#METABOLOMICS WORKBENCH rgn5011_20170926_112858 DATATRACK_ID:1246 VERSION 1 CREATED_ON December 1, 2017, 10:46 am #PROJECT PR:PROJECT_TITLE Murine vitamin A deficiency results in a hypermetabolic state and alterations in PR:PROJECT_TITLE bacterial community structure and metabolism PR:PROJECT_SUMMARY Vitamin A deficiency (A-) is a significant public health problem. To better PR:PROJECT_SUMMARY understand how vitamin A status influences gut microbiota and host metabolism, PR:PROJECT_SUMMARY we systematically analyzed urine, cecum, serum, and liver samples from vitamin A PR:PROJECT_SUMMARY sufficient (A+) and A- mice using 1H NMR-based metabolomics, quantitative PR:PROJECT_SUMMARY (q)PCR, and 16S rRNA gene sequencing coupled with multivariate data analysis. PR:PROJECT_SUMMARY The microbiota in the cecum of A- mice showed compositional as well as PR:PROJECT_SUMMARY functional shifts compared to the microbiota from A+ mice. Targeted 1H NMR PR:PROJECT_SUMMARY analyses revealed significant changes in microbial metabolite concentrations PR:PROJECT_SUMMARY including higher butyrate and hippurate and decreased acetate and PR:PROJECT_SUMMARY 4-hydroxyphenylacetate in A+ relative to A- mice. Bacterial butyrate-producing PR:PROJECT_SUMMARY genes including butyryl-CoA:acetate CoA-transferase and butyrate kinase were PR:PROJECT_SUMMARY significantly higher in bacteria from A+ versus bacteria from A- mice. A - mice PR:PROJECT_SUMMARY had disturbances in multiple metabolic pathways including alterations in energy PR:PROJECT_SUMMARY metabolism (hyperglycemia, glycogenesis, TCA cycle, and lipoprotein PR:PROJECT_SUMMARY biosynthesis) and the A- host showed metabolites indicative of a hypermetabolic PR:PROJECT_SUMMARY state (higher levels of amino acids and nucleic acids). A- mice had PR:PROJECT_SUMMARY hyperglycemia, liver dysfunction, changes in bacterial metabolism, and altered PR:PROJECT_SUMMARY gut microbial communities. Moreover, integrative analyses indicated a strong PR:PROJECT_SUMMARY correlation between gut microbiota and host energy metabolism pathways in the PR:PROJECT_SUMMARY liver. Vitamin A regulates the microbiota, bacterial metabolism and the effects PR:PROJECT_SUMMARY of vitamin A on the microbiota results in alterations to host metabolism. PR:INSTITUTE The Pennsylvania State University (Penn State) PR:LAST_NAME Nichols PR:FIRST_NAME Robert PR:ADDRESS 101 Life science building, University Park, State college, PA, 16803 PR:EMAIL rgn5011@psu.edu PR:PHONE 7247662694 #STUDY ST:STUDY_TITLE Murine vitamin A deficiency results in a hypermetabolic state and alterations in ST:STUDY_TITLE bacterial community structure and metabolism. (Liver) ST:STUDY_SUMMARY Vitamin A deficiency (A-) is a significant public health problem. To better ST:STUDY_SUMMARY understand how vitamin A status influences gut microbiota and host metabolism, ST:STUDY_SUMMARY we systematically analyzed urine, cecum, serum, and liver samples from vitamin A ST:STUDY_SUMMARY sufficient (A+) and A- mice using 1H NMR-based metabolomics, quantitative ST:STUDY_SUMMARY (q)PCR, and 16S rRNA gene sequencing coupled with multivariate data analysis. ST:STUDY_SUMMARY The microbiota in the cecum of A- mice showed compositional as well as ST:STUDY_SUMMARY functional shifts compared to the microbiota from A+ mice. Targeted 1H NMR ST:STUDY_SUMMARY analyses revealed significant changes in microbial metabolite concentrations ST:STUDY_SUMMARY including higher butyrate and hippurate and decreased acetate and ST:STUDY_SUMMARY 4-hydroxyphenylacetate in A+ relative to A- mice. Bacterial butyrate-producing ST:STUDY_SUMMARY genes including butyryl-CoA:acetate CoA-transferase and butyrate kinase were ST:STUDY_SUMMARY significantly higher in bacteria from A+ versus bacteria from A- mice. A - mice ST:STUDY_SUMMARY had disturbances in multiple metabolic pathways including alterations in energy ST:STUDY_SUMMARY metabolism (hyperglycemia, glycogenesis, TCA cycle, and lipoprotein ST:STUDY_SUMMARY biosynthesis) and the A- host showed metabolites indicative of a hypermetabolic ST:STUDY_SUMMARY state (higher levels of amino acids and nucleic acids). A- mice had ST:STUDY_SUMMARY hyperglycemia, liver dysfunction, changes in bacterial metabolism, and altered ST:STUDY_SUMMARY gut microbial communities. Moreover, integrative analyses indicated a strong ST:STUDY_SUMMARY correlation between gut microbiota and host energy metabolism pathways in the ST:STUDY_SUMMARY liver. Vitamin A regulates the microbiota, bacterial metabolism and the effects ST:STUDY_SUMMARY of vitamin A on the microbiota results in alterations to host metabolism. ST:INSTITUTE Pennsylvania State University ST:LAST_NAME Nichols ST:FIRST_NAME Robert ST:ADDRESS 101 Life science building, University park, PA, 16803 ST:EMAIL rgn5011@psu.edu ST:PHONE 17247662694 #SUBJECT SU:SUBJECT_TYPE mouse SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS Vit A sufficient C1 Treatment:Control Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A sufficient C2 Treatment:Control Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A sufficient C3 Treatment:Control Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A sufficient C4 Treatment:Control Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A sufficient C5 Treatment:Control Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A sufficient C6 Treatment:Control Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A deficient T1 Treatment:Vit-A deficient food Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A deficient T2 Treatment:Vit-A deficient food Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A deficient T3 Treatment:Vit-A deficient food Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A deficient T4 Treatment:Vit-A deficient food Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A deficient T5 Treatment:Vit-A deficient food Genotype=Wild-Type SUBJECT_SAMPLE_FACTORS Vit A deficient T6 Treatment:Vit-A deficient food Genotype=Wild-Type #COLLECTION CO:COLLECTION_SUMMARY liver #TREATMENT TR:TREATMENT_SUMMARY Twelve male litters were weaned at 3 wks and continuously fed the vitamin A TR:TREATMENT_SUMMARY sufficient diet, vitamin A deficient diet, or the vitamin A deficient diet, TR:TREATMENT_SUMMARY supplemented with retenoic acid until the end of the experiment. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY The NMR sample prep for the urine, liver, cecal contents and serum are attached. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE - CH:INSTRUMENT_NAME - CH:COLUMN_NAME - #ANALYSIS AN:ANALYSIS_TYPE NMR #NMR NM:INSTRUMENT_NAME Bruker Avance III NM:INSTRUMENT_TYPE FT-NMR NM:NMR_EXPERIMENT_TYPE 1D-1H NM:SPECTROMETER_FREQUENCY 600 Mhz #NMR_METABOLITE_DATA NMR_METABOLITE_DATA:UNITS total peak intensity per metabolite NMR_METABOLITE_DATA_START Samples C1 C2 C3 C4 C5 C6 T1 T2 T3 T4 T5 T6 Factors Treatment:Control Treatment:Control Treatment:Control Treatment:Control Treatment:Control Treatment:Control Treatment:Vit-A deficient food Treatment:Vit-A deficient food Treatment:Vit-A deficient food Treatment:Vit-A deficient food Treatment:Vit-A deficient food Treatment:Vit-A deficient food glucose 12015.65492 72472.88534 17927.2833 9531.049805 14294.53916 17704.63314 96898.34287 47100.38347 76095.38697 155694.1842 48629.00336 74656.94524 lactate 161886.1291 198892.2169 123861.7989 121554.8352 163156.3906 132839.6231 279165.6674 224486.1705 250233.6072 251799.3421 229155.8168 244246.8974 glycogen 2349.094908 7173.3389 3909.400159 2632.755152 5359.155386 6134.789147 20383.11611 5591.55842 11145.61456 64484.14621 4584.146468 13465.73732 succinate 15706.30317 16442.23729 15270.34804 12950.04446 16026.28599 13486.89551 23053.49591 17216.93152 15256.47045 20607.1424 19707.22238 22208.43353 BCAAs 132013.6187 162492.9719 126971.3318 124048.1017 140937.6802 127717.3096 180762.5002 160995.9293 177343.7505 165435.8146 157255.1047 188546.9253 alanine 75054.08916 108762.8525 75769.39019 64490.36028 68200.97678 71122.84451 121720.2335 106094.1133 132088.4748 135036.5476 115460.9514 127246.3854 glutamate 40741.84481 56019.12333 54079.83285 47600.32915 47385.3142 52259.4766 57844.05783 56815.78892 62683.56465 66781.16194 51022.87917 62127.26378 glutamine 43552.23847 49902.68018 47830.58514 46551.14984 39488.17806 43917.00349 36706.62887 38793.56967 36676.21574 46242.17452 48410.79001 51062.67361 tyrosine 284200.7019 383035.9965 302451.9332 274682.1998 303522.7255 300027.822 443022.5511 383507.6283 445146.0912 439690.8273 380603.1886 455947.0038 phe 11023.46762 16463.3022 13578.27463 11370.43035 14067.99023 15063.82263 26663.5597 18714.19566 23149.05544 22838.66178 17241.23648 24857.36407 histidine 3804.04569 6648.647028 5489.925141 5008.855962 5167.727258 5199.117482 7648.415466 5615.789461 7165.62523 7577.772376 6160.735435 7803.761819 AMP 955.4507362 1662.256705 1493.615061 1187.296495 1781.567301 1455.547969 1587.846532 1113.32879 1214.759438 1280.939623 1187.864166 1444.586954 ADP 909.1448682 1252.431513 1211.142286 973.9537553 1498.038541 1227.922589 1370.846901 993.2669455 1230.138149 1180.017287 937.5775517 1331.171235 guanosine 493.9259458 1181.872262 766.5074976 630.691472 1072.852497 946.1263678 1068.824115 712.8371627 812.632488 1161.267183 860.0419906 1060.468966 hypo 11253.66227 9161.784238 10228.69632 9479.028815 10078.69897 11170.07335 12317.61251 13607.61028 11253.12765 10963.01126 12357.64572 12105.29011 inosine 36576.08842 53051.42092 50224.90507 42011.1712 40506.03223 51112.92668 57262.15873 47528.90191 50046.99017 62238.66548 49441.47992 58075.00063 uracil 1081.140972 1047.922807 1422.749833 1166.559554 1672.735634 2130.796614 2130.676052 1643.677552 1950.726821 1769.035424 1577.360345 1744.301699 uridine 8484.392662 11587.33336 10654.79374 9727.329239 8918.935456 11348.54152 14031.14017 13119.50839 12724.72366 15908.72291 11902.84377 14487.79007 lipid 17875.37 14925.09372 12893.6472 13053.8698 18695.12846 20678.96803 12257.32006 14405.34099 16576.57156 16037.47458 13568.07008 10046.60649 3HB 39543.24272 36965.38504 41291.46826 43182.68385 40846.26043 44255.90733 37584.30642 38622.97533 32544.50331 33789.29425 39150.94783 35858.93598 NMR_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name glucose lactate glycogen succinate BCAAs alanine glutamate glutamine tyrosine phe histidine AMP ADP guanosine hypo inosine uracil uridine lipid 3HB METABOLITES_END #END