Summary of Study ST001688

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 PR001074. The data can be accessed directly via it's Project DOI: 10.21228/M8W11P 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 IDST001688
Study TitleA gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism (part-II)
Study TypeBacterial Metabolomics
Study SummaryThe C18 positive mode data for A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism.
Institute
Stanford University
DepartmentMicrobiology and Immunology
LaboratoryJustin Sonnenburg
Last NameVan Treuren
First NameWill
AddressSherman Fairchild Building, 299 Campus Drive, Stanford CA, 94305
Emailwdwvt@stanford.edu
Phone7209370980
Submit Date2021-01-20
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-05-17
Release Version1
Will Van Treuren Will Van Treuren
https://dx.doi.org/10.21228/M8W11P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001074
Project DOI:doi: 10.21228/M8W11P
Project Title:A gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism
Project Summary:Gut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules1–3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse body fluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.
Institute:Stanford University
Department:Microbiology and Immunology
Laboratory:Justin Sonnenburg
Last Name:Van Treuren
First Name:Will
Address:Sherman Fairchild Building, 299 Campus Drive, Stanford CA, 94305
Email:wdwvt@stanford.edu
Phone:7209370980
Contributors:Shuo Han1,*, Will Van Treuren1,2,*, Curt R. Fischer3, 4, Bryan D. Merrill1,2, Leah Guthrie1, Brian C. DeFelice4, Lalla A. Fall3,5, Dylan Dodd1,5,^, Michael A. Fischbach4,6,^, and Justin L. Sonnenburg1,4,7,^.

Subject:

Subject ID:SU001765
Subject Type:Bacteria
Subject Species:Bacteria
Subject Comments:178 Bacterial strains

Factors:

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

mb_sample_id local_sample_id experiment sample_type
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SA155508ncbimw_076220180512.0 media_blank
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Collection:

Collection ID:CO001758
Collection Summary:Please see 'methods.pdf' associated with this submission.
Collection Protocol Filename:wdwvt1_20210120_100719_PR_CO_methods.pdf
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001778
Treatment Summary:The 'treatment' groups are specified in Supplemental Table 5 of the associated Han*, Van Treuren* et al. manuscript. An abbreviated version is shown in the 'study_guide' file associated with this study.

Sample Preparation:

Sampleprep ID:SP001771
Sampleprep Summary:Please see 'methods.pdf' associated with this project.
Sampleprep Protocol Filename:wdwvt1_20210120_100719_PR_CO_methods.pdf

Combined analysis:

Analysis ID AN002756 AN002757 AN002758
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase HILIC
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 1290 Infinity II
Column Waters Acquity BEH C18 (100 x 2mm,1.7um) Waters Acquity BEH C18 (100 x 2mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI
MS instrument type QTOF QTOF QTOF
MS instrument name Agilent 6540 QTOF Agilent 6540 QTOF Agilent 6540 QTOF
Ion Mode POSITIVE NEGATIVE POSITIVE
Units counts (area) counts (area) Counts

Chromatography:

Chromatography ID:CH002036
Chromatography Summary:Please see 'methods.pdf' associated with this project. This is the data from the C18 positive method.
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002037
Chromatography Summary:Please see 'methods.pdf' associated with this project. This is the data from the C18 negative method.
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002038
Chromatography Summary:Please see 'methods.pdf' associated with this project. This is the data from the HILIC positive method method.
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS002553
Analysis ID:AN002756
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Please see 'methods.pdf' associated with this project. This is the data from the C18 positive method.
Ion Mode:POSITIVE
  
MS ID:MS002554
Analysis ID:AN002757
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Please see 'methods.pdf' associated with this project. This is the data from the C18 negative method.
Ion Mode:NEGATIVE
  
MS ID:MS002555
Analysis ID:AN002758
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Please see 'methods.pdf' associated with this project. This is the data from the HILIC positive method.
Ion Mode:POSITIVE
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