Summary of Study ST003941
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 PR002470. The data can be accessed directly via it's Project DOI: 10.21228/M8C82T This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003941 |
| Study Title | Lipidomic analysis of Bacteroides thetaiotaomicron WT vs SPT KO (sphingolipid-deficient) outer membrane vesicles (OMVs) and whole cells. |
| Study Summary | We performed a lipidomic analysis of outer membrane vesicles (OMVs) from Bacteroides thetaiotaomicron vs whole cell bacteria to understand whether there are lipids enriched in the OMVs of Bacteroides. We also utilized a sphingolipid-deficient Bacteroides thetaiotaomicron strain with a knockout of the serine palmitoyltransferase gene (spt) and compared the lipidomic signature to the wild-type strain in OMVs and whole cell bacteria. Overall we report the differences in lipids from each strain in OMVs and in whole cell bacteria and which sphingolipids are enriched in OMVs. |
| Institute | Broad Institute of MIT and Harvard |
| Department | IDMP |
| Laboratory | Xavier Lab and Clish Lab |
| Last Name | Brown |
| First Name | Eric |
| Address | 415 Main Street, Cambridge, MA, USA 02142 |
| ericmichbrown@gmail.com | |
| Phone | 6176826566 |
| Submit Date | 2025-04-21 |
| Study Comments | Bacterial lipidomics on OMVs and whole cell bacteria on B. thetaiotaomicron WT vs SPT KO strains |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-06-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002470 |
| Project DOI: | doi: 10.21228/M8C82T |
| Project Title: | Sphingolipids promote anti-inflammatory responses of Bacteroides through the mevalonate pathway |
| Project Type: | Bacterial lipidomics |
| Project Summary: | A lipidomics analysis to identify sphingolipids of interest in Bacteroides thetaiotaomicron outer membrane vesicles (OMVs) and whole cell bacteria. |
| Institute: | Broad Institute of MIT and Harvard |
| Department: | IDMP |
| Laboratory: | Xavier Lab and Clish Lab |
| Last Name: | Brown |
| First Name: | Eric |
| Address: | 415 Main Street, Cambridge, Massachusetts, 02142, USA |
| Email: | erbrown@broadinstitute.org |
| Phone: | 6176826566 |
| Contributors: | Clary Clish, Sarah Jeanfavre, Julian Avila-Pacheco |
Subject:
| Subject ID: | SU004077 |
| Subject Type: | Bacteria |
| Subject Species: | Bacteroides thetaiotaomicron |
| Taxonomy ID: | 8188 |
| Genotype Strain: | Wild-type vs SPT Knockout strain |
Factors:
Subject type: Bacteria; Subject species: Bacteroides thetaiotaomicron (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Sample type |
|---|---|---|---|---|
| SA450445 | BTSPTWC_2 | Bacteria | SPT KO | Bacteria |
| SA450446 | BTSPTWC_1 | Bacteria | SPT KO | Bacteria |
| SA450447 | BTSPTWC_3 | Bacteria | SPT KO | Bacteria |
| SA450448 | BTWTWC_1 | Bacteria | Wild-type | Bacteria |
| SA450449 | BTWTWC_2 | Bacteria | Wild-type | Bacteria |
| SA450450 | BTWTWC_3 | Bacteria | Wild-type | Bacteria |
| SA450451 | BTSPTOMV_1 | OMVs | SPT KO | OMVs |
| SA450452 | BTSPTOMV_2 | OMVs | SPT KO | OMVs |
| SA450453 | BTSPTOMV_3 | OMVs | SPT KO | OMVs |
| SA450454 | BTWTOMV_1 | OMVs | Wild-type | OMVs |
| SA450455 | BTWTOMV_2 | OMVs | Wild-type | OMVs |
| SA450456 | BTWTOMV_3 | OMVs | Wild-type | OMVs |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO004070 |
| Collection Summary: | Bacteroides thetaiotaomicron wild-type or spt-knockout OMVs were collected after 2 days of culture in BHI media by ultra-centrifugation and frozen at -80 degrees until analysis. To obtain the whole cell lipidomic data, either wild-type or spt knockout Bacteroides thetaiotaomicron strains were centrifuged at 8000g for 20 min and pellets were snap frozen before analysis. |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004086 |
| Treatment Summary: | Cells were not treated |
| Cell Storage: | -80 |
| Cell Media: | Brain Heart Infusion Agar |
Sample Preparation:
| Sampleprep ID: | SP004083 |
| Sampleprep Summary: | Metabolites were extracted from the samples by adding isopropanol to the OMVs or cells. The extract was then subjected to LC-MS analysis. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH004919 |
| Chromatography Summary: | Solvent A - 95:5:0.1 vol/vol/vol 10 mM ammonium acetate/methanol/formic acid |
| Methods Filename: | Lipidomic_profiling_methods_Metabolomics_Workbench_Sphingolipids.pdf |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACQUITY BEH C8 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | The column was eluted isocratically with 80% A for 1 minute followed by a linear gradient to 80% B over 2 minutes, a linear gradient to 100% B over 7 minutes, then 3 minutes at 100% B |
| Flow Rate: | 0.45mL/min |
| Solvent A: | 95% water/5% methanol; 10 mM ammonium acetate; 0.1% formic acid |
| Solvent B: | 100% water; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006477 |
| Analysis Type: | MS |
| Analysis Protocol File: | Lipidomic_profiling_methods_Metabolomics_Workbench_Sphingolipids.pdf |
| Chromatography ID: | CH004919 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Seconds |
| Results File: | ST003941_AN006477_Results.txt |
| Units: | Intensity |
