Summary of Study ST002472

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 PR001596. The data can be accessed directly via it's Project DOI: 10.21228/M8D701 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 IDST002472
Study TitleLinking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation. Veillonella parvula cell and media profiling
Study SummaryUnderstanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.
Institute
Broad Institute of MIT and Harvard
Last NameXavier
First NameRamnik
Address415 Main Street
Emailrxavier@broadinstitute.org
Phone617717084
Submit Date2023-02-10
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-02-12
Release Version1
Ramnik Xavier Ramnik Xavier
https://dx.doi.org/10.21228/M8D701
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001596
Project DOI:doi: 10.21228/M8D701
Project Title:Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation
Project Type:Metabolomic profiling of human fecal and plasma samples and bacterial strains
Project Summary:Understanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.
Institute:Broad Institute of MIT and Harvard
Last Name:Xavier
First Name:Ramnik
Address:415 Main Street
Email:rxavier@broadinstitute.org
Phone:6177147080
Publications:Schirmer, M., Stražar, M., Avila-Pacheco, J., Rojas-Tapias, D. F., Brown, E. M., Temple, E., Deik, A., Bullock, K., Jeanfavre, S., Pierce, K., Jin, S., Invernizzi, R., Pust, M.-M., Costliow, Z., Mack, D. R., Griffiths, A. M., Walters, T., Boyle, B. M., Kugathasan, S., … Xavier, R. J. (2024). Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2023.12.013
Contributors:Melanie Schirmer, Martin Strazar, Julian Avila-Pacheco, Daniel F. Rojas-Tapias, Eric Brown, Emily Temple, Subra Kugathasan, Zach Costliow, Hera Vlamakis, Jeff Hyams, Lee Denson, Clary B. Clish, Ramnik J. Xavier

Subject:

Subject ID:SU002562
Subject Type:Bacteria
Subject Species:Veillonella parvula
Taxonomy ID:29466

Factors:

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

mb_sample_id local_sample_id Matrix Sample Type Tretment
SA247708C_40Cell_pool QC_Titration -
SA247709C_80Cell_pool QC_Titration -
SA247710C_100Cell_pool QC_Titration -
SA247711C_20Cell_pool QC_Titration -
SA247712C_60Cell_pool QC_Titration -
SA247699L_C1Cell Experiment Lactate
SA247700L_C3Cell Experiment Lactate
SA247701L_C2Cell Experiment Lactate
SA247702LN_C3Cell Experiment Lactate+Nitrate
SA247703LN_C2Cell Experiment Lactate+Nitrate
SA247704LN_C1Cell Experiment Lactate+Nitrate
SA247705N_C2Cell Experiment Nitrate
SA247706N_C3Cell Experiment Nitrate
SA247707N_C1Cell Experiment Nitrate
SA247713SM_80Media_pool QC_Titration -
SA247714SM_40Media_pool QC_Titration -
SA247715SM_20Media_pool QC_Titration -
SA247716SM_60Media_pool QC_Titration -
SA247717SM_100Media_pool QC_Titration -
SA247718L_SM1Spent Media Experiment Lactate
SA247719L_SM2Spent Media Experiment Lactate
SA247720L_SM3Spent Media Experiment Lactate
SA247721LN_SM1Spent Media Experiment Lactate+Nitrate
SA247722LN_SM3Spent Media Experiment Lactate+Nitrate
SA247723LN_SM2Spent Media Experiment Lactate+Nitrate
SA247724N_SM3Spent Media Experiment Nitrate
SA247725N_SM1Spent Media Experiment Nitrate
SA247726N_SM2Spent Media Experiment Nitrate
SA247727L_UM1Unspent Media Experiment Lactate
SA247728L_UM3Unspent Media Experiment Lactate
SA247729L_UM2Unspent Media Experiment Lactate
SA247730LN_UM3Unspent Media Experiment Lactate+Nitrate
SA247731LN_UM1Unspent Media Experiment Lactate+Nitrate
SA247732LN_UM2Unspent Media Experiment Lactate+Nitrate
SA247733N_UM3Unspent Media Experiment Nitrate
SA247734N_UM2Unspent Media Experiment Nitrate
SA247735N_UM1Unspent Media Experiment Nitrate
Showing results 1 to 37 of 37

Collection:

Collection ID:CO002555
Collection Summary:The strain Veillonella parvula SKV38 xdh::cat*. Briefly, V. parvula was grown on SK agar (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with either DL-lactate (50 mM lactate), potassium nitrate (40 mM KNO3), or both, incubated under anaerobic conditions at 37ºC overnight and then inoculated into the respective liquid media in biological triplicates. Cells and supernatants were harvested at mid-exponential phase (OD600=0.3), after centrifugation at 10,000g for 5 min. Both cell pellets and resulting supernatants were stored at -80C until processing for metabolite extraction and metabolomic analysis. A titration of cell pools and media pools was conducted (10,20,40,60,80,100%) and used to filter the data based on the correlation of the abundance of detected features with
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR002574
Treatment Summary:The strain was first streaked on an agar plate with SK media (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with 50 mM lactate and 40 mM KNO3 (SKLN medium) and antibiotics if required. From this agar plate, a single colony was selected and inoculated in 5mL SKLN media and grown for 24 hours. Next, overnight cells from this inoculum were grown using a 1/50 inoculum of the overnight culture, on either SK, SK + 50 mM lactate (SKL), SK + 40 mM nitrate (SKN), and SKLN.

Sample Preparation:

Sampleprep ID:SP002568
Sampleprep Summary:Bacterial metabolites were profiled using the HILIC-pos and C8-pos methods for mapping Veillonella metabolites present in human stool. Bacterial samples were prepared as follows: mid-exponential Veillonella cultures (OD600 = 0.3-0.4) were harvested by centrifugation at 20,000g at 4°C for 1 minute, supernatants (spent media) were aliquoted, while cell pellets were resuspended in ice-cold PBS. Cells were then spun twice at 20,000g for 1 minute and all PBS supernatant removed and discarded. Cell pellet weights were estimated and all the samples harvested were stored at -80°C until metabolite profiling was conducted. For cells profiled in the C8-pos, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using 380 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL), 10 ul of media was extracted using 190 µL of isopropanol containing internal standards. Extracts were incubated at room temperature in the dark before centrifugation (10 min, 9,000 x g, Room Temperature). For cells profiled in the HILIC-pos mode, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using180 µL HILIC extraction solution with internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA), while 10 µL of media was extracted with 90 µL of extraction solution. Extracts were cleared by centrifugation (10 min, 9,000 x g, 4C) prior to analysis.

Combined analysis:

Analysis ID AN004037 AN004038
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2 mm, 3 μm) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE POSITIVE
Units Abundance Abundance

Chromatography:

Chromatography ID:CH002985
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2 mm, 3 μm)
Column Temperature:30C
Flow Gradient:Isocratically with 5% mobile phase A for 1 minute followed by a linear gradient to 40% mobile phase B over 10 minutes
Flow Rate:250 µL/min
Solvent A:100% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH002986
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Column Temperature:40C
Flow Gradient:The column was eluted at a flow rate of 450 µL/min isocratically for 1 minute at 80% mobile phase A, followed by a linear gradient to 80% mobile-phase B over 2 minutes, a linear gradient to 100% mobile phase B over 7 minutes, and then 3 minutes at 100% mobile-phase B.
Flow Rate:450 µL/min
Solvent A:95% water/5% methanol; 10 mM ammonium acetate; 0.1% acetic acid
Solvent B:100% methanol; 0.1% acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003784
Analysis ID:AN004037
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:POSITIVE
  
MS ID:MS003785
Analysis ID:AN004038
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:POSITIVE
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