Summary of Study ST003011

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 PR001874. The data can be accessed directly via it's Project DOI: 10.21228/M8GM8G 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.

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Study IDST003011
Study TitleUntargeted metabolomics analysis of murine colon content
Study Summarywe used the minimal consortium Oligo-Mouse Microbiota (OMM)12 to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without addition of the dominant gut bacterium Eggerthella lenta were fed with diets varying in fat content or supplemented with primary bile acids.
Institute
Helmholtz Centre for Environmental Research
DepartmentMolecular Systems Biology
Last NameEngelmann
First NameBeatrice
AddressPermoserstrasse 15, 04318 Leipzig, Germany
Emailbeatrice.engelmann@ufz.de
Phone+493411099
Submit Date2023-12-12
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-01-04
Release Version1
Beatrice Engelmann Beatrice Engelmann
https://dx.doi.org/10.21228/M8GM8G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001874
Project DOI:doi: 10.21228/M8GM8G
Project Title:Effects of the human intestinal bacterium Eggerthella lenta in gut of gnotobiotic mice
Project Summary:In this work, we used the minimal consortium Oligo-Mouse Microbiota (OMM)12 to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without addition of the dominant gut bacterium Eggerthella lenta were fed with diets varying in fat content or supplemented with primary bile acids.
Institute:Helmholtz Centre for Environmental Research
Department:Molecular Systems Biology
Last Name:Engelmann
First Name:Beatrice
Address:Permoserstrasse 15, 04318 Leipzig, Germany
Email:beatrice.engelmann@ufz.de
Phone:00493411099

Subject:

Subject ID:SU003125
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Diet colonization
SA32695724_Corio.O_BABA Corio_OligoMM
SA32695823_Corio.O_BABA Corio_OligoMM
SA32695922_Corio.O_BABA Corio_OligoMM
SA326960422_Corio.O_BABA Corio_OligoMM
SA32696145_Corio.O_BABA Corio_OligoMM
SA32696243_Corio.O_BABA Corio_OligoMM
SA32696344_Corio.O_BABA Corio_OligoMM
SA32696421_Corio.O_BA_posBA Corio_OligoMM
SA32696521_Corio.O_BABA Corio_OligoMM
SA32696622_Corio.O_BA_posBA Corio_OligoMM
SA32696743_Corio.O_BA_posBA Corio_OligoMM
SA32696824_Corio.O_BA_posBA Corio_OligoMM
SA32696923_Corio.O_BA_posBA Corio_OligoMM
SA32697044_Corio.O_BA_posBA Corio_OligoMM
SA326971422_Corio.O_BA_posBA Corio_OligoMM
SA32697245_Corio.O_BA_posBA Corio_OligoMM
SA32697357_O_BABA OligoMM
SA32697455_O_BABA OligoMM
SA32697511_6_O_BABA OligoMM
SA32697654_O_BABA OligoMM
SA32697756_O_BA_posBA OligoMM
SA3269788_O_BA_posBA OligoMM
SA32697911_O_BA_posBA OligoMM
SA32698054_O_BA_posBA OligoMM
SA32698142_O_BABA OligoMM
SA32698255_O_BA_posBA OligoMM
SA32698342_O_BA_posBA OligoMM
SA32698457_O_BA_posBA OligoMM
SA32698556_O_BABA OligoMM
SA32698611_O_BABA OligoMM
SA3269878_O_BABA OligoMM
SA32698811_6_O_BA_posBA OligoMM
SA32698917_Corio.O_CD_posCD Corio_OligoMM
SA32699020_Corio.O_CDCD Corio_OligoMM
SA32699119_Corio.O_CD_posCD Corio_OligoMM
SA32699217_Corio.O_CDCD Corio_OligoMM
SA32699333_Corio.O_CD_posCD Corio_OligoMM
SA32699435_Corio.O_CD_posCD Corio_OligoMM
SA32699534_Corio.O_CD_posCD Corio_OligoMM
SA32699633_Corio.O_CDCD Corio_OligoMM
SA32699720_Corio.O_CD_posCD Corio_OligoMM
SA32699819_Corio.O_CDCD Corio_OligoMM
SA32699934_Corio.O_CDCD Corio_OligoMM
SA32700035_Corio.O_CDCD Corio_OligoMM
SA32700113_O_CDCD OligoMM
SA32700214_O_CDCD OligoMM
SA32700314_O_CD_posCD OligoMM
SA32700413_O_CD_posCD OligoMM
SA32700536_O_CDCD OligoMM
SA32700638_O_CD_posCD OligoMM
SA32700746_O_CD_posCD OligoMM
SA32700837_O_CD_posCD OligoMM
SA32700936_O_CD_posCD OligoMM
SA32701037_O_CDCD OligoMM
SA32701138_O_CDCD OligoMM
SA32701246_O_CDCD OligoMM
SA32701331_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32701447_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32701530_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32701632_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32701731_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32701849_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32701929_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32702030_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA327021462_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32702248_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32702332_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32702447_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32702549_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA327026462_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32702748_Corio.O_HFD.BA_posHFD.BA Corio_OligoMM
SA32702829_Corio.O_HFD.BAHFD.BA Corio_OligoMM
SA32702959_O_HFD.BA_posHFD.BA OligoMM
SA32703058_O_HFD.BA_posHFD.BA OligoMM
SA32703160_O_HFD.BAHFD.BA OligoMM
SA32703261_O_HFD.BA_posHFD.BA OligoMM
SA3270339_O_HFD.BA_posHFD.BA OligoMM
SA32703460_O_HFD.BA_posHFD.BA OligoMM
SA3270359_O_HFD.BAHFD.BA OligoMM
SA32703661_O_HFD.BAHFD.BA OligoMM
SA32703759_O_HFD.BAHFD.BA OligoMM
SA32703858_O_HFD.BAHFD.BA OligoMM
SA32703951_Corio.O_HFD_posHFD Corio_OligoMM
SA32704052_Corio.O_HFDHFD Corio_OligoMM
SA32704150_Corio.O_HFD_posHFD Corio_OligoMM
SA32704253_Corio.O_HFDHFD Corio_OligoMM
SA32704327_Corio.O_HFD_posHFD Corio_OligoMM
SA32704453_Corio.O_HFD_posHFD Corio_OligoMM
SA32704525_Corio.O_HFDHFD Corio_OligoMM
SA32704627_Corio.O_HFDHFD Corio_OligoMM
SA32704752_Corio.O_HFD_posHFD Corio_OligoMM
SA32704851_Corio.O_HFDHFD Corio_OligoMM
SA32704928_Corio.O_HFD_posHFD Corio_OligoMM
SA32705028_Corio.O_HFDHFD Corio_OligoMM
SA32705125_Corio.O_HFD_posHFD Corio_OligoMM
SA32705250_Corio.O_HFDHFD Corio_OligoMM
SA3270532_O_HFD_posHFD OligoMM
SA3270547_O_HFDHFD OligoMM
SA32705539_O_HFDHFD OligoMM
SA32705640_O_HFDHFD OligoMM
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Collection:

Collection ID:CO003118
Collection Summary:Mice were euthanized with CO2 and colon was extracted.
Sample Type:Colon

Treatment:

Treatment ID:TR003134
Treatment Summary:Germfree male C57BL/6N mice were associated with 0.2 ml of the freshly thawed microbial mixtures via oral gavage three times within one week at the age of five weeks. From week 8 onwards, diet was changed from autoclaved standard chow to synthetic control diet (CD) for two weeks. Thereafter, the mice were randomly assigned to four different groups fed the following diets for eight weeks (the references and main differences in composition between the diets are provided in Figure S1B): CD, control diet; CD-BA, control diet supplemented with the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) (each 0.1%); HFD, lard-based high-fat diet (48% energy from fat); HFD-BA, HFD supplemented with CA and CDCA. These diets were used due to the link between Coriobacteriia/E. lenta and bile acid metabolism as well as host metabolic health.

Sample Preparation:

Sampleprep ID:SP003131
Sampleprep Summary:Colon content was mixed with 5x ACN:H2O solvent and 4 steel beads for subsequent extraction in the bead mill. After centrifugation, 100 µL of the supernatant were mixed with 500 µL methanol:acetonitrile (ACN):water (2:3:1) followed by vortex and sonication. After centrifugation, 100 µL of the supernatant were dried in a SpeedVac™ vacuum concentrator (Eppendorf, Hamburg, Germany).

Combined analysis:

Analysis ID AN004942 AN004943
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II
Column Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um) Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6546 QTOF Agilent 6546 QTOF
Ion Mode NEGATIVE POSITIVE
Units Peak AUC Peak AUC

Chromatography:

Chromatography ID:CH003731
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent ZORBAX Eclipse Plus C18 (100 x 2.1mm,1.8um)
Column Temperature:45
Flow Gradient:0-5.5 min: 1% B; 5-20 min: 1-100% B; 20-22 min: 100% B; 22-22.5: 100-1% B; 22.5-25 min: 1% B
Flow Rate:0.3 ml/min
Solvent A:Water + 0.1% FA
Solvent B:ACN + 0.1% FA
Chromatography Type:Reversed phase

MS:

MS ID:MS004685
Analysis ID:AN004942
Instrument Name:Agilent 6546 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 50 – 1000 m/z. After each full scan, the 2 most intense ions were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.4, Waters Corporation) for further analysis.
Ion Mode:NEGATIVE
  
MS ID:MS004686
Analysis ID:AN004943
Instrument Name:Agilent 6546 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 50 – 1000 m/z. After each full scan, the 2 most intense ions were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.4, Waters Corporation) for further analysis.
Ion Mode:POSITIVE
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