Summary of study ST001127

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 IDST001127
Study TitleLipid profiling of caecal samples from GF mice colonized with B. thetaiotaomicron WT or the ΔSPT mutants (part III)
Study SummaryTo study Bacteroidetes sphingolipids in intestinal health, we colonized germ-free mice with wild type or a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides derived sphingolipids increased intestinal inflammation, dysregulated innate immunity and altered the host ceramide pool.
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Submit Date2019-01-17
Num Groups3
Total Subjects14
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:SU001188
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6 germ-free mice
Animal Animal Supplier:Taconic


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Inoculum Strain
SA078054BTSPR Cecal_3Bacteroides thetaiotaomicron SPT K.O. (BT_0870)
SA078055BTSPR Cecal_4Bacteroides thetaiotaomicron SPT K.O. (BT_0870)
SA078056BTSPR Cecal_6Bacteroides thetaiotaomicron SPT K.O. (BT_0870)
SA078057BTSPR Cecal_1Bacteroides thetaiotaomicron SPT K.O. (BT_0870)
SA078058BTSPR Cecal_5Bacteroides thetaiotaomicron SPT K.O. (BT_0870)
SA078059BTSPR Cecal_2Bacteroides thetaiotaomicron SPT K.O. (BT_0870)
SA078060BTWT Cecal_3Bacteroides thetaiotaomicron WT (VPI-5482)
SA078061BTWT Cecal_2Bacteroides thetaiotaomicron WT (VPI-5482)
SA078062BTWT Cecal_1Bacteroides thetaiotaomicron WT (VPI-5482)
SA078063BTWT Cecal_4Bacteroides thetaiotaomicron WT (VPI-5482)
SA078064BTWT Cecal_5Bacteroides thetaiotaomicron WT (VPI-5482)
SA078065BTWT Cecal_6Bacteroides thetaiotaomicron WT (VPI-5482)
SA078066GF Cecal_1None None
SA078067GF Cecal_2None None
Showing results 1 to 14 of 14


Collection ID:CO001182
Collection Summary:Caecal samples from GF mice colonized with B. thetaiotaomicron WT or the ΔSPT mutant were weighed, and 20 mg of each wet-weight sample was used for lipid profiling.
Sample Type:Cecum
Storage Conditions:-80℃


Treatment ID:TR001203
Treatment Summary:In an anaerobic chamber, bacterial cultures from frozen stocks were first plated on BHI supplemented with hemin and vitamin K, and subsequently pure cultures were selected and mixed together at a 1:1 ratio in sterile, reduced PBS. Bacterial mixtures in PBS were removed from the anaerobic chamber and immediately transported to the animal facility for gavage experiments. The volume of the mixture received per mouse was 100 μL, at a concentration of 10^9 cells/mL. The concentration of the mixture in cell/mL was determined using a UV spectrometer, and gavage doses were confirmed by back-titering the inocula.

Sample Preparation:

Sampleprep ID:SP001196
Sampleprep Summary:20 mg of each wet-weight cecal sample was extracted using 200 μL isopropanol + 0.1 ng/μL C24:0 PC as internal standard, incubated at RT for 1 hr, and centrifuged for 10 min at 10,000g.

Combined analysis:

Analysis ID AN001852
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:CH001340
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Chromatography Type:Reversed phase


MS ID:MS001713
Analysis ID:AN001852
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).