Summary of Study ST001650

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 PR001056. The data can be accessed directly via it's Project DOI: 10.21228/M86D8X 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 IDST001650
Study TitleChanges to gut microbiota metabolism based on Clostridium difficile-induced inflammation
Study SummaryDetermine changes to metabolites in lumen (cecal contents) of mice due to toxin production by Clostridium difficile R20291.
Stanford University
DepartmentMicrobiology & Immunology
Last NameUniversity
First NameStanford
Address299 Campus Drive Fairchild Building Rm D315
Submit Date2020-12-21
Num Groups3
Total Subjects14
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2021-01-25
Release Version1
Stanford University Stanford University application/zip

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Project ID:PR001056
Project DOI:doi: 10.21228/M86D8X
Project Title:Clostridium difficile toxin production in vivo
Project Summary:Gnotobiotic mice harboring a defined community of bacteria were infected with wild-type Clostridium difficile R20291, its isogenic triple-toxin knockout mutant, or uninfected. Cecal contents were collected for untargeted GC-TOF MS.
Institute:Stanford University
Department:Microbiology & Immunology
Last Name:University
First Name:Stanford
Address:299 Campus Drive Fairchild Building Rm D315


Subject ID:SU001727
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Swiss Webster


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

mb_sample_id local_sample_id Colonization
Showing results 1 to 14 of 14


Collection ID:CO001720
Collection Summary:Cecal contents from gnotobiotic mice were collected under sterile conditions, flash-frozen in liquid nitrogen and stored at -80 C.
Sample Type:Feces
Storage Vials:-80


Treatment ID:TR001740
Treatment Summary:Swiss Webster germ-free mice were tri-colonized with Bacteroides thetaiotaomicron, Clostridium sporogenes and Escherichia coli for 10 days. Mice were subsequently infected with wild-type Clostridium difficile R20291 (n=5), the isogenic toxin-deficient mutant TcdA-B-CDT- (n=5), or gavaged with PBS as an uninfected control (n=4). Cecal contents were colleged 5 days after C. difficile infection.

Sample Preparation:

Sampleprep ID:SP001733
Sampleprep Summary:Metabolites were extracted according to the methodology described in Fiehn 2017 Curr Protoc Mol Biol. ; 114: 30.4.1–30.4.32. doi:10.1002/0471142727.mb3004s114. Briefly, 1 mL 3:3:2 acetonitrile:isopropanol:water was added to ~4 mg cecal contents/feces. Samples were homogenized and then shaken at 4 C for 6 min prior to centrifugation at 14,000 x g for 2 minutes. An aliquot of 475 µl supernatant was taken for subsequent analysis, evaporated, cleaned with acetonitrile and water (1:1), and fully evaporated to dryness. 10 µl MeOH and 91 µl MSTFA were added to all samples for derivatization.

Combined analysis:

Analysis ID AN002696
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890 GC
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Units preak area


Chromatography ID:CH001989
Chromatography Summary:Agilent 6890 GC is equipped with a Gerstel automatic liner exchange system (ALEX) that includes a multipurpose sample (MPS2) dual rail, and a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany) with temperature program as follows: 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume is 0.5 μl with 10 μl/s injection speed on a splitless injector with purge time of 25 seconds. Liner (Gerstel #011711-010-00) is changed after every 10 samples, (using the Maestro1 Gerstel software vs. Before and after each injection, the 10 μl injection syringe is washed three times with 10 μl ethyl acetate A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 μm 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min.
Instrument Name:Agilent 6890 GC
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Flow Rate:1 ml/min
Chromatography Type:GC


MS ID:MS002494
Analysis ID:AN002696
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da.