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 ID	ST001260
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
Department	Graduate School of Dentistry, Department of Preventive Dentistry
Last Name	Kuboniwa
First Name	Masae
Address	Yamadaoka 1-8
Email	kuboniwa@dent.osaka-u.ac.jp
Phone	81668792922
Submit Date	2019-09-26
Analysis Type Detail	LC-MS
Release Date	2021-04-01
Release Version	1

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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 subsp. nucleatum ATCC 25586
Taxonomy ID:	190304
Genotype Strain:	ATCC 25586
Cell Biosource Or Supplier:	ATCC 25586
Species Group:	Bacteria

Factors:

Subject type: Bacteria; Subject species: Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (Factor headings shown in green)

mb_sample_id	local_sample_id	partner
SA091500	Fn_2	none
SA091501	Fn_1	none
SA091502	Fn_3	none
SA091491	Fn-Sg_3	Sg
SA091492	Fn-Sg_2	Sg
SA091493	Fn-Sg_1	Sg
SA091494	Fn-SgVp_1	SgVp
SA091495	Fn-SgVp_2	SgVp
SA091496	Fn-SgVp_3	SgVp
SA091497	Fn-Vp_3	Vp
SA091498	Fn-Vp_1	Vp
SA091499	Fn-Vp_2	Vp

Showing results 1 to 12 of 12

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.

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.

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.

Chromatography:

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

Analysis:

Analysis ID:	AN002090
Analysis Type:	MS
Chromatography ID:	CH001527
Num Factors:	4
Num Metabolites:	57
Units:	AU

Analysis ID:	AN002091
Analysis Type:	MS
Chromatography ID:	CH001527
Num Factors:	4
Num Metabolites:	28
Units:	AU