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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| 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 |
| 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 |
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 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 |
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 |
|---|---|---|
| Chromatography ID | CH001527 | CH001527 |
| MS ID | MS001941 | MS001942 |
| 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 |
