Summary of Study ST001671

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

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Study IDST001671
Study TitleA gut microbe-focused metabolomics pipeline enables mechanistic interrogation of microbiome metabolism
Study SummaryGut 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
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)raw
Analysis Type DetailLC-MS
Release Date2021-06-01
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:SU001748
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 sample_type media taxonomy strain
SA153406ncbimw_0217media_blank bhis - -
SA153407ncbimw_0216media_blank bhis - -
SA153408ncbimw_0604media_blank bhis - -
SA153409ncbimw_0218media_blank bhis - -
SA153410ncbimw_0602media_blank bhis - -
SA153411ncbimw_0603media_blank bhis - -
SA153412ncbimw_0752media_blank cm - -
SA153413ncbimw_0751media_blank cm - -
SA153414ncbimw_0770media_blank cm - -
SA153415ncbimw_0750media_blank cm - -
SA153416ncbimw_0646media_blank cm - -
SA153417ncbimw_0645media_blank cm - -
SA153418ncbimw_0644media_blank cm - -
SA153464ncbimw_0755media_blank mml - -
SA153465ncbimw_0753media_blank mml - -
SA153466ncbimw_0754media_blank mml - -
SA153461ncbimw_0630media_blank mm_s04_citrate - -
SA153462ncbimw_0631media_blank mm_s04_citrate - -
SA153463ncbimw_0629media_blank mm_s04_citrate - -
SA153467ncbimw_0740media_blank mms - -
SA153468ncbimw_0741media_blank mms - -
SA153469ncbimw_0749media_blank mms - -
SA153470ncbimw_0739media_blank mms - -
SA153419ncbimw_0757media_blank mm - -
SA153420ncbimw_0758media_blank mm - -
SA153421ncbimw_0760media_blank mm - -
SA153422ncbimw_0756media_blank mm - -
SA153423ncbimw_0761media_blank mm - -
SA153424ncbimw_1036media_blank mm - -
SA153425ncbimw_0094media_blank mm - -
SA153426ncbimw_0123media_blank mm - -
SA153427ncbimw_1035media_blank mm - -
SA153428ncbimw_0762media_blank mm - -
SA153429ncbimw_1037media_blank mm - -
SA153430ncbimw_0767media_blank mm - -
SA153431ncbimw_0205media_blank mm - -
SA153432ncbimw_0204media_blank mm - -
SA153433ncbimw_0203media_blank mm - -
SA153434ncbimw_0206media_blank mm - -
SA153435ncbimw_0244media_blank mm - -
SA153436ncbimw_0246media_blank mm - -
SA153437ncbimw_0245media_blank mm - -
SA153438ncbimw_0776media_blank mm - -
SA153439ncbimw_0775media_blank mm - -
SA153440ncbimw_0766media_blank mm - -
SA153441ncbimw_0765media_blank mm - -
SA153442ncbimw_0764media_blank mm - -
SA153443ncbimw_1038media_blank mm - -
SA153444ncbimw_0768media_blank mm - -
SA153445ncbimw_0774media_blank mm - -
SA153446ncbimw_0769media_blank mm - -
SA153447ncbimw_0763media_blank mm - -
SA153448ncbimw_0444media_blank mm - -
SA153449ncbimw_1045media_blank mm - -
SA153450ncbimw_1046media_blank mm - -
SA153451ncbimw_1048media_blank mm - -
SA153452ncbimw_1040media_blank mm - -
SA153453ncbimw_1047media_blank mm - -
SA153454ncbimw_0593media_blank mm - -
SA153455ncbimw_1039media_blank mm - -
SA153456ncbimw_0002media_blank mm - -
SA153457ncbimw_1044media_blank mm - -
SA153458ncbimw_0001media_blank mm - -
SA153459ncbimw_0032media_blank mm - -
SA153460ncbimw_0003media_blank mm - -
SA153471ncbimw_1031media_blank paf - -
SA153472ncbimw_1030media_blank paf - -
SA153473ncbimw_1042media_blank paf - -
SA153474ncbimw_1041media_blank paf - -
SA153475ncbimw_1043media_blank paf - -
SA153476ncbimw_1029media_blank paf - -
SA153477ncbimw_1034media_blank paf - -
SA153478ncbimw_1033media_blank paf - -
SA153479ncbimw_1032media_blank paf - -
SA153493ncbimw_0347media_blank pyg_muc - -
SA153494ncbimw_0348media_blank pyg_muc - -
SA153495ncbimw_0346media_blank pyg_muc - -
SA153480ncbimw_0150media_blank pyg - -
SA153481ncbimw_0152media_blank pyg - -
SA153482ncbimw_0375media_blank pyg - -
SA153483ncbimw_0417media_blank pyg - -
SA153484ncbimw_0747media_blank pyg - -
SA153485ncbimw_0748media_blank pyg - -
SA153486ncbimw_0746media_blank pyg - -
SA153487ncbimw_0745media_blank pyg - -
SA153488ncbimw_0419media_blank pyg - -
SA153489ncbimw_0773media_blank pyg - -
SA153490ncbimw_0151media_blank pyg - -
SA153491ncbimw_0772media_blank pyg - -
SA153492ncbimw_0771media_blank pyg - -
SA153497ncbimw_0381media_blank rcml - -
SA153498ncbimw_0380media_blank rcml - -
SA153499ncbimw_0382media_blank rcml - -
SA153500ncbimw_0418media_blank rcml - -
SA153501ncbimw_0059media_blank rcml - -
SA153502ncbimw_0321media_blank rcml - -
SA153503ncbimw_0573media_blank rcmsg - -
SA153504ncbimw_0574media_blank rcmsg - -
SA153505ncbimw_0572media_blank rcmsg - -
SA153496ncbimw_0759media_blank rcm - -
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Collection:

Collection ID:CO001741
Collection Summary:Please see the methods associated with this submission. In short, this data is from mono-cultured anaerobic gut bacteria grown in a variety of different media, harvested, and subjected to multiple LCMS detection methods.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001761
Treatment Summary:Please see the methods associated with this submission.

Sample Preparation:

Sampleprep ID:SP001754
Sampleprep Summary:Please see the methods associated with this submission.

Combined analysis:

Analysis ID AN002727 AN002728 AN002729
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 (area)

Chromatography:

Chromatography ID:CH002013
Chromatography Summary:Please see `methods.pdf` associated with this submission for full details. In short, this analysis is processed data associated with standard reverse phase LCMS with positive ionization.
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40
Flow Rate:350 uL/min
Solvent A:Water with 0.1% formic acid
Solvent B:Methanol with 0.1% formic acid
Capillary Voltage:4000
Chromatography Type:Reversed phase
  
Chromatography ID:CH002014
Chromatography Summary:Please see `methods.pdf` associated with this submission for full details. In short, this analysis is processed data associated with standard reverse phase LCMS with negative ionization.
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40
Flow Rate:350 uL/min
Solvent A:Water with 6.5 mM ammonium bicarbonate
Solvent B:95:5 (V/V) Methanol:Water with 6.5 mM ammonium bicarbonate
Capillary Voltage:4000
Chromatography Type:Reversed phase
  
Chromatography ID:CH002015
Chromatography Summary:Please see `methods.pdf` associated with this submission for full details. In short, this analysis is processed data associated with HILIC LCMS with positive ionization.
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:40
Flow Rate:400 uL/min
Solvent A:Water with 0.125% Formic Acid and 10 mM Ammonium Formate
Solvent B:95:5 (V/V) Acetonitrile:Water with 0.125% Formic Acid and 10 mM Ammonium Formate
Capillary Voltage:4000
Chromatography Type:HILIC

MS:

MS ID:MS002524
Analysis ID:AN002727
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Please see `methods.pdf` associated with this submission.
Ion Mode:POSITIVE
Capillary Voltage:4000
Dry Gas Temp:250C
Fragment Voltage:140V
  
MS ID:MS002525
Analysis ID:AN002728
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Please see `methods.pdf` associated with this submission.
Ion Mode:NEGATIVE
Capillary Voltage:4000
Dry Gas Temp:250C
Fragment Voltage:140V
  
MS ID:MS002526
Analysis ID:AN002729
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Please see `methods.pdf` associated with this submission.
Ion Mode:POSITIVE
Capillary Voltage:4000
Dry Gas Temp:250C
Fragment Voltage:140V
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