{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000259","ANALYSIS_ID":"AN000411","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Effects of synthetic large-scale genome reduction on metabolism and metabolic in a nutritionally complex environment","PROJECT_SUMMARY":"The soil bacterium Sinorhizobium meliloti forms nodules on the roots of plants, where N2 is reduced to ammonia. Its genome includes a 3.65 Mb a 1.35 Mb pSymA megaplasmid, and a 1.68 Mb pSymB chromid. pSymA and pSymB ~45% of the genome and here a non-targeted approach was used to identify the consequences of the removal of these replicons. Polar and non-polar metabolites wild-type, ?pSymA, ?pSymB, and ?pSymAB cells and supernatants across a growth were analyzed by LC-HILIC-TOF-MS. 2008 metabolite features were identified in extracellular metabolome of cells grown in LBmc containing yeast extract and hydrolysate. 1474 features were found from the intracellular metabolites of grown in minimal M9-sucrose medium. Analysis revealed both time and genotype the metabolome, with the removal of pSymB having a much greater effect than the of pSymA. Strains lacking pSymB showed an increase in sugar, amino acid, and metabolites in the intracellular metabolome, and the loss of pSymB clearly the cell’s ability to catabolize exogenous amino acids. We conclude that the ability of wild-type, ?pSymA, ?pSymB, and ?pSymAB strains to grow in both and LBmc media, the removal of pSymA, and particularly pSymB, had clear and effects on the S. meliloti metabolome. The larger effect associated with the chromid is consistent with the large number of metabolic genes on this replicon the greater genetic and metabolic integration of this replicon with the S. chromosome.","INSTITUTE":"McMaster University","DEPARTMENT":"Department of Biology","LAST_NAME":"Finan","FIRST_NAME":"Turlough","ADDRESS":"Department of Biology, McMaster University, Hamilton, Canada L8S4K1","EMAIL":"finan@mcmaster.ca","PHONE":"(+1)905-525-9140 ext 22932"},

"STUDY":{"STUDY_TITLE":"metabolic contriubtion of pSymA and pSymB megaplasmid/chromid for multipartite meliloti cultured in rich LBmc medium","STUDY_TYPE":"megaplasmid deletion","STUDY_SUMMARY":"We wished to evaluate the contribution of pSymA and pSymB towards the of various metabolites in a nutritionally complex environment and to examine S. meliloti influences its surrounding environment.","INSTITUTE":"McMaster University","DEPARTMENT":"Department of Biology","LAST_NAME":"Finan","FIRST_NAME":"Turlough","ADDRESS":"Department of Biology, McMaster University, Hamilton, Canada L8S4K1","EMAIL":"finan@mcmaster.ca","PHONE":"(+1)905-525-9140 ext 22932","NUM_GROUPS":"14","TOTAL_SUBJECTS":"82"},

"SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Sinorhizobium meliloti","TAXONOMY_ID":"382","GENOTYPE_STRAIN":"Rm2011 (SU47 str-3)|SmA818|RmP3009|RmP2917","HUMAN_ETHNICITY":"wild type|Rm2011 lack pSymA|Rm2011 lack pSymB|Rm2011 lack pSymA and pSymB | a and the smb20996-engA operon from pSymB were integrated to chromosome in RmP3009 and RmP2917"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"L1AB",
"Sample ID":"AB_L1a",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.29"}
},
{
"Subject ID":"L1AB",
"Sample ID":"AB_L1b",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.29"}
},
{
"Subject ID":"L1AB",
"Sample ID":"AB_L1c",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.31"}
},
{
"Subject ID":"L1AB",
"Sample ID":"AB_L1d",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.31"}
},
{
"Subject ID":"L1AB",
"Sample ID":"AB_L1e",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.32"}
},
{
"Subject ID":"L1AB",
"Sample ID":"AB_L1f",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.32"}
},
{
"Subject ID":"L2AB",
"Sample ID":"AB_L2a",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.79"}
},
{
"Subject ID":"L2AB",
"Sample ID":"AB_L2b",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.85"}
},
{
"Subject ID":"L2AB",
"Sample ID":"AB_L2c",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.85"}
},
{
"Subject ID":"L2AB",
"Sample ID":"AB_L2d",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.87"}
},
{
"Subject ID":"L2AB",
"Sample ID":"AB_L2e",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.88"}
},
{
"Subject ID":"L2AB",
"Sample ID":"AB_L2f",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"0.89"}
},
{
"Subject ID":"L3AB",
"Sample ID":"AB_L3a",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"1.10"}
},
{
"Subject ID":"L3AB",
"Sample ID":"AB_L3b",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"1.08"}
},
{
"Subject ID":"L3AB",
"Sample ID":"AB_L3c",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"1.09"}
},
{
"Subject ID":"L3AB",
"Sample ID":"AB_L3d",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"1.09"}
},
{
"Subject ID":"L3AB",
"Sample ID":"AB_L3e",
"Factors":{"strains":"ΔpSymAB","time":"N/A"},
"Additional sample data":{"od600":"1.07"}
},
{
"Subject ID":"L1A",
"Sample ID":"A_L1a",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"0.91"}
},
{
"Subject ID":"L1A",
"Sample ID":"A_L1b",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"1.04"}
},
{
"Subject ID":"L1A",
"Sample ID":"A_L1c",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"1.05"}
},
{
"Subject ID":"L1A",
"Sample ID":"A_L1d",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"1.03"}
},
{
"Subject ID":"L1A",
"Sample ID":"A_L1e",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"1.03"}
},
{
"Subject ID":"L1A",
"Sample ID":"A_L1f",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"0.93"}
},
{
"Subject ID":"L2A",
"Sample ID":"A_L2a",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"4.69"}
},
{
"Subject ID":"L2A",
"Sample ID":"A_L2b",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"5.06"}
},
{
"Subject ID":"L2A",
"Sample ID":"A_L2c",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"5.35"}
},
{
"Subject ID":"L2A",
"Sample ID":"A_L2d",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"4.93"}
},
{
"Subject ID":"L2A",
"Sample ID":"A_L2e",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"4.90"}
},
{
"Subject ID":"L2A",
"Sample ID":"A_L2f",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"4.89"}
},
{
"Subject ID":"L3A",
"Sample ID":"A_L3a",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"6.03"}
},
{
"Subject ID":"L3A",
"Sample ID":"A_L3b",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"6.78"}
},
{
"Subject ID":"L3A",
"Sample ID":"A_L3c",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"6.60"}
},
{
"Subject ID":"L3A",
"Sample ID":"A_L3d",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"6.72"}
},
{
"Subject ID":"L3A",
"Sample ID":"A_L3e",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"7.25"}
},
{
"Subject ID":"L3A",
"Sample ID":"A_L3f",
"Factors":{"strains":"ΔpSymA","time":"N/A"},
"Additional sample data":{"od600":"6.76"}
},
{
"Subject ID":"L1B",
"Sample ID":"B_L1a",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"0.50"}
},
{
"Subject ID":"L1B",
"Sample ID":"B_L1b",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"0.45"}
},
{
"Subject ID":"L1B",
"Sample ID":"B_L1c",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"0.43"}
},
{
"Subject ID":"L1B",
"Sample ID":"B_L1d",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"0.46"}
},
{
"Subject ID":"L1B",
"Sample ID":"B_L1e",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"0.42"}
},
{
"Subject ID":"L1B",
"Sample ID":"B_L1f",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"0.53"}
},
{
"Subject ID":"L2B",
"Sample ID":"B_L2a",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.40"}
},
{
"Subject ID":"L2B",
"Sample ID":"B_L2b",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.33"}
},
{
"Subject ID":"L2B",
"Sample ID":"B_L2c",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.29"}
},
{
"Subject ID":"L2B",
"Sample ID":"B_L2d",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.36"}
},
{
"Subject ID":"L2B",
"Sample ID":"B_L2e",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.33"}
},
{
"Subject ID":"L2B",
"Sample ID":"B_L2f",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.50"}
},
{
"Subject ID":"L3B",
"Sample ID":"B_L3a",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.39"}
},
{
"Subject ID":"L3B",
"Sample ID":"B_L3b",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.43"}
},
{
"Subject ID":"L3B",
"Sample ID":"B_L3c",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.37"}
},
{
"Subject ID":"L3B",
"Sample ID":"B_L3d",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.48"}
},
{
"Subject ID":"L3B",
"Sample ID":"B_L3e",
"Factors":{"strains":"ΔpSymB","time":"N/A"},
"Additional sample data":{"od600":"1.53"}
},
{
"Subject ID":"L1LB",
"Sample ID":"LB_L1a",
"Factors":{"strains":"Luria Broth only","time":"0 hr"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L1LB",
"Sample ID":"LB_L1b",
"Factors":{"strains":"Luria Broth only","time":"0 hr"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L1LB",
"Sample ID":"LB_L1c",
"Factors":{"strains":"Luria Broth only","time":"0 hr"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L1LB",
"Sample ID":"LB_L1d",
"Factors":{"strains":"Luria Broth only","time":"0 hr"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L1LB",
"Sample ID":"LB_L1e",
"Factors":{"strains":"Luria Broth only","time":"0 hr"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L1LB",
"Sample ID":"LB_L1f",
"Factors":{"strains":"Luria Broth only","time":"0 hr"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L3LB",
"Sample ID":"LB_L2a",
"Factors":{"strains":"Luria Broth only","time":"45 hrs"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L3LB",
"Sample ID":"LB_L2b",
"Factors":{"strains":"Luria Broth only","time":"45 hrs"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L3LB",
"Sample ID":"LB_L2c",
"Factors":{"strains":"Luria Broth only","time":"45 hrs"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L3LB",
"Sample ID":"LB_L2d",
"Factors":{"strains":"Luria Broth only","time":"45 hrs"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L3LB",
"Sample ID":"LB_L2e",
"Factors":{"strains":"Luria Broth only","time":"45 hrs"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L3LB",
"Sample ID":"LB_L2f",
"Factors":{"strains":"Luria Broth only","time":"45 hrs"},
"Additional sample data":{"od600":"N/A"}
},
{
"Subject ID":"L1WT",
"Sample ID":"WT_L1a",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"0.99"}
},
{
"Subject ID":"L1WT",
"Sample ID":"WT_L1b",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"1.06"}
},
{
"Subject ID":"L1WT",
"Sample ID":"WT_L1c",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"1.08"}
},
{
"Subject ID":"L1WT",
"Sample ID":"WT_L1d",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"1.08"}
},
{
"Subject ID":"L1WT",
"Sample ID":"WT_L1e",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"1.07"}
},
{
"Subject ID":"L1WT",
"Sample ID":"WT_L1f",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"1.08"}
},
{
"Subject ID":"L2WT",
"Sample ID":"WT_L2a",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"5.43"}
},
{
"Subject ID":"L2WT",
"Sample ID":"WT_L2b",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"5.71"}
},
{
"Subject ID":"L2WT",
"Sample ID":"WT_L2c",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"5.69"}
},
{
"Subject ID":"L2WT",
"Sample ID":"WT_L2d",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"5.65"}
},
{
"Subject ID":"L2WT",
"Sample ID":"WT_L2e",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"5.63"}
},
{
"Subject ID":"L2WT",
"Sample ID":"WT_L2f",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"5.75"}
},
{
"Subject ID":"L3WT",
"Sample ID":"WT_L3a",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"6.44"}
},
{
"Subject ID":"L3WT",
"Sample ID":"WT_L3b",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"6.67"}
},
{
"Subject ID":"L3WT",
"Sample ID":"WT_L3c",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"6.63"}
},
{
"Subject ID":"L3WT",
"Sample ID":"WT_L3d",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"6.75"}
},
{
"Subject ID":"L3WT",
"Sample ID":"WT_L3e",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"6.79"}
},
{
"Subject ID":"L3WT",
"Sample ID":"WT_L3f",
"Factors":{"strains":"wild type","time":"N/A"},
"Additional sample data":{"od600":"6.52"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"cell supernatant","VOLUMEORAMOUNT_COLLECTED":"20 ΔL","STORAGE_CONDITIONS":"-80ºC freezer","COLLECTION_VIALS":"eppendorf tube"},

"TREATMENT":{"TREATMENT_SUMMARY":"-","ANIMAL_VET_TREATMENTS":"-80ºC freezer","ANIMAL_ANESTHESIA":"test tube","ANIMAL_ENDP_CLINICAL_SIGNS":"n/a","HUMAN_FASTING":"30ºC incubator","HUMAN_ENDP_CLINICAL_SIGNS":"supernatant collected at mid-exponential phase, early stationary phase, and stationary phase"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","SAMPLEPREP_PROTOCOL_FILENAME":"Fei,_F.,_Bowdish,_D._M._E.,_&_McCarry,_B._E._(2014)._Analytical_and_Bioanalytical_Chemistry,_406,_3723?3733.","EXTRACTION_METHOD":"dilute 10 fold in 1:1 MeOH/EtOH","EXTRACT_STORAGE":"-80ºC freezer","SAMPLE_SPIKING":"L-methionine-d3, L-tryptophan-d5 as standards for recovery determination ; diphenylalanine and glycine-phenylalanine as internal standards for peak area","CELL_TYPE":"Gram negative bacterium"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1200 RR Series II","COLUMN_NAME":"Phenomenex Kinetex HILIC 100A (50 x 2.1 mm, 2.6um)","METHODS_FILENAME":"Opt_silicaHILIC.m","COLUMN_TEMPERATURE":"40C","FLOW_GRADIENT":"0-0.5 min, 95%A; 0.5-12.5 min, 35%A; 12.5-13.0 min, 35%A; 13.0-14.0 min, 95%A; min, 95%A","FLOW_RATE":"200 ΔL/min","INTERNAL_STANDARD":"L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine","SAMPLE_INJECTION":"2 ΔL","SOLVENT_A":"HPLC grade acetonitrile","SOLVENT_B":"10 mM ammonium acetate in HPLC grade water adjusted to pH 3 with formic acid","ANALYTICAL_TIME":"24 min"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","SOFTWARE_VERSION":"Bruker Hystar","OPERATOR_NAME":"Fan Fei","DETECTOR_TYPE":"electron multiplier detector","DATA_FORMAT":".d"},

"MS":{"INSTRUMENT_NAME":"Bruker MicrOTOF II","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_VOLTAGE":"-3800 V","DRY_GAS_FLOW":"8.0 L/min","DRY_GAS_TEMP":"250ºC","SCAN_RANGE_MOVERZ":"50-1000 m/z","MS_COMMENTS":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"Normalized Peak area",

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