgt/FoxP3+ T reg cells important for resistance to colitis.","INSTITUTE":"The Pennsylvania State University (Penn State)","LAST_NAME":"Nichols","FIRST_NAME":"Robert","ADDRESS":"917 Old Boalsburg Road, State College, Pennsylvania, 16801, USA","EMAIL":"rgn5011@psu.edu","PHONE":"7247662694"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-1",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-2",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-3",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-4",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-5",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-6",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-7",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-8",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-9",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-10",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-11",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-12",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-13",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-14",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-15",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-16",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-17",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-18",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-19",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-20",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-21",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-22",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-23",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-24",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-25",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-26",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-27",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4A-28",
"Factors":{"Group":"Vitamin D-"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-1",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-2",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-3",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-4",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-5",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-6",
"Factors":{"Group":"Vitamin D -"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-7",
"Factors":{"Group":"Vitamin D -"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-8",
"Factors":{"Group":"Vitamin D -"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-9",
"Factors":{"Group":"Vitamin D -"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-10",
"Factors":{"Group":"Vitamin D -"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4B-11",
"Factors":{"Group":"Vitamin D -"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-1",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-2",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-3",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-4",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-5",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-6",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-7",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-8",
"Factors":{"Group":"Vitamin D+"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-9",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-10",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-11",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-12",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-13",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-14",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-15",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-16",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-17",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-18",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-19",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-20",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-21",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-22",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-23",
"Factors":{"Group":"Vitamin D-, +1,25D"}
},
{
"Subject ID":"-",
"Sample ID":"Sup_Fig4C-24",
"Factors":{"Group":"Vitamin D-, +1,25D"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"C57BL/6 mice were originally from Jackson Labs (Bar Harbor, MN) and maintained at the Pennsylvania State University (University Park, PA). All mice used were housed within the same rooms in the animal facility. Mice were fed purified diets made in the lab as described that either contained vitamin D (D+) or did not (D-) 24. GF C57BL/6 mice were bred and maintained at the Pennsylvania State University gnotobiotic animal research facility. For some experiments, 1,25D was started in the diets of 3-5 week old mice (25ng/d until 5 weeks of age) and mice that were >5 weeks old were fed 50ng/d 1,25D exactly as described 24. For microbial transplantation experiments (two independent experiments), the 4 week old GF mice were gavaged with 100 µl/10 µg cecal contents from D+ and D- mice, and used for experiments after 2 weeks 25. All of the experimental procedures were approved by the Institutional Animal Care and Use Committee at the Pennsylvania State University","SAMPLE_TYPE":"Cecum"},

"TREATMENT":{"TREATMENT_SUMMARY":"C57BL/6 mice were originally from Jackson Labs (Bar Harbor, MN) and maintained at the Pennsylvania State University (University Park, PA). All mice used were housed within the same rooms in the animal facility. Mice were fed purified diets made in the lab as described that either contained vitamin D (D+) or did not (D-) 24. GF C57BL/6 mice were bred and maintained at the Pennsylvania State University gnotobiotic animal research facility. For some experiments, 1,25D was started in the diets of 3-5 week old mice (25ng/d until 5 weeks of age) and mice that were >5 weeks old were fed 50ng/d 1,25D exactly as described 24. For microbial transplantation experiments (two independent experiments), the 4 week old GF mice were gavaged with 100 µl/10 µg cecal contents from D+ and D- mice, and used for experiments after 2 weeks 25. All of the experimental procedures were approved by the Institutional Animal Care and Use Committee at the Pennsylvania State University"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extract metabolites from cecal contents, then run samples. Pleas see the NMR protocol doc attached to this file"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance II","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"600"},

"NMR_METABOLITE_DATA":{
"Units":"umol/mg",

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"Metabolites":[{"Metabolite":"Acetate","Type":"SCFA"},{"Metabolite":"Propionate","Type":"SCFA"},{"Metabolite":"Butyrate","Type":"SCFA"},{"Metabolite":"Total SCFA","Type":"SCFA"},{"Metabolite":"bile acids","Type":"Bile acid"},{"Metabolite":"5-aminovalerate","Type":"5-aminovalerate"}]
}

}