Summary of Study ST001128

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 PR000754. The data can be accessed directly via it's Project DOI: 10.21228/M8709G This work is supported by NIH grant, U2C- DK119886.

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Study IDST001128
Study TitleWT and ΔSPT cultures of B. thetaiotaomicron grown in Minimal Media with or without d4-alanine (part IV)
Study SummaryLipid profiling was applied on WT and ΔSPT cultures of B. thetaiotaomicron grown in minimal liquid media supplemented with or without deuterium (D4)-labelled alanine, in order to elucidate the production pathways of Bacteroides-derived sphingolipids.
Institute
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone617-714-8264
Submit Date2019-01-17
Num Groups3
Total Subjects9
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-03-06
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M8709G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000754
Project DOI:doi: 10.21228/M8709G
Project Title:Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis
Project Summary:Sphingolipids are structural membrane components and important eukaryotic signaling molecules. We hypothesized that sphingolipids mediate intestinal health as they were identified as the most upregulated metabolite feature in stool of inflammatory bowel disease (IBD) patients. Commensal Bacteroidetes also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To study Bacteroidetes sphingolipids in intestinal health, we colonized germ-free mice with a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides-derived sphingolipids increased intestinal inflammation, dysregulated innate immunity and altered the host ceramide pool. Using metabolomic analysis, we described the Bacteroides sphingolipid biosynthesis pathway and revealed a greater variety of Bacteroides-derived sphingolipids than previously recognized, including ceramide phosphoinositol and deoxy-sphingolipids. We annotated Bacteroides sphingolipids in an IBD metabolomic dataset, discovering lower abundances in IBD and negative correlations with gut inflammation and host sphingolipid production. These data highlight the role of sphingolipids in maintaining host-bacterial symbiosis and intestinal homeostasis.
Institute:Broad Institute of MIT and Harvard
Last Name:Avila-Pacheco
First Name:Julian
Address:415 Main Street, Cambridge MA
Email:jravilap@broadinstitute.org
Phone:617-714-8264
Funding Source:National Institutes of Health (P30 DK043351 and R01 AT009708)
Contributors:Eric M. Brown, Xiaobo Ke, Daniel Hitchcock, Timothy D. Arthur, Toru Nakata, Nadine Fornelos, Cortney Heim, Eric A. Franzosa1,4, Curtis Huttenhower1,4, Henry J. Haiser3, Glen 6 Dillow3, Daniel B. Graham1, B. Brett Finlay, Aleksandar D. Kostic, Jeffrey A. Porter, Hera Vlamakis, Sarah Jeanfavre, Julian Avila-Pacheco, Clary B. Clish, and Ramnik J. Xavier

Subject:

Subject ID:SU001189
Subject Type:Bacteria
Subject Species:Bacteroides thetaiotaomicron VPI-5482
Taxonomy ID:226186
Genotype Strain:WT (VPI-5482), SPT K.O. (BT_0870)
Cell Biosource Or Supplier:ATCC
Cell Strain Details:Wild type Bacteroides tethaiotamicron strains and serine palmitoyltransferase (SPT) knockouts
Subject Comments:Grown in Minimal Media with or without d4-alanine

Factors:

Subject type: Bacteria; Subject species: Bacteroides thetaiotaomicron VPI-5482 (Factor headings shown in green)

mb_sample_id local_sample_id Strain
SA078068SPT3SPT K.O. (BT_0870) + d4-Ala
SA078069SPT1SPT K.O. (BT_0870) + d4-Ala
SA078070SPT2SPT K.O. (BT_0870) + d4-Ala
SA078071MM2WT (VPI-5482)
SA078072MM1WT (VPI-5482)
SA078073MM3WT (VPI-5482)
SA078074WT3WT (VPI-5482) + d4-Ala
SA078075WT1WT (VPI-5482) + d4-Ala
SA078076WT2WT (VPI-5482) + d4-Ala
Showing results 1 to 9 of 9

Collection:

Collection ID:CO001183
Collection Summary:After 48 hrs of labeling, resulting cultures were pelleted by centrifugation at 8000 rpm for 10 min and cell density was normalized. Lipids were extracted using isopropanol and stored at -80C for lipidomic analysis.
Sample Type:Bacterial cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001204
Treatment Summary:WT and ΔSPT cultures of B. thetaiotaomicron and B. ovatus were grown in 5 mL of minimal media (M9 salts (Teknova), 1% vitamin K1-hemin solution (Becton Dickinson), 1% trace mineral supplement (ATCC), 1% trace vitamin supplement (ATCC), 2% lactose), supplemented with 10μM of deuterium (D4)-labelled alanine (Sigma), or 10μM of -alanine (Sigma).
Cell Storage:-80C
Cell Growth Container:anaerobic chamber (Coy Laboratory Products) with an atmosphere of 20% CO2, 5% H2, and 75% N2 at 37°C.

Sample Preparation:

Sampleprep ID:SP001197
Sampleprep Summary:After 48 hrs, resulting cultures were pelleted by centrifugation at 8000 rpm for 10 min and cell density was normalized. Lipids were extracted using isopropanol and stored at -80C until ready for lipidomic analysis.

Combined analysis:

Analysis ID AN001853
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu Nexera X2
Column Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Focus
Ion Mode POSITIVE
Units Abundances

Chromatography:

Chromatography ID:CH001341
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS001714
Analysis ID:AN001853
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were processed using TraceFinder 3.1 (Thermo Fisher) and Progenesis QI (Nonlinear dynamics). Retention time, m/z, MS/MS fragmentation were used to confirm the identity of metabolite using authentic reference standards when available (level 1 identifications), in addition to monitoring the product ions produced and the retention time and mass of species belonging to the each lipid class (level 2-3 annotation).
Ion Mode:POSITIVE
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