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.

Study ID	ST002472
Study Title	Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation. Veillonella parvula cell and media profiling
Study 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	617717084
Submit Date	2023-02-10
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2024-02-12
Release Version	1

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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.

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.