Summary of Study ST002289

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 PR001468. The data can be accessed directly via it's Project DOI: 10.21228/M8ZT5R 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 IDST002289
Study TitleMap of microbially induced metabolic changes across diverse body sites in mice - Bacterial culture data
Study SummaryMetabolite profiles of culture supernatants from individual commensal bacteria isolated from the intestine of mice.
Institute
University of Calgary
DepartmentPhysiology and Pharmacology
LaboratoryMcCoy
Last NameBROWN
First NameKIRSTY
Address3330 Hospital Dr NW
Emailkirsty.brown1@ucalgary.ca
Phone2508692232
Submit Date2022-05-26
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-02-05
Release Version1
KIRSTY BROWN KIRSTY BROWN
https://dx.doi.org/10.21228/M8ZT5R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001468
Project DOI:doi: 10.21228/M8ZT5R
Project Title:Microbiota alter the metabolome in an age and sex dependent manner in mice
Project Summary:Tissue samples from contents along the intestinal tract and systemic sites in mice that did not have any bacteria (germ free) or colonized with a simplified microbiota or more complex microbiota.
Institute:University of Calgary
Department:Physiology and Pharmacology
Laboratory:McCoy
Last Name:BROWN
First Name:KIRSTY
Address:2500 University Dr NW, CALGARY, AB, T2N 1N4, Canada
Email:kirsty.brown1@ucalgary.ca; Kathy.mccoy@ucalgary.ca
Phone:2508692232
Funding Source:Canadian Institute of Health Research, Natural Science and Engineering Research Council of Canada, Alberta Innovates Health Solutions
Publications:Microbiota alter the metabolome in an age and sex dependent manner in mice
Contributors:Kirsty Brown, Carolyn A. Thomson, Ryan Groves, Vina Fan, Ian A. Lewis, Kathy D. McCoy

Subject:

Subject ID:SU002375
Subject Type:Bacteria
Subject Species:Several mouse commensals
Age Or Age Range:8-16 hours

Factors:

Subject type: Bacteria; Subject species: Several mouse commensals (Factor headings shown in green)

mb_sample_id local_sample_id Factor species
SA219960I46.1I46 Clostridium inocuum
SA219961I46.2I46 Clostridium inocuum
SA219962I46.3I46 Clostridium inocuum
SA219963I46.4I46 Clostridium inocuum
SA219964I48.1I48 Bacteroides caecimuris
SA219965I48.2I48 Bacteroides caecimuris
SA219966I48.3I48 Bacteroides caecimuris
SA219967I48.4I48 Bacteroides caecimuris
SA219968I49.1I49 Lactobacillus reuteri
SA219969I49.2I49 Lactobacillus reuteri
SA219970I49.3I49 Lactobacillus reuteri
SA219971I49.4I49 Lactobacillus reuteri
SA219972KB18.1KB18 Acutalibacter muris
SA219973KB18.2KB18 Acutalibacter muris
SA219974KB18.5KB18 Acutalibacter muris
SA219975KB18.6KB18 Acutalibacter muris
SA219976KB1.1KB1 Enterococcus faecalis
SA219977KB1.2KB1 Enterococcus faecalis
SA219978KB1.3KB1 Enterococcus faecalis
SA219979KB1.4KB1 Enterococcus faecalis
SA219980Media.1Media Media
SA219981Media.2Media Media
SA219982Media.3Media Media
SA219983Media.4Media Media
SA219984YL27.1YL27 Muribaculun intestinale
SA219985YL27.2YL27 Muribaculun intestinale
SA219986YL27.3YL27 Muribaculun intestinale
SA219987YL27.4YL27 Muribaculun intestinale
SA219988YL2.1YL2 Bifidobacterium animalis
SA219989YL2.2YL2 Bifidobacterium animalis
SA219990YL2.3YL2 Bifidobacterium animalis
SA219991YL2.4YL2 Bifidobacterium animalis
SA219992YL31.1YL31 Faecalibacter plautii
SA219993YL31.2YL31 Faecalibacter plautii
SA219994YL31.3YL31 Faecalibacter plautii
SA219995YL31.4YL31 Faecalibacter plautii
SA219996YL32.1YL32 Enterocloster clostridioforme
SA219997YL32.2YL32 Enterocloster clostridioforme
SA219998YL32.3YL32 Enterocloster clostridioforme
SA219999YL32.4YL32 Enterocloster clostridioforme
SA220000YL44.1YL44 Akkermansia muciniphila
SA220001YL44.2YL44 Akkermansia muciniphila
SA220002YL44.3YL44 Akkermansia muciniphila
SA220003YL44.4YL44 Akkermansia muciniphila
SA220004YL45.1YL45 Turicimonas muris
SA220005YL45.2YL45 Turicimonas muris
SA220006YL45.3YL45 Turicimonas muris
SA220007YL45.4YL45 Turicimonas muris
SA220008YL58.1YL58 Blautia coccoides
SA220009YL58.2YL58 Blautia coccoides
SA220010YL58.3YL58 Blautia coccoides
SA220011YL58.4YL58 Blautia coccoides
Showing results 1 to 52 of 52

Collection:

Collection ID:CO002368
Collection Summary:Bacteria were grown in 15mL culture tubes in 3mL of modified brain heart infusion broth [37g/L BHI powder, 0.025% Cystiene-HCl.H2O, 0.025% Na2S.9H2O, 1ug/mL Hemin, 0.5ug/mL menadione, 0.025% mucin]. Media was pre-reduced in an anaerobic chamber (Whitley A95 Workstation; 90% N2, 5% H2 & 5% CO2) for 48 hours then bacterial cultures were started from glycerol stocks. 200µL of glycerol stock was added to each culture tube and cultures were incubated for 6-36 hours until early plateau phase. After incubation, cultures were removed from the anaerobic chamber, and 50uL was collected to extract DNA for 16S sequencing to confirm accurate identification of bacteria and absence of contamination. The remaining culture was centrifuged (max. speed, 15 minutes, 4°C) and the supernatant was collected and combined 1:1 with 100% methanol. Samples were then incubated at - 20°C for 1 hour. Samples were centrifuged (max. speed, 15 minutes, 4°C), supernatant was recovered and combined 1:4 with 50% methanol to obtain a final dilution of D20.
Sample Type:Bacterial cells
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR002387
Treatment Summary:Culture conditions and extractions methods described in protocol.

Sample Preparation:

Sampleprep ID:SP002381
Sampleprep Summary:The remaining culture was centrifuged (max. speed, 15 minutes, 4°C) and the supernatant was collected and combined 1:1 with 100% methanol. Samples were then incubated at - 20°C for 1 hour. Samples were centrifuged (max. speed, 15 minutes, 4°C), supernatant was recovered and combined 1:4 with 50% methanol to obtain a final dilution of D20.

Combined analysis:

Analysis ID AN003741
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column Thermo Syncronis HILIC (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode NEGATIVE
Units AUC

Chromatography:

Chromatography ID:CH002772
Methods Filename:culture_protocol_kb.docx
Instrument Name:Thermo Vanquish
Column Name:Thermo Syncronis HILIC (100 x 2.1mm,1.7um)
Column Temperature:30C
Flow Gradient:2 stage linear gradient
Flow Rate:600uL/min
Sample Injection:2uL
Solvent A:100% water; 20 mM ammonium formate, pH 3
Solvent B:100% acetonitrile; 0.1% formic acid
Analytical Time:15 minutes
Washing Buffer:10% MeOH in H2O + 0.1% formic acid
Target Sample Temperature:4
Chromatography Type:HILIC

MS:

MS ID:MS003489
Analysis ID:AN003741
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:50-750 m/z, peak integration and assignment using El-Maven software matching to authentic standard library (~150 compounds).
Ion Mode:NEGATIVE
Analysis Protocol File:culture_protocol_kb.docx
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