{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001260","ANALYSIS_ID":"AN002091","VERSION":"1","CREATED_ON":"October 2, 2019, 9:13 am"},

"PROJECT":{"PROJECT_TITLE":"Fusobacterium nucleatum metabolome","PROJECT_SUMMARY":"CE-TOFMS-based untargeted analysis of the intracellular metabolite changes of F. nucleatum when co-cultured with other oral microbes","INSTITUTE":"Osaka University Graduate School of Dentistry","DEPARTMENT":"Department of Preventive Dentistry","LAST_NAME":"Kuboniwa","FIRST_NAME":"Masae","ADDRESS":"Yamadaoka 1-8","EMAIL":"kuboniwa@dent.osaka-u.ac.jp","PHONE":"81668792922"},

"STUDY":{"STUDY_TITLE":"Metabolic changes of Fusobacterium nucleatum when co-cultured with other oral microbes (part-I)","STUDY_SUMMARY":"We used membrane-separated co-culture systems to globally assess metabolomic changes of Fusobacterium nucleatum when co-cultured with Streptococcus gordonii and/or Veillonella parvula.","INSTITUTE":"Osaka University Graduate School of Dentistry","DEPARTMENT":"Department of Preventive Dentistry","LAST_NAME":"Kuboniwa","FIRST_NAME":"Masae","ADDRESS":"Yamadaoka 1-8","EMAIL":"kuboniwa@dent.osaka-u.ac.jp","PHONE":"81668792922"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Fusobacterium nucleatum subsp. nucleatum ATCC 25586","TAXONOMY_ID":"190304"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Fn_1",
"Factors":{"partner":"none"}
},
{
"Subject ID":"-",
"Sample ID":"Fn_2",
"Factors":{"partner":"none"}
},
{
"Subject ID":"-",
"Sample ID":"Fn_3",
"Factors":{"partner":"none"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-Sg_1",
"Factors":{"partner":"Sg"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-Sg_2",
"Factors":{"partner":"Sg"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-Sg_3",
"Factors":{"partner":"Sg"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-Vp_1",
"Factors":{"partner":"Vp"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-Vp_2",
"Factors":{"partner":"Vp"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-Vp_3",
"Factors":{"partner":"Vp"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-SgVp_1",
"Factors":{"partner":"SgVp"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-SgVp_2",
"Factors":{"partner":"SgVp"}
},
{
"Subject ID":"-",
"Sample ID":"Fn-SgVp_3",
"Factors":{"partner":"SgVp"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After 6 h of co-culture, F. nucleatum cells were collected by pipetting from the lower chamber and washed with Milli-Q water by centrifugation. Bacterial pellets were immediately fixed by adding methanol containing 5 µM internal standard.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Co-culture growth was performed by inoculating 1.4E+10 cells of F. nucleatum in CDM in the lower chamber of a Transwell unit with 0.4-µm pore polystyrene membrane inserts (Corning, NY, USA), into which 1.4E+10 cells of S. gordonii, V. parvula or their mixture (7E+9 cells each) in CDM, or an equal volume of CDM (as a control) were added. The setup was anaerobically incubated in triplicate for 37°C."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"To remove protein, 2 ml of chloroform and 0.8 ml of ultrapure water were added to the samples, which were thoroughly mixed and centrifuged at 2300 × g for 5 minutes at 4˚C. The upper aqueous layer was then transferred to ultrafilter tips (Amicon ultrafilter system™) and centrifuged at 9100 × g for 120 minutes at 4˚C. Filtered material was dried under reduced pressure, followed by suspension in 50 µl of ultrapure water."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"CE","INSTRUMENT_NAME":"Agilent 6210","COLUMN_NAME":"None"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6210 TOF","INSTRUMENT_TYPE":"CE-TOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"The conditions for measurement of anionic metabolites were as follows. Run buffer: Anion Buffer Solution (H3302-1023), CE voltage: +30kV, MS ionization: ESI negative, MS capillary voltage: 3,500V, MS scan range: m/z 50-1,000, and sheath liquid: HMT Sheath Liquid (H3301-1020). Identification of metabolites and evaluation of the relative amounts were conducted using Master Hands (version 2.16.0.15 and 2.17.1.11; Keio University, Tokyo, Japan) with the HMT metabolite database. The relative amount of each metabolite was calculated with reference to the internal standard material (HMT)."},

"MS_METABOLITE_DATA":{
"Units":"AU",

"Data":[{"Metabolite":"Isovaleric acid","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.001358","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.001127","Fn-Vp_1":"0.001376","Fn-Vp_2":"0.001464","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.001204","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"Heptanoic acid","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.000632","Fn-Sg_2":"0.000596","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000000","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000379","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"Sedoheptulose 7-phosphate","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000377","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000000","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"dTMP","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000262","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000000","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"UMP","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000292","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000000","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"AMP","Fn_1":"0.000965","Fn_2":"0.001390","Fn_3":"0.000921","Fn-Sg_1":"0.003579","Fn-Sg_2":"0.003365","Fn-Sg_3":"0.002824","Fn-Vp_1":"0.000608","Fn-Vp_2":"0.000658","Fn-Vp_3":"0.000619","Fn-SgVp_1":"0.001669","Fn-SgVp_2":"0.001632","Fn-SgVp_3":"0.001693"},{"Metabolite":"NAD+","Fn_1":"0.000571","Fn_2":"0.000443","Fn_3":"0.000728","Fn-Sg_1":"0.001089","Fn-Sg_2":"0.001201","Fn-Sg_3":"0.001658","Fn-Vp_1":"0.000694","Fn-Vp_2":"0.000679","Fn-Vp_3":"0.000791","Fn-SgVp_1":"0.000742","Fn-SgVp_2":"0.001158","Fn-SgVp_3":"0.000828"},{"Metabolite":"Decanoic acid","Fn_1":"0.001530","Fn_2":"0.001790","Fn_3":"0.001149","Fn-Sg_1":"0.002379","Fn-Sg_2":"0.002445","Fn-Sg_3":"0.001720","Fn-Vp_1":"0.002092","Fn-Vp_2":"0.001779","Fn-Vp_3":"0.001170","Fn-SgVp_1":"0.002078","Fn-SgVp_2":"0.000882","Fn-SgVp_3":"0.002270"},{"Metabolite":"Hexanoic acid","Fn_1":"0.000912","Fn_2":"0.001072","Fn_3":"0.000834","Fn-Sg_1":"0.001746","Fn-Sg_2":"0.001352","Fn-Sg_3":"0.000970","Fn-Vp_1":"0.001134","Fn-Vp_2":"0.001225","Fn-Vp_3":"0.000919","Fn-SgVp_1":"0.001120","Fn-SgVp_2":"0.000997","Fn-SgVp_3":"0.000881"},{"Metabolite":"2-Hydroxyvaleric acid","Fn_1":"0.000416","Fn_2":"0.000638","Fn_3":"0.000679","Fn-Sg_1":"0.000997","Fn-Sg_2":"0.000825","Fn-Sg_3":"0.000589","Fn-Vp_1":"0.001023","Fn-Vp_2":"0.000867","Fn-Vp_3":"0.000734","Fn-SgVp_1":"0.000815","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000623"},{"Metabolite":"Octanoic acid","Fn_1":"0.000977","Fn_2":"0.001298","Fn_3":"0.000855","Fn-Sg_1":"0.001678","Fn-Sg_2":"0.001551","Fn-Sg_3":"0.001022","Fn-Vp_1":"0.000959","Fn-Vp_2":"0.001042","Fn-Vp_3":"0.000621","Fn-SgVp_1":"0.001132","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.001032"},{"Metabolite":"Glucose 6-phosphate","Fn_1":"0.000437","Fn_2":"0.000619","Fn_3":"0.000722","Fn-Sg_1":"0.000733","Fn-Sg_2":"0.000707","Fn-Sg_3":"0.000966","Fn-Vp_1":"0.000608","Fn-Vp_2":"0.000753","Fn-Vp_3":"0.000605","Fn-SgVp_1":"0.000586","Fn-SgVp_2":"0.000493","Fn-SgVp_3":"0.000507"},{"Metabolite":"Pelargonic acid","Fn_1":"0.000562","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.000758","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000883","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"Quinic acid","Fn_1":"0.000541","Fn_2":"0.000395","Fn_3":"0.000000","Fn-Sg_1":"0.000892","Fn-Sg_2":"0.000370","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000000","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000714","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000557"},{"Metabolite":"Flavin adenine dinucleotide","Fn_1":"0.001566","Fn_2":"0.001180","Fn_3":"0.002385","Fn-Sg_1":"0.001672","Fn-Sg_2":"0.002329","Fn-Sg_3":"0.002695","Fn-Vp_1":"0.001931","Fn-Vp_2":"0.002125","Fn-Vp_3":"0.001855","Fn-SgVp_1":"0.001835","Fn-SgVp_2":"0.002835","Fn-SgVp_3":"0.002168"},{"Metabolite":"Lauric acid","Fn_1":"0.019638","Fn_2":"0.029437","Fn_3":"0.020191","Fn-Sg_1":"0.025143","Fn-Sg_2":"0.027660","Fn-Sg_3":"0.031016","Fn-Vp_1":"0.028379","Fn-Vp_2":"0.026942","Fn-Vp_3":"0.021742","Fn-SgVp_1":"0.022735","Fn-SgVp_2":"0.021155","Fn-SgVp_3":"0.028440"},{"Metabolite":"3-Phenylpropionic acid","Fn_1":"0.000375","Fn_2":"0.000679","Fn_3":"0.000597","Fn-Sg_1":"0.000628","Fn-Sg_2":"0.000725","Fn-Sg_3":"0.000563","Fn-Vp_1":"0.000724","Fn-Vp_2":"0.000727","Fn-Vp_3":"0.000489","Fn-SgVp_1":"0.000770","Fn-SgVp_2":"0.000432","Fn-SgVp_3":"0.000675"},{"Metabolite":"ADP","Fn_1":"0.001195","Fn_2":"0.000794","Fn_3":"0.001659","Fn-Sg_1":"0.000953","Fn-Sg_2":"0.001698","Fn-Sg_3":"0.001497","Fn-Vp_1":"0.001571","Fn-Vp_2":"0.001769","Fn-Vp_3":"0.001545","Fn-SgVp_1":"0.001081","Fn-SgVp_2":"0.001404","Fn-SgVp_3":"0.002108"},{"Metabolite":"Terephthalic acid","Fn_1":"0.001144","Fn_2":"0.000876","Fn_3":"0.000850","Fn-Sg_1":"0.001202","Fn-Sg_2":"0.000927","Fn-Sg_3":"0.001124","Fn-Vp_1":"0.001322","Fn-Vp_2":"0.001159","Fn-Vp_3":"0.000922","Fn-SgVp_1":"0.000851","Fn-SgVp_2":"0.000910","Fn-SgVp_3":"0.001151"},{"Metabolite":"Flavin mononucleotide","Fn_1":"0.003893","Fn_2":"0.003594","Fn_3":"0.004566","Fn-Sg_1":"0.004733","Fn-Sg_2":"0.003969","Fn-Sg_3":"0.004557","Fn-Vp_1":"0.004148","Fn-Vp_2":"0.003115","Fn-Vp_3":"0.003713","Fn-SgVp_1":"0.004700","Fn-SgVp_2":"0.005776","Fn-SgVp_3":"0.004572"},{"Metabolite":"Lactic acid","Fn_1":"0.007329","Fn_2":"0.011481","Fn_3":"0.006691","Fn-Sg_1":"0.010364","Fn-Sg_2":"0.009224","Fn-Sg_3":"0.006099","Fn-Vp_1":"0.008312","Fn-Vp_2":"0.007431","Fn-Vp_3":"0.005224","Fn-SgVp_1":"0.010405","Fn-SgVp_2":"0.005350","Fn-SgVp_3":"0.007540"},{"Metabolite":"Dihydroxyacetone phosphate","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000741","Fn-Sg_1":"0.000671","Fn-Sg_2":"0.000558","Fn-Sg_3":"0.000849","Fn-Vp_1":"0.001047","Fn-Vp_2":"0.000784","Fn-Vp_3":"0.001063","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000884","Fn-SgVp_3":"0.000000"},{"Metabolite":"Myristoleic acid","Fn_1":"0.000724","Fn_2":"0.000587","Fn_3":"0.001115","Fn-Sg_1":"0.000689","Fn-Sg_2":"0.000454","Fn-Sg_3":"0.000794","Fn-Vp_1":"0.001419","Fn-Vp_2":"0.001383","Fn-Vp_3":"0.001059","Fn-SgVp_1":"0.000549","Fn-SgVp_2":"0.000983","Fn-SgVp_3":"0.001257"},{"Metabolite":"Glycerol 3-phosphate","Fn_1":"0.001583","Fn_2":"0.001629","Fn_3":"0.001218","Fn-Sg_1":"0.001160","Fn-Sg_2":"0.000999","Fn-Sg_3":"0.000998","Fn-Vp_1":"0.001242","Fn-Vp_2":"0.001245","Fn-Vp_3":"0.000976","Fn-SgVp_1":"0.000929","Fn-SgVp_2":"0.001056","Fn-SgVp_3":"0.000868"},{"Metabolite":"Benzoic acid","Fn_1":"0.001105","Fn_2":"0.001285","Fn_3":"0.000000","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.001283","Fn-Vp_2":"0.001696","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"5-Oxoproline","Fn_1":"0.000441","Fn_2":"0.000572","Fn_3":"0.000000","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000292","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000624","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"},{"Metabolite":"Glyceraldehyde 3-phosphate","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000349","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000000","Fn-Vp_3":"0.000000","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000320"},{"Metabolite":"5-Oxohexanoic acid","Fn_1":"0.000000","Fn_2":"0.000000","Fn_3":"0.000000","Fn-Sg_1":"0.000000","Fn-Sg_2":"0.000000","Fn-Sg_3":"0.000000","Fn-Vp_1":"0.000000","Fn-Vp_2":"0.000999","Fn-Vp_3":"0.000764","Fn-SgVp_1":"0.000000","Fn-SgVp_2":"0.000000","Fn-SgVp_3":"0.000000"}],

"Metabolites":[{"Metabolite":"Isovaleric acid","KEGG ID":"C08262","HMDB ID":"HMDB00718","m/z":"101.0616388","MT":"8.8371834"},{"Metabolite":"Heptanoic acid","KEGG ID":"","HMDB ID":"HMDB00666","m/z":"129.09239","MT":"8.206988333"},{"Metabolite":"Sedoheptulose 7-phosphate","KEGG ID":"C05382","HMDB ID":"HMDB01068","m/z":"289.03384","MT":"9.194174"},{"Metabolite":"dTMP","KEGG ID":"C00364","HMDB ID":"HMDB01227","m/z":"321.05112","MT":"9.160733"},{"Metabolite":"UMP","KEGG ID":"C00105","HMDB ID":"HMDB00288","m/z":"323.0299","MT":"9.390243"},{"Metabolite":"AMP","KEGG ID":"C00020","HMDB ID":"HMDB00045","m/z":"346.0568242","MT":"8.846265583"},{"Metabolite":"NAD+","KEGG ID":"C00003","HMDB ID":"HMDB00902","m/z":"662.1030592","MT":"6.235059758"},{"Metabolite":"Decanoic acid","KEGG ID":"C01571","HMDB ID":"HMDB00511","m/z":"171.1394908","MT":"7.574135883"},{"Metabolite":"Hexanoic acid","KEGG ID":"C01585","HMDB ID":"HMDB00535","m/z":"115.0769255","MT":"8.522434667"},{"Metabolite":"2-Hydroxyvaleric acid","KEGG ID":"","HMDB ID":"HMDB01863","m/z":"117.0559795","MT":"8.724931045"},{"Metabolite":"Octanoic acid","KEGG ID":"C06423","HMDB ID":"HMDB00482","m/z":"143.1081927","MT":"7.957609736"},{"Metabolite":"Glucose 6-phosphate","KEGG ID":"C00668","HMDB ID":"HMDB01401","m/z":"259.0239142","MT":"9.42149875"},{"Metabolite":"Pelargonic acid","KEGG ID":"C01601","HMDB ID":"HMDB00847","m/z":"157.12334","MT":"7.684384267"},{"Metabolite":"Quinic acid","KEGG ID":"C00296","HMDB ID":"HMDB03072","m/z":"191.0569883","MT":"7.715836183"},{"Metabolite":"Flavin adenine dinucleotide","KEGG ID":"C00016","HMDB ID":"HMDB01248","m/z":"391.5727842","MT":"7.486915667"},{"Metabolite":"Lauric acid","KEGG ID":"C02679","HMDB ID":"HMDB00638","m/z":"199.1716717","MT":"7.291103458"},{"Metabolite":"3-Phenylpropionic acid","KEGG ID":"C05629","HMDB ID":"HMDB00764","m/z":"149.0604833","MT":"8.3869645"},{"Metabolite":"ADP","KEGG ID":"C00008","HMDB ID":"HMDB01341","m/z":"426.0236725","MT":"10.41607963"},{"Metabolite":"Terephthalic acid","KEGG ID":"C06337","HMDB ID":"HMDB02428","m/z":"165.0197483","MT":"16.35139942"},{"Metabolite":"Flavin mononucleotide","KEGG ID":"C00061","HMDB ID":"HMDB01520","m/z":"455.0992458","MT":"7.952716567"},{"Metabolite":"Lactic acid","KEGG ID":"C00186","HMDB ID":"HMDB00190","m/z":"89.02549667","MT":"10.32700825"},{"Metabolite":"Dihydroxyacetone phosphate","KEGG ID":"C00111","HMDB ID":"HMDB01473","m/z":"168.9920325","MT":"12.24683125"},{"Metabolite":"Myristoleic acid","KEGG ID":"C08322","HMDB ID":"HMDB02000","m/z":"225.1869658","MT":"7.1148007"},{"Metabolite":"Glycerol 3-phosphate","KEGG ID":"C00093","HMDB ID":"HMDB00126","m/z":"171.0068908","MT":"11.70746775"},{"Metabolite":"Benzoic acid","KEGG ID":"C00180","HMDB ID":"HMDB01870","m/z":"121.0302688","MT":"9.43087725"},{"Metabolite":"5-Oxoproline","KEGG ID":"C01879","HMDB ID":"HMDB00267","m/z":"128.035305","MT":"9.0731555"},{"Metabolite":"Glyceraldehyde 3-phosphate","KEGG ID":"C00118","HMDB ID":"HMDB01112","m/z":"168.99168","MT":"11.2315135"},{"Metabolite":"5-Oxohexanoic acid","KEGG ID":"C02129","HMDB ID":"","m/z":"129.05674","MT":"8.685487"}]
}

}