Summary of Study ST002394

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 PR001541. The data can be accessed directly via it's Project DOI: 10.21228/M8HB00 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 IDST002394
Study TitleShort-chain fatty acid (SCFA) analysis of DSS-treated murine intestinal microbiota using continuous cultivation in bioreactors
Study SummaryWe cultivated murine faecal microbiota in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared to the untreated control bioreactors.
Institute
Helmholtz Centre for Environmental Research
DepartmentMolecular Systems Biology
Last NameEngelmann
First NameBeatrice
AddressPermoserstraße 15, Leipzipg, Saxony, 03418, Germany
Emailbeatrice.engelmann@ufz.de
Phone00493412351099
Submit Date2022-12-06
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2022-12-30
Release Version1
Beatrice Engelmann Beatrice Engelmann
https://dx.doi.org/10.21228/M8HB00
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001541
Project DOI:doi: 10.21228/M8HB00
Project Title:Short-chain fatty acid (SCFA) analysis of DSS-treated murine intestinal microbiota using continuous cultivation in bioreactors
Project Summary:We cultivated murine faecal microbiota in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared to the untreated control bioreactors.
Institute:Helmholtz Centre for Environmental Research
Department:Molecular Systems Biology
Last Name:Engelmann
First Name:Beatrice
Address:Permoserstraße 15, Leipzipg, Saxony, 03418, Germany
Email:beatrice.engelmann@ufz.de
Phone:00493412351099

Subject:

Subject ID:SU002483
Subject Type:Bacteria
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Day Treatment
SA238935F_d1111 1%DSS
SA238936B_d1111 1%DSS
SA238937D_d1111 1%DSS
SA238938A_d1111 control
SA238939E_d1111 control
SA238940C_d1111 control
SA238941B_d1212 1%DSS
SA238942F_d1212 1%DSS
SA238943D_d1212 1%DSS
SA238944C_d1212 control
SA238945E_d1212 control
SA238946A_d1212 control
SA238947F_d1313 1%DSS
SA238948D_d1313 1%DSS
SA238949B_d1313 1%DSS
SA238950E_d1313 control
SA238951A_d1313 control
SA238952C_d1313 control
SA238953B_d1414 1%DSS
SA238954F_d1414 1%DSS
SA238955D_d1414 1%DSS
SA238956A_d1414 control
SA238957E_d1414 control
SA238958C_d1414 control
SA238959B_d1515 1%DSS
SA238960F_d1515 1%DSS
SA238961D_d1515 1%DSS
SA238962C_d1515 control
SA238963A_d1515 control
SA238964E_d1515 control
SA238965F_d1818 1%DSS
SA238966D_d1818 1%DSS
SA238967B_d1818 1%DSS
SA238968E_d1818 control
SA238969A_d1818 control
SA238970C_d1818 control
SA238971F_d1919 1%DSS
SA238972B_d1919 1%DSS
SA238973D_d1919 1%DSS
SA238974A_d1919 control
SA238975E_d1919 control
SA238976C_d1919 control
SA238977F_d2020 1%DSS
SA238978D_d2020 1%DSS
SA238979B_d2020 1%DSS
SA238980C_d2020 control
SA238981E_d2020 control
SA238982A_d2020 control
Showing results 1 to 48 of 48

Collection:

Collection ID:CO002476
Collection Summary:Samples were taken at day 1 and as a multiple of 24 h during the control phase (day 12-14) and the early (day 15) and late treatment phase (day 18 to day 20) from the bioreactors under unaerobic conditions.
Sample Type:Feces

Treatment:

Treatment ID:TR002495
Treatment Summary:Faecal pellets were isolated from the colon under aseptic conditions. Directly after collection, faecal pellets were stored at anaerobic conditions. The murine microbiota was cultivated in the chemostats from day 1 to day 13. At day 14, the bioreactors B, D and F were spiked with 1% DSS.

Sample Preparation:

Sampleprep ID:SP002489
Sampleprep Summary:In brief, 20 µl of each sample was mixed with ACN to a final concentration of 50 %. SCFAs were derivatized with 200 mM 3-nitrophenylhydrazine and 120 mM N-(3-dimethylaminopropyl)-N‘-ethylcarbodiimide hydrochloride in pyridine and then diluted in 10 % ACN.

Combined analysis:

Analysis ID AN003900
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode NEGATIVE
Units µM

Chromatography:

Chromatography ID:CH002887
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003639
Analysis ID:AN003900
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:For identification and quantitation, a scheduled MRM method was used, with specific transitions for every SCFA. Data acquisition and peak integration were performed in Analyst® software (Version 1.6.2). Calculation of concentration was done using external calibration curves and statistics were performed using the R software programme.
Ion Mode:NEGATIVE
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