{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001261","ANALYSIS_ID":"AN002093","VERSION":"1","CREATED_ON":"October 2, 2019, 9:23 am"},
"PROJECT":{"PROJECT_TITLE":"Fusobacterium nucleatum metabolome","PROJECT_SUMMARY":"CE-TOFMS-based untargeted analysis of the extracellular 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 culture supernatants of Fusobacterium nucleatum co-cultured with other oral microbes (part-II)","STUDY_SUMMARY":"We used membrane-separated co-culture systems to globally assess extracellular metabolomic changes of Fusobacterium nucleatum 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":"Other","SUBJECT_SPECIES":"Fusobacterium nucleatum"},
"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":"Spent medium from cultures and sterile CDM were centrifuged, filtered through 0.22-µm filtration devices (Millipore) and lyophilized.","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 (I3302-1023), 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":"5-Oxoproline","Fn_1":"0.0000000","Fn_2":"0.0000000","Fn_3":"0.0000000","Fn-Sg_1":"0.0000718","Fn-Sg_2":"0.0000941","Fn-Sg_3":"0.0000781","Fn-Vp_1":"0.0000000","Fn-Vp_2":"0.0000000","Fn-Vp_3":"0.0000495","Fn-SgVp_1":"0.0000869","Fn-SgVp_2":"0.0000983","Fn-SgVp_3":"0.0001049"},{"Metabolite":"2-Hydroxy-4-methylpentanoic acid","Fn_1":"0.0000000","Fn_2":"0.0000000","Fn_3":"0.0000000","Fn-Sg_1":"0.0000444","Fn-Sg_2":"0.0000525","Fn-Sg_3":"0.0000000","Fn-Vp_1":"0.0000742","Fn-Vp_2":"0.0000867","Fn-Vp_3":"0.0000818","Fn-SgVp_1":"0.0001794","Fn-SgVp_2":"0.0001587","Fn-SgVp_3":"0.0001838"},{"Metabolite":"Fructose 1,6-diphosphate","Fn_1":"0.0000000","Fn_2":"0.0000000","Fn_3":"0.0000000","Fn-Sg_1":"0.0000319","Fn-Sg_2":"0.0000000","Fn-Sg_3":"0.0000000","Fn-Vp_1":"0.0000000","Fn-Vp_2":"0.0000000","Fn-Vp_3":"0.0000325","Fn-SgVp_1":"0.0000000","Fn-SgVp_2":"0.0000000","Fn-SgVp_3":"0.0000000"},{"Metabolite":"Lactic 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}
}