{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001938","ANALYSIS_ID":"AN003151","VERSION":"1","CREATED_ON":"October 12, 2021, 6:37 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics characterized concentration-dependent metabolic influence of magnesium on biofilm formation in Escherichia coli","PROJECT_TYPE":"Targeted MS quantitative analysis","PROJECT_SUMMARY":"Metabolomics characterized concentration-dependent metabolic influence of magnesium on biofilm formation in Escherichia coli","INSTITUTE":"Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University","DEPARTMENT":"Shanghai Center for Systems Biomedicine","LABORATORY":"Lu Group","LAST_NAME":"Lu","FIRST_NAME":"Haitao","ADDRESS":"800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China","EMAIL":"haitao_lu@sjtu.edu.cn","PHONE":"15221478139"},

"STUDY":{"STUDY_TITLE":"Metabolomics characterized concentration-dependent metabolic influence of magnesium on biofilm formation in Escherichia coli (Part1)","STUDY_SUMMARY":"Biofilms are broadly formed by a diversity of microorganisms that enable them to adapt stressful environments. Biofilms often impose harmful influences in many niches, as they can cause food contamination, antibiotics resistance, and environmental issues. However, eradicating biofilms remains difficult since the formation mechanism of biofilms are still incompletely clarified. In this study, we aimed at exploring the regulatory role of magnesium (Mg2+) on biofilm formation in Escherichia coli (E. coli) using phenotype visualization combined with targeted metabolomics method. We found that Mg2+ could exert significant influence on biofilm formation in a concentration-dependent manner by regulating phenotypic morphology and triggering metabolic modifications of biofilm. Phenotypic imaging revealed that increasing concentration of Mg2+ gradually inhibited biofilm formation, Mg2+ was observed to restore the microstructure of E. coli strain in biofilms to that in the relevant planktonic cells. In addition, our metabolomics analysis characterized 20 differential metabolites and associated 2 metabolic pathways including nucleotide metabolism and amino acid metabolism that were notably modified during biofilm formation under the treatments of different concentrations of Mg2+. Altogether, our work provides a novel insight into the influence of Mg2+ on biofilm formation at a metabolic level, which are implicated in the novel solution to disturb biofilm formation through the regulation of Mg2+ and functional metabolite interaction, then biofilms associated harmful impacts in different niches could be well tangled accordingly.","INSTITUTE":"Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University","DEPARTMENT":"Shanghai Center for Systems Biomedicine","LABORATORY":"Lu Group","LAST_NAME":"Lu","FIRST_NAME":"Haitao","ADDRESS":"800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China","EMAIL":"haitao_lu@sjtu.edu.cn","PHONE":"15221478139"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"20210306-4-C-1",
"Factors":{"Concentration of MgSO4(w/v)":"0.01%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-C-1"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-C-2",
"Factors":{"Concentration of MgSO4(w/v)":"0.01%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-C-2"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-C-4",
"Factors":{"Concentration of MgSO4(w/v)":"0.01%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-C-4"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-C-5",
"Factors":{"Concentration of MgSO4(w/v)":"0.01%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-C-5"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-C-6",
"Factors":{"Concentration of MgSO4(w/v)":"0.01%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-C-6"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-30-1",
"Factors":{"Concentration of MgSO4(w/v)":"0.15%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-30-1"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-30-2",
"Factors":{"Concentration of MgSO4(w/v)":"0.15%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-30-2"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-30-4",
"Factors":{"Concentration of MgSO4(w/v)":"0.15%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-30-4"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-30-5",
"Factors":{"Concentration of MgSO4(w/v)":"0.15%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-30-5"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-30-6",
"Factors":{"Concentration of MgSO4(w/v)":"0.15%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-30-6"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-50-1",
"Factors":{"Concentration of MgSO4(w/v)":"0.25%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-50-1"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-50-2",
"Factors":{"Concentration of MgSO4(w/v)":"0.25%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-50-2"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-50-3",
"Factors":{"Concentration of MgSO4(w/v)":"0.25%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-50-3"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-50-4",
"Factors":{"Concentration of MgSO4(w/v)":"0.25%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-50-4"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-50-5",
"Factors":{"Concentration of MgSO4(w/v)":"0.25%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-50-5"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-50-6",
"Factors":{"Concentration of MgSO4(w/v)":"0.25%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-50-6"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-80-1",
"Factors":{"Concentration of MgSO4(w/v)":"0.40%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-80-1"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-80-2",
"Factors":{"Concentration of MgSO4(w/v)":"0.40%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-80-2"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-80-3",
"Factors":{"Concentration of MgSO4(w/v)":"0.40%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-80-3"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-80-4",
"Factors":{"Concentration of MgSO4(w/v)":"0.40%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-80-4"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-80-5",
"Factors":{"Concentration of MgSO4(w/v)":"0.40%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-80-5"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-80-6",
"Factors":{"Concentration of MgSO4(w/v)":"0.40%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-80-6"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-100-1",
"Factors":{"Concentration of MgSO4(w/v)":"0.50%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-100-1"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-100-2",
"Factors":{"Concentration of MgSO4(w/v)":"0.50%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-100-2"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-100-3",
"Factors":{"Concentration of MgSO4(w/v)":"0.50%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-100-3"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-100-4",
"Factors":{"Concentration of MgSO4(w/v)":"0.50%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-100-4"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-100-5",
"Factors":{"Concentration of MgSO4(w/v)":"0.50%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-100-5"}
},
{
"Subject ID":"-",
"Sample ID":"20210306-4-100-6",
"Factors":{"Concentration of MgSO4(w/v)":"0.50%"},
"Additional sample data":{"RAW_FILE_NAME":"20210306-4-100-6"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After 72 hours of culture, the planktonic cells were isolated, and the biofilms were washed with PBS solvent for three times. Then, planktonic cells and biofilm solutions were centrifuged at 2000 rpm and 4°C for 15 minutes, to collect the strain pellets.","SAMPLE_TYPE":"Biofilm"},

"TREATMENT":{"TREATMENT_SUMMARY":"Colony-forming antigen (CFA) medium (1% casamino acids, 0.15% yeast extract, 0.005% magnesium sulfate, and 0.0005% manganese chloride) was used to form biofilms. The E. coli strain was incubated in LB-agar plate for 12 hours, one colony was isolated to LB broth for further 4 hours incubation, then diluted the solution into CFA medium at a ratio of 1:1000 and the cultures were incubated for another 72 h at 30°C to form mature biofilms. To test the influence of MgSO4 on biofilm formation, the purified compound of MgSO4 was added to the CFA medium at different concentrations for the preparation of treated culture medium; The left cultural procedures were kept as the same as the protocol listed above."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Each pellet sample was mixed with 2 mL of 80% ice-cold methanol, and the mixed solution was homogenized on ice for 2 minutes and repeated the same procedure for three times. Next, the collected samples were centrifuged at 12000 rpm and 4°C for 15 minutes, to collect the supernatants. The supernatants were further mixed with 800 μL of ice-cold acetonitrile for 20 minutes before further centrifuge at 12000 rpm and 4°C for 15 minutes. At last, the isolated supernatants were gone through a 0.22 μm filter membrane (nylon) before the lyophilization. The lyophilized samples were stored at -80°C for metabolomics analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The chromatographic separation of biological samples was implemented on a Waters ACQUITY UPLC HSS T3 column (2.1×100 mm, 1.8 μm) with an optimized gradient-elution program (mobile phase A and B were 0.1% formic acid in water and acetonitrile (v/v)): 0-2 minutes, 98% A; 2-10 minutes, 98%-65% A; 10-12 minutes, 65%-20% A; 12-14 minutes, 20%-2% A; 14-30 minutes, 2% A. The column temperature was at 40°C and the flow rate was set at 0.3 mL/ minutes.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6495 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Agilent MassHunter Workstation Data Acquisition Agilent MassHunter QualitativeAnalysis B.07.00 Agilent MassHunter Quantitative Analysis (for QQQ)"},

"MS_METABOLITE_DATA":{
"Units":"-",

"Data":[{"Metabolite":"Citrate","20210306-4-C-1":"2326.255528","20210306-4-C-2":"1280.785882","20210306-4-C-4":"4063.517177","20210306-4-C-5":"1839.75724","20210306-4-C-6":"3062.152221","20210306-4-30-1":"3603.364042","20210306-4-30-2":"2142.995903","20210306-4-30-4":"1532.07668","20210306-4-30-5":"1929.731169","20210306-4-30-6":"3623.052209","20210306-4-50-1":"2479.242136","20210306-4-50-2":"2258.901048","20210306-4-50-3":"2665.656664","20210306-4-50-4":"2991.956826","20210306-4-50-5":"2898.325035","20210306-4-50-6":"1893.672754","20210306-4-80-1":"3258.477249","20210306-4-80-2":"3655.46426","20210306-4-80-3":"5053.056551","20210306-4-80-4":"3609.94553","20210306-4-80-5":"2634.883083","20210306-4-80-6":"1966.503815","20210306-4-100-1":"2680.175269","20210306-4-100-2":"3955.084539","20210306-4-100-3":"2980.199756","20210306-4-100-4":"3281.84596","20210306-4-100-5":"6983.01619","20210306-4-100-6":"2799.920457"},{"Metabolite":"Isocitric acid","20210306-4-C-1":"2363.674418","20210306-4-C-2":"977.3233325","20210306-4-C-4":"3246.91494","20210306-4-C-5":"1439.187121","20210306-4-C-6":"2239.935192","20210306-4-30-1":"3102.968352","20210306-4-30-2":"2467.309266","20210306-4-30-4":"1385.704266","20210306-4-30-5":"1724.373602","20210306-4-30-6":"3077.912221","20210306-4-50-1":"2122.658304","20210306-4-50-2":"1979.950073","20210306-4-50-3":"3009.109463","20210306-4-50-4":"2771.458397","20210306-4-50-5":"2436.872019","20210306-4-50-6":"1675.732229","20210306-4-80-1":"2693.766891","20210306-4-80-2":"3232.695035","20210306-4-80-3":"4496.944736","20210306-4-80-4":"3241.793694","20210306-4-80-5":"2178.865465","20210306-4-80-6":"2028.805872","20210306-4-100-1":"2630.943088","20210306-4-100-2":"3391.765592","20210306-4-100-3":"2339.642917","20210306-4-100-4":"3452.600213","20210306-4-100-5":"5437.795245","20210306-4-100-6":"2656.892993"},{"Metabolite":"Methylmalonic acid","20210306-4-C-1":"2926.428312","20210306-4-C-2":"8150.115441","20210306-4-C-4":"1012.942125","20210306-4-C-5":"5513.15038","20210306-4-C-6":"6155.366251","20210306-4-30-1":"2793.235585","20210306-4-30-2":"5007.874268","20210306-4-30-4":"3386.216981","20210306-4-30-5":"4332.459064","20210306-4-30-6":"6080.478854","20210306-4-50-1":"1740.726768","20210306-4-50-2":"3780.173302","20210306-4-50-3":"2681.150377","20210306-4-50-4":"2379.626905","20210306-4-50-5":"4755.901578","20210306-4-50-6":"1944.229911","20210306-4-80-1":"1314.720304","20210306-4-80-2":"1613.028121","20210306-4-80-3":"3416.610655","20210306-4-80-4":"1531.017025","20210306-4-80-5":"1157.048244","20210306-4-80-6":"1935.058023","20210306-4-100-1":"629.1302272","20210306-4-100-2":"1748.992993","20210306-4-100-3":"2087.466195","20210306-4-100-4":"1779.099056","20210306-4-100-5":"2170.881705","20210306-4-100-6":"2826.916187"},{"Metabolite":"3-Hydroxybenzoic acid","20210306-4-C-1":"18.76240298","20210306-4-C-2":"30.79886472","20210306-4-C-4":"29.35188962","20210306-4-C-5":"41.41673102","20210306-4-C-6":"30.99202664","20210306-4-30-1":"15.10462575","20210306-4-30-2":"22.13970915","20210306-4-30-4":"23.38463559","20210306-4-30-5":"21.92432696","20210306-4-30-6":"36.25491714","20210306-4-50-1":"9.255997122","20210306-4-50-2":"28.79412661","20210306-4-50-3":"17.75897871","20210306-4-50-4":"17.03680109","20210306-4-50-5":"23.74617928","20210306-4-50-6":"12.32026423","20210306-4-80-1":"14.66703969","20210306-4-80-2":"27.63990409","20210306-4-80-3":"41.78024559","20210306-4-80-4":"24.71013153","20210306-4-80-5":"20.93464966","20210306-4-80-6":"16.78210231","20210306-4-100-1":"26.99752722","20210306-4-100-2":"23.21767019","20210306-4-100-3":"34.45204222","20210306-4-100-4":"17.06517425","20210306-4-100-5":"23.15365437","20210306-4-100-6":"18.06970494"},{"Metabolite":"4-Hydroxybenzoic acid","20210306-4-C-1":"23.97068518","20210306-4-C-2":"37.28448714","20210306-4-C-4":"35.80039583","20210306-4-C-5":"47.57974898","20210306-4-C-6":"40.6241692","20210306-4-30-1":"17.80980685","20210306-4-30-2":"28.30878892","20210306-4-30-4":"29.33949763","20210306-4-30-5":"27.15919256","20210306-4-30-6":"47.34984522","20210306-4-50-1":"11.63402516","20210306-4-50-2":"32.87402399","20210306-4-50-3":"20.75054316","20210306-4-50-4":"21.45699885","20210306-4-50-5":"30.24104854","20210306-4-50-6":"14.58768105","20210306-4-80-1":"15.31053362","20210306-4-80-2":"30.29997575","20210306-4-80-3":"52.21065753","20210306-4-80-4":"29.40070846","20210306-4-80-5":"26.07177797","20210306-4-80-6":"18.45998862","20210306-4-100-1":"32.61508751","20210306-4-100-2":"29.59493325","20210306-4-100-3":"39.22712295","20210306-4-100-4":"20.33972259","20210306-4-100-5":"28.75106059","20210306-4-100-6":"23.01199679"},{"Metabolite":"Azelaic acid","20210306-4-C-1":"21.97977978","20210306-4-C-2":"38.84546483","20210306-4-C-4":"21.9193774","20210306-4-C-5":"41.73451978","20210306-4-C-6":"14.44504189","20210306-4-30-1":"16.94088258","20210306-4-30-2":"20.95855382","20210306-4-30-4":"20.30574829","20210306-4-30-5":"25.7573133","20210306-4-30-6":"34.77674194","20210306-4-50-1":"14.86363567","20210306-4-50-2":"18.38195523","20210306-4-50-3":"22.90784587","20210306-4-50-4":"29.44807428","20210306-4-50-5":"21.27124601","20210306-4-50-6":"10.82718653","20210306-4-80-1":"19.85409845","20210306-4-80-2":"20.61193267","20210306-4-80-3":"39.24820295","20210306-4-80-4":"17.60966047","20210306-4-80-5":"18.5894389","20210306-4-80-6":"20.52981363","20210306-4-100-1":"27.64584774","20210306-4-100-2":"23.9040124","20210306-4-100-3":"27.3327934","20210306-4-100-4":"13.84091431","20210306-4-100-5":"26.19881862","20210306-4-100-6":"26.08334096"},{"Metabolite":"Maleic acid","20210306-4-C-1":"377.7946379","20210306-4-C-2":"532.0387637","20210306-4-C-4":"1649.623714","20210306-4-C-5":"1356.460457","20210306-4-C-6":"735.7244064","20210306-4-30-1":"50.73052084","20210306-4-30-2":"188.5843367","20210306-4-30-4":"239.0247669","20210306-4-30-5":"132.9212231","20210306-4-30-6":"183.4763432","20210306-4-50-1":"58.30458619","20210306-4-50-2":"236.9671009","20210306-4-50-3":"60.79903257","20210306-4-50-4":"47.01126716","20210306-4-50-5":"68.60007347","20210306-4-50-6":"77.00266851","20210306-4-80-1":"55.05072746","20210306-4-80-2":"804.6002578","20210306-4-80-3":"211.3623364","20210306-4-80-4":"213.083865","20210306-4-80-5":"352.4346377","20210306-4-80-6":"132.6420958","20210306-4-100-1":"234.3103389","20210306-4-100-2":"308.8754442","20210306-4-100-3":"321.1345056","20210306-4-100-4":"140.1653686","20210306-4-100-5":"123.8412433","20210306-4-100-6":"182.0579385"},{"Metabolite":"Lithocholic 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}