Summary of study ST001260

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000846. The data can be accessed directly via it's Project DOI: 10.21228/M8B97R This work is supported by NIH grant, U2C- DK119886.

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Study IDST001260
Study TitleMetabolic changes of Fusobacterium nucleatum when co-cultured with other oral microbes (part-I)
Study SummaryWe 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
DepartmentGraduate School of Dentistry, Department of Preventive Dentistry
Last NameKuboniwa
First NameMasae
AddressYamadaoka 1-8
Emailkuboniwa@dent.osaka-u.ac.jp
Phone81668792922
Submit Date2019-09-26
Analysis Type DetailLC-MS
Release Date2021-04-01
Release Version1
Masae Kuboniwa Masae Kuboniwa
https://dx.doi.org/10.21228/M8B97R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000846
Project DOI:doi: 10.21228/M8B97R
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

Subject:

Subject ID:SU001328
Subject Type:Bacteria
Subject Species:Fusobacterium nucleatum
Taxonomy ID:190304
Genotype Strain:Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Cell Biosource Or Supplier:ATCC 25586

Factors:

Subject type: Bacteria; Subject species: Fusobacterium nucleatum (Factor headings shown in green)

mb_sample_id local_sample_id partner
SA091500Fn_2none
SA091501Fn_1none
SA091502Fn_3none
SA091491Fn-Sg_3Sg
SA091492Fn-Sg_2Sg
SA091493Fn-Sg_1Sg
SA091494Fn-SgVp_1SgVp
SA091495Fn-SgVp_2SgVp
SA091496Fn-SgVp_3SgVp
SA091497Fn-Vp_3Vp
SA091498Fn-Vp_1Vp
SA091499Fn-Vp_2Vp
Showing results 1 to 12 of 12

Collection:

Collection ID:CO001322
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 ID:TR001343
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.

Sample Preparation:

Sampleprep ID:SP001336
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.

Combined analysis:

Analysis ID AN002090 AN002091
Analysis type MS MS
Chromatography type CE CE
Chromatography system Agilent 6210 Agilent 6210
Column None None
MS Type ESI ESI
MS instrument type CE-TOF CE-TOF
MS instrument name Agilent 6210 TOF Agilent 6210 TOF
Ion Mode POSITIVE NEGATIVE
Units AU AU

Chromatography:

Chromatography ID:CH001527
Instrument Name:Agilent 6210
Column Name:None
Chromatography Type:CE

MS:

MS ID:MS001941
Analysis ID:AN002090
Instrument Name:Agilent 6210 TOF
Instrument Type:CE-TOF
MS Type:ESI
MS Comments:The conditions for measurement of cationic metabolites were as follows. Run buffer: Cation Buffer Solution (H3301-1001; Human Metabolome Technologies (HMT)), CE voltage: +27kV, MS ionization: ESI positive, MS capillary voltage: 4,000V, 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).
Ion Mode:POSITIVE
  
MS ID:MS001942
Analysis ID:AN002091
Instrument Name:Agilent 6210 TOF
Instrument Type:CE-TOF
MS Type:ESI
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).
Ion Mode:NEGATIVE
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