{
"METABOLOMICS WORKBENCH":{"VERSION":"1","CREATED_ON":"December 1, 2017, 10:46 am"},

"PROJECT":{"PROJECT_TITLE":"Murine vitamin A deficiency results in a hypermetabolic state and alterations in bacterial community structure and metabolism","PROJECT_SUMMARY":"Vitamin A deficiency (A-) is a significant public health problem. To better understand how vitamin A status influences gut microbiota and host metabolism, we systematically analyzed urine, cecum, serum, and liver samples from vitamin A sufficient (A+) and A- mice using 1H NMR-based metabolomics, quantitative (q)PCR, and 16S rRNA gene sequencing coupled with multivariate data analysis. The microbiota in the cecum of A- mice showed compositional as well as functional shifts compared to the microbiota from A+ mice. Targeted 1H NMR analyses revealed significant changes in microbial metabolite concentrations including higher butyrate and hippurate and decreased acetate and 4-hydroxyphenylacetate in A+ relative to A- mice. Bacterial butyrate-producing genes including butyryl-CoA:acetate CoA-transferase and butyrate kinase were significantly higher in bacteria from A+ versus bacteria from A- mice. A - mice had disturbances in multiple metabolic pathways including alterations in energy metabolism (hyperglycemia, glycogenesis, TCA cycle, and lipoprotein biosynthesis) and the A- host showed metabolites indicative of a hypermetabolic state (higher levels of amino acids and nucleic acids). A- mice had hyperglycemia, liver dysfunction, changes in bacterial metabolism, and altered gut microbial communities. Moreover, integrative analyses indicated a strong correlation between gut microbiota and host energy metabolism pathways in the liver. Vitamin A regulates the microbiota, bacterial metabolism and the effects of vitamin A on the microbiota results in alterations to host metabolism.","INSTITUTE":"The Pennsylvania State University (Penn State)","LAST_NAME":"Nichols","FIRST_NAME":"Robert","ADDRESS":"101 Life science building, University Park, State college, PA, 16803","EMAIL":"rgn5011@psu.edu","PHONE":"7247662694"},

"STUDY":{"STUDY_TITLE":"Murine vitamin A deficiency results in a hypermetabolic state and alterations in bacterial community structure and metabolism. (Liver)","STUDY_SUMMARY":"Vitamin A deficiency (A-) is a significant public health problem. To better understand how vitamin A status influences gut microbiota and host metabolism, we systematically analyzed urine, cecum, serum, and liver samples from vitamin A sufficient (A+) and A- mice using 1H NMR-based metabolomics, quantitative (q)PCR, and 16S rRNA gene sequencing coupled with multivariate data analysis. The microbiota in the cecum of A- mice showed compositional as well as functional shifts compared to the microbiota from A+ mice. Targeted 1H NMR analyses revealed significant changes in microbial metabolite concentrations including higher butyrate and hippurate and decreased acetate and 4-hydroxyphenylacetate in A+ relative to A- mice. Bacterial butyrate-producing genes including butyryl-CoA:acetate CoA-transferase and butyrate kinase were significantly higher in bacteria from A+ versus bacteria from A- mice. A - mice had disturbances in multiple metabolic pathways including alterations in energy metabolism (hyperglycemia, glycogenesis, TCA cycle, and lipoprotein biosynthesis) and the A- host showed metabolites indicative of a hypermetabolic state (higher levels of amino acids and nucleic acids). A- mice had hyperglycemia, liver dysfunction, changes in bacterial metabolism, and altered gut microbial communities. Moreover, integrative analyses indicated a strong correlation between gut microbiota and host energy metabolism pathways in the liver. Vitamin A regulates the microbiota, bacterial metabolism and the effects of vitamin A on the microbiota results in alterations to host metabolism.","INSTITUTE":"Pennsylvania State University","LAST_NAME":"Nichols","FIRST_NAME":"Robert","ADDRESS":"101 Life science building, University park, PA, 16803","EMAIL":"rgn5011@psu.edu","PHONE":"17247662694"},

"SUBJECT":{"SUBJECT_TYPE":"mouse","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Vit A sufficient",
"Sample ID":"C1",
"Factors":{"Treatment":"Control"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A sufficient",
"Sample ID":"C2",
"Factors":{"Treatment":"Control"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A sufficient",
"Sample ID":"C3",
"Factors":{"Treatment":"Control"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A sufficient",
"Sample ID":"C4",
"Factors":{"Treatment":"Control"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A sufficient",
"Sample ID":"C5",
"Factors":{"Treatment":"Control"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A sufficient",
"Sample ID":"C6",
"Factors":{"Treatment":"Control"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A deficient",
"Sample ID":"T1",
"Factors":{"Treatment":"Vit-A deficient food"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A deficient",
"Sample ID":"T2",
"Factors":{"Treatment":"Vit-A deficient food"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A deficient",
"Sample ID":"T3",
"Factors":{"Treatment":"Vit-A deficient food"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A deficient",
"Sample ID":"T4",
"Factors":{"Treatment":"Vit-A deficient food"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A deficient",
"Sample ID":"T5",
"Factors":{"Treatment":"Vit-A deficient food"},
"Additional sample data":{"Genotype":"Wild-Type"}
},
{
"Subject ID":"Vit A deficient",
"Sample ID":"T6",
"Factors":{"Treatment":"Vit-A deficient food"},
"Additional sample data":{"Genotype":"Wild-Type"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"liver"},

"TREATMENT":{"TREATMENT_SUMMARY":"Twelve male litters were weaned at 3 wks and continuously fed the vitamin A sufficient diet, vitamin A deficient diet, or the vitamin A deficient diet, supplemented with retenoic acid until the end of the experiment."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The NMR sample prep for the urine, liver, cecal contents and serum are attached."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"-","INSTRUMENT_NAME":"-","COLUMN_NAME":"-"},

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

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

"NMR_METABOLITE_DATA":{
"Units":"total peak intensity per metabolite",

"Data":[{"Metabolite":"glucose","C1":"12015.65492","C2":"72472.88534","C3":"17927.2833","C4":"9531.049805","C5":"14294.53916","C6":"17704.63314","T1":"96898.34287","T2":"47100.38347","T3":"76095.38697","T4":"155694.1842","T5":"48629.00336","T6":"74656.94524"},{"Metabolite":"lactate","C1":"161886.1291","C2":"198892.2169","C3":"123861.7989","C4":"121554.8352","C5":"163156.3906","C6":"132839.6231","T1":"279165.6674","T2":"224486.1705","T3":"250233.6072","T4":"251799.3421","T5":"229155.8168","T6":"244246.8974"},{"Metabolite":"glycogen","C1":"2349.094908","C2":"7173.3389","C3":"3909.400159","C4":"2632.755152","C5":"5359.155386","C6":"6134.789147","T1":"20383.11611","T2":"5591.55842","T3":"11145.61456","T4":"64484.14621","T5":"4584.146468","T6":"13465.73732"},{"Metabolite":"succinate","C1":"15706.30317","C2":"16442.23729","C3":"15270.34804","C4":"12950.04446","C5":"16026.28599","C6":"13486.89551","T1":"23053.49591","T2":"17216.93152","T3":"15256.47045","T4":"20607.1424","T5":"19707.22238","T6":"22208.43353"},{"Metabolite":"BCAAs","C1":"132013.6187","C2":"162492.9719","C3":"126971.3318","C4":"124048.1017","C5":"140937.6802","C6":"127717.3096","T1":"180762.5002","T2":"160995.9293","T3":"177343.7505","T4":"165435.8146","T5":"157255.1047","T6":"188546.9253"},{"Metabolite":"alanine","C1":"75054.08916","C2":"108762.8525","C3":"75769.39019","C4":"64490.36028","C5":"68200.97678","C6":"71122.84451","T1":"121720.2335","T2":"106094.1133","T3":"132088.4748","T4":"135036.5476","T5":"115460.9514","T6":"127246.3854"},{"Metabolite":"glutamate","C1":"40741.84481","C2":"56019.12333","C3":"54079.83285","C4":"47600.32915","C5":"47385.3142","C6":"52259.4766","T1":"57844.05783","T2":"56815.78892","T3":"62683.56465","T4":"66781.16194","T5":"51022.87917","T6":"62127.26378"},{"Metabolite":"glutamine","C1":"43552.23847","C2":"49902.68018","C3":"47830.58514","C4":"46551.14984","C5":"39488.17806","C6":"43917.00349","T1":"36706.62887","T2":"38793.56967","T3":"36676.21574","T4":"46242.17452","T5":"48410.79001","T6":"51062.67361"},{"Metabolite":"tyrosine","C1":"284200.7019","C2":"383035.9965","C3":"302451.9332","C4":"274682.1998","C5":"303522.7255","C6":"300027.822","T1":"443022.5511","T2":"383507.6283","T3":"445146.0912","T4":"439690.8273","T5":"380603.1886","T6":"455947.0038"},{"Metabolite":"phe","C1":"11023.46762","C2":"16463.3022","C3":"13578.27463","C4":"11370.43035","C5":"14067.99023","C6":"15063.82263","T1":"26663.5597","T2":"18714.19566","T3":"23149.05544","T4":"22838.66178","T5":"17241.23648","T6":"24857.36407"},{"Metabolite":"histidine","C1":"3804.04569","C2":"6648.647028","C3":"5489.925141","C4":"5008.855962","C5":"5167.727258","C6":"5199.117482","T1":"7648.415466","T2":"5615.789461","T3":"7165.62523","T4":"7577.772376","T5":"6160.735435","T6":"7803.761819"},{"Metabolite":"AMP","C1":"955.4507362","C2":"1662.256705","C3":"1493.615061","C4":"1187.296495","C5":"1781.567301","C6":"1455.547969","T1":"1587.846532","T2":"1113.32879","T3":"1214.759438","T4":"1280.939623","T5":"1187.864166","T6":"1444.586954"},{"Metabolite":"ADP","C1":"909.1448682","C2":"1252.431513","C3":"1211.142286","C4":"973.9537553","C5":"1498.038541","C6":"1227.922589","T1":"1370.846901","T2":"993.2669455","T3":"1230.138149","T4":"1180.017287","T5":"937.5775517","T6":"1331.171235"},{"Metabolite":"guanosine","C1":"493.9259458","C2":"1181.872262","C3":"766.5074976","C4":"630.691472","C5":"1072.852497","C6":"946.1263678","T1":"1068.824115","T2":"712.8371627","T3":"812.632488","T4":"1161.267183","T5":"860.0419906","T6":"1060.468966"},{"Metabolite":"hypo","C1":"11253.66227","C2":"9161.784238","C3":"10228.69632","C4":"9479.028815","C5":"10078.69897","C6":"11170.07335","T1":"12317.61251","T2":"13607.61028","T3":"11253.12765","T4":"10963.01126","T5":"12357.64572","T6":"12105.29011"},{"Metabolite":"inosine","C1":"36576.08842","C2":"53051.42092","C3":"50224.90507","C4":"42011.1712","C5":"40506.03223","C6":"51112.92668","T1":"57262.15873","T2":"47528.90191","T3":"50046.99017","T4":"62238.66548","T5":"49441.47992","T6":"58075.00063"},{"Metabolite":"uracil","C1":"1081.140972","C2":"1047.922807","C3":"1422.749833","C4":"1166.559554","C5":"1672.735634","C6":"2130.796614","T1":"2130.676052","T2":"1643.677552","T3":"1950.726821","T4":"1769.035424","T5":"1577.360345","T6":"1744.301699"},{"Metabolite":"uridine","C1":"8484.392662","C2":"11587.33336","C3":"10654.79374","C4":"9727.329239","C5":"8918.935456","C6":"11348.54152","T1":"14031.14017","T2":"13119.50839","T3":"12724.72366","T4":"15908.72291","T5":"11902.84377","T6":"14487.79007"},{"Metabolite":"lipid","C1":"17875.37","C2":"14925.09372","C3":"12893.6472","C4":"13053.8698","C5":"18695.12846","C6":"20678.96803","T1":"12257.32006","T2":"14405.34099","T3":"16576.57156","T4":"16037.47458","T5":"13568.07008","T6":"10046.60649"},{"Metabolite":"3HB","C1":"39543.24272","C2":"36965.38504","C3":"41291.46826","C4":"43182.68385","C5":"40846.26043","C6":"44255.90733","T1":"37584.30642","T2":"38622.97533","T3":"32544.50331","T4":"33789.29425","T5":"39150.94783","T6":"35858.93598"}],

"Metabolites":[{"metabolite_name":"glucose"},{"metabolite_name":"lactate"},{"metabolite_name":"glycogen"},{"metabolite_name":"succinate"},{"metabolite_name":"BCAAs"},{"metabolite_name":"alanine"},{"metabolite_name":"glutamate"},{"metabolite_name":"glutamine"},{"metabolite_name":"tyrosine"},{"metabolite_name":"phe"},{"metabolite_name":"histidine"},{"metabolite_name":"AMP"},{"metabolite_name":"ADP"},{"metabolite_name":"guanosine"},{"metabolite_name":"hypo"},{"metabolite_name":"inosine"},{"metabolite_name":"uracil"},{"metabolite_name":"uridine"},{"metabolite_name":"lipid"},{"metabolite_name":"3HB"}]
}

}