Summary of study ST001126

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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.

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Study IDST001126
Study TitleWT and ΔSPT cultures of B. thetaiotaomicron grown in Minimal Media (part II)
Study SummaryLipid profiling was applied on WT and ΔSPT cultures of B. thetaiotaomicron grown in minimal liquid media in order to confirm the production of Bacteroides-derived sphingolipids.
Broad Institute of MIT and Harvard
DepartmentGastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, University Medical Center Groningen
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Submit Date2019-01-17
Num Groups2
Total Subjects6
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2019-03-06
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco application/zip

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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
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 ID:SU001187
Subject Type:Bacteria
Subject Species:Bacteroides tethaiotamicron
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


Subject type: Bacteria; Subject species: Bacteroides tethaiotamicron (Factor headings shown in green)

mb_sample_id local_sample_id Bacterial Species / Inoculum
SA078048KO1_1SPT K.O. (BT_0870)
SA078049KO3_3SPT K.O. (BT_0870)
SA078050KO2_2SPT K.O. (BT_0870)
SA078051WT3_6WT (VPI-5482)
SA078052WT1_4WT (VPI-5482)
SA078053WT2_5WT (VPI-5482)
Showing results 1 to 6 of 6


Collection ID:CO001181
Collection Summary:WT and ΔSPT cultures of B. thetaiotaomicron were grown in 5 mL of minimal 714 media (M9 salts (Teknova), 1% vitamin K1-hemin solution (Becton Dickinson), 1% trace mineral 715 supplement (ATCC), 1% trace vitamin supplement (ATCC), 2% lactose).
Sample Type:Bacterial cells
Storage Conditions:-80℃


Treatment ID:TR001202
Treatment Summary:In-frame deletion of the serine palmitoyl transferase gene (spt) in B. thetaiotaomicron Δtdk was generated using a counter-selectable allelic exchange procedure (Koropatkin et al., 2008).
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:SP001195
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 AN001851
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu Nexera X2
Column Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Focus
Units abundance


Chromatography ID:CH001339
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase


MS ID:MS001712
Analysis ID:AN001851
Instrument Name:Thermo Q Exactive Focus
Instrument Type:Orbitrap
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).