Summary of Study ST002473

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	ST002473
Study Title	Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation. Veillonella parvula media profiling of IBD drug metabolites
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:	SP002569
Sampleprep Summary:	Bacterial supernatant (media) metabolites were profiled using the HILIC-pos and HILIC-neg methods in order to estimate purines and thiopurines metabolism. Media 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 and stored at -80°C until metabolite profiling was conducted. For the HILIC-pos method, media samples (10 µL) were extracted using 90 µL HILIC extraction solution (74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid) with internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8) and extracts were cleared by centrifugation (10 min, 9,000 x g, Room Temperature). For media profiled in the HILIC-neg mode, 30 µL of media and metabolites extracted using 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). Extracts were cleared by centrifugation (10 min, 9,000 x g, 4C) prior to analysis.

Sampleprep ID:

SP002569

Sampleprep Summary:

Bacterial supernatant (media) metabolites were profiled using the HILIC-pos and HILIC-neg methods in order to estimate purines and thiopurines metabolism. Media 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 and stored at -80°C until metabolite profiling was conducted. For the HILIC-pos method, media samples (10 µL) were extracted using 90 µL HILIC extraction solution (74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid) with internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8) and extracts were cleared by centrifugation (10 min, 9,000 x g, Room Temperature). For media profiled in the HILIC-neg mode, 30 µL of media and metabolites extracted using 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). Extracts were cleared by centrifugation (10 min, 9,000 x g, 4C) prior to analysis.