{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000351","ANALYSIS_ID":"AN000569","VERSION":"1","CREATED_ON":"February 18, 2016, 3:29 pm"},

"PROJECT":{"PROJECT_TITLE":"Application of a targeted metabolomic profiling for the delineation of mechanisms of autolytic systems in Streptococcus mutans cells under oxidative stresses","PROJECT_SUMMARY":"Streptococcus mutans is capable of withstanding a variety of stressors encountered in the oral cavity. The ability to efficiently and rapidly adjust to the changing environment is essential for its pathogenic lifestyle. Oxidative stress is one of the most important environmental variables affecting the pathogenic potential of S. mutans, as high oxygen concentrations disfavor growth of S. mutans and other oral bacteria. In order to fulfill its role as a major constituent of cariogenic oral biofilms and sustain virulence, S. mutans must overcome oxidative stress. Oxidation sensing and response is a complex yet highly-regulated process, particularly because it is cross-regulated with other metabolic pathways, stress responses and virulence physiology. In addition, we previously showed that exposure of S. mutans to oxygen strongly inhibits biofilm formation and alters cell surface biogenesis, possibly through AtlA, a major autolysin of the organism. More recently, we have also shown that S. mutans Cid/Lrg system, potentially mediating cell lysis/death in a programmed fashion, uniquely leads a global readjustment in central metabolism and virulence processes, particularly in coping with oxidative stress. To this end, a targeted metabolomics approach will be employed to understand how these autolytic systems influence the metabolism of S. mutans, ultimately leading to a more complete appreciation of how S. mutans survives and persists in hostile host microenvironment.","INSTITUTE":"University of Florida","DEPARTMENT":"College of Dentistry","LAST_NAME":"Ahn","FIRST_NAME":"Sang-Joon","ADDRESS":"1395 Center Drive, Room D5-29 Gainesville FL 32610","EMAIL":"sahn@dental.ufl.edu","PHONE":"352-273-8834","FUNDING_SOURCE":"NIH R03"},

"STUDY":{"STUDY_TITLE":"Determining the metabolic profile of wildtype, lrgAB, and atlA mutant Steptococcus mutans grown aerobically and anaerobically","STUDY_TYPE":"Single time point, aerobic vs. anaerobic cultures","STUDY_SUMMARY":"Whole cells from both aerobic and anaerobic cultures of wild-type,lrgAB and atlA strain will be isolated for analysis of the whole cytosolic metabolome. Supernatants will be also analyzed for their metabolite profile in wild type and lrgAB cultures.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LAST_NAME":"Ahn","FIRST_NAME":"Sang-Joon","ADDRESS":"1395 Center Drive, Room D5-29 Gainesville FL 32610","EMAIL":"sahn@dental.ufl.edu","PHONE":"352-273-8834","NUM_GROUPS":"3","TOTAL_SUBJECTS":"36"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Streptococcus mutans"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1",
"Factors":{"Strain":"UA159 wild type","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"2",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"3",
"Factors":{"Strain":"atlA mutant","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"4",
"Factors":{"Strain":"UA159 wild type","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"5",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"6",
"Factors":{"Strain":"atlA mutant","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"7",
"Factors":{"Strain":"UA159 wild type","Sample type":"Supernatant","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"8",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Supernatant","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"9",
"Factors":{"Strain":"UA159 wild type","Sample type":"Supernatant","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"10",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Supernatant","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"11",
"Factors":{"Strain":"UA159 wild type","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"12",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"13",
"Factors":{"Strain":"atlA mutant","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"14",
"Factors":{"Strain":"UA159 wild type","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"15",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"16",
"Factors":{"Strain":"atlA mutant","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"17",
"Factors":{"Strain":"UA159 wild type","Sample type":"Supernatant","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"18",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Supernatant","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"19",
"Factors":{"Strain":"UA159 wild type","Sample type":"Supernatant","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"20",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Supernatant","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"21",
"Factors":{"Strain":"UA159 wild type","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"22",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"23",
"Factors":{"Strain":"atlA mutant","Sample type":"Whole cells","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"24",
"Factors":{"Strain":"UA159 wild type","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"25",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"26",
"Factors":{"Strain":"atlA mutant","Sample type":"Whole cells","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"27",
"Factors":{"Strain":"UA159 wild type","Sample type":"Supernatant","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"28",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Supernatant","Growth condition":"anaerobically"}
},
{
"Subject ID":"-",
"Sample ID":"29",
"Factors":{"Strain":"UA159 wild type","Sample type":"Supernatant","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"30",
"Factors":{"Strain":"lrgAB mutant","Sample type":"Supernatant","Growth condition":"aerobically"}
},
{
"Subject ID":"-",
"Sample ID":"C1-1",
"Factors":{"Strain":"N/A","Sample type":"Media only","Growth condition":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"C1-2",
"Factors":{"Strain":"N/A","Sample type":"Media only","Growth condition":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"C1-3",
"Factors":{"Strain":"N/A","Sample type":"Media only","Growth condition":"N/A"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Bacterial cells were harvested at mid-exponential phase of growth by centrifugation. The cell pellets were washed with PBS buffer and then flash frozen in liquid nitrogen. The culture supernatants were filtered and then flash frozen in liquid nitrogen","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Bacterial cells were grown under aerobic and anaerobic conditions."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"see attached protocols"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Organic acid method","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Quantiva QQQ","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2mm, 1.7um) 186002352"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Quantiva QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"nmol/mg",

"Data":[{"Metabolite":"Lactate","1":"6.99","11":"20.96","21":"22.95","4":"6.77","14":"25.69","24":"18.74","2":"17.05","12":"34.34","22":"5.02","5":"18.25","15":"32.29","25":"9.85","7":"9480.21","17":"15638.59","27":"18050.89","9":"13280.34","19":"8697.85","29":"12169.74","8":"9311.2","18":"10866.09","28":"17582.52","10":"12737.47","20":"12996.5","30":"11676.53","C1-1":"1799.28","C1-2":"1816.68","C1-3":"1530.12"},{"Metabolite":"Pyruvate","1":"12.03","11":"12.44","21":"20.18","4":"7.23","14":"8.79","24":"3.11","2":"19.1","12":"16","22":"9.37","5":"6.11","15":"4.71","25":"7.49","7":"157.94","17":"246.61","27":"176.19","9":"194.8","19":"125.57","29":"121.52","8":"213.66","18":"227.06","28":"156.51","10":"167.53","20":"231","30":"97.74","C1-1":"322.5","C1-2":"335.31","C1-3":"98.11"},{"Metabolite":"_3_HBA","1":"BLOQ","11":"BLOQ","21":"BLOQ","4":"BLOQ","14":"BLOQ","24":"BLOQ","2":"BLOQ","12":"BLOQ","22":"BLOQ","5":"BLOQ","15":"BLOQ","25":"BLOQ","7":"11.2","17":"18.88","27":"21.56","9":"16.98","19":"12.87","29":"18.34","8":"14.86","18":"21.77","28":"20.47","10":"14.35","20":"18.04","30":"16.88","C1-1":"30.32","C1-2":"30.29","C1-3":"25.79"},{"Metabolite":"Succinate","1":"0.85","11":"0.97","21":"1.54","4":"0.73","14":"0.61","24":"0.49","2":"0.93","12":"0.79","22":"1.75","5":"1.2","15":"0.77","25":"1.2","7":"334.52","17":"540.26","27":"647.72","9":"442.01","19":"322.95","29":"582.49","8":"259.92","18":"503.38","28":"662.7","10":"363.9","20":"499.17","30":"414.77","C1-1":"756.08","C1-2":"833.24","C1-3":"707.47"},{"Metabolite":"Fumarate","1":"BLOQ","11":"0.23","21":"0.28","4":"0.22","14":"0.38","24":"BLOQ","2":"0.32","12":"0.43","22":"0.41","5":"BLOQ","15":"BLOQ","25":"BLOQ","7":"13.34","17":"23.85","27":"27.85","9":"22.04","19":"13.06","29":"15.38","8":"18.3","18":"26.45","28":"26.68","10":"17.34","20":"21.98","30":"21.96","C1-1":"15","C1-2":"14.35","C1-3":"11.32"},{"Metabolite":"Malate","1":"BLOQ","11":"BLOQ","21":"BLOQ","4":"BLOQ","14":"BLOQ","24":"BLOQ","2":"BLOQ","12":"BLOQ","22":"BLOQ","5":"BLOQ","15":"BLOQ","25":"BLOQ","7":"42.08","17":"73.37","27":"86.67","9":"65.69","19":"48.86","29":"83.51","8":"57.97","18":"88.53","28":"83.98","10":"51.78","20":"80.95","30":"65.45","C1-1":"136.15","C1-2":"138.15","C1-3":"118.95"},{"Metabolite":"a-KG","1":"3","11":"2.94","21":"3.97","4":"3.3","14":"3.03","24":"3.41","2":"4.46","12":"3.46","22":"4.71","5":"3.77","15":"4.2","25":"4.88","7":"9.49","17":"15.01","27":"12.6","9":"11.99","19":"7.25","29":"6.49","8":"13.1","18":"16.63","28":"11.86","10":"11.06","20":"15.31","30":"7.42","C1-1":"20.94","C1-2":"20.55","C1-3":"10.24"},{"Metabolite":"Citrate","1":"BLOQ","11":"BLOQ","21":"BLOQ","4":"BLOQ","14":"BLOQ","24":"BLOQ","2":"BLOQ","12":"BLOQ","22":"BLOQ","5":"0.77","15":"0.34","25":"0.47","7":"641.29","17":"1087.81","27":"1258.4","9":"835.92","19":"604.92","29":"1020.47","8":"569.71","18":"730.79","28":"1234.89","10":"635.58","20":"860.2","30":"682.61","C1-1":"1404.9","C1-2":"1519.71","C1-3":"1245.6"}],

"Metabolites":[{"Metabolite":"Lactate","Retention Index":"3.98","Moverz Quant":"196.1, 91.062","PubChem CID":"107689"},{"Metabolite":"Pyruvate","Retention Index":"6.68","Moverz Quant":"299.1, 91.186","PubChem CID":"1060"},{"Metabolite":"_3_HBA","Retention Index":"4.21","Moverz Quant":"210.1, 91.153","PubChem CID":"441"},{"Metabolite":"Succinate","Retention Index":"5.44","Moverz Quant":"329.1, 206.233","PubChem CID":"1110"},{"Metabolite":"Fumarate","Retention Index":"5.59","Moverz Quant":"327.1, 91.192","PubChem CID":"444972"},{"Metabolite":"Malate","Retention Index":"5.28","Moverz Quant":"345.1, 91.18","PubChem CID":"525"},{"Metabolite":"a-KG","Retention Index":"6.59","Moverz Quant":"462.2, 91.2","PubChem CID":"164533"},{"Metabolite":"Citrate","Retention Index":"5.95","Moverz Quant":"508.25, 385","PubChem CID":"311"}]
}

}