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 |
| 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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Collection:
| Collection ID: | CO002556 |
| Collection Summary: | All strain experiments were done in the Xavier lab. Strains and growth conditions: we utilized the following strains of Veillonella for growth and metabolic analysis; Veillonella parvula SKV38 [DR071], Veillonella parvula SKV38 xdh::cat* [DR214], Veillonella parvula SKV38 pucD::cat* [DR213]. All strains were 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 5 mL 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. Supernatants were collected at the mid-exponential phase (OD600~0.4) and collected for metabolomic analyses (HILIC-pos metabolite profiling method described above). For analysis of the metabolism of the IBD drugs, cells were prepared as described above, and mid-exponential phase cells were collected, washed twice with sterile SK, and resuspended in 100 µl of SK. A volume of 6 ml of SKN was then inoculated using 90 µl of the bacterial suspension. Those 6 ml were split in three parts: a) 1.5 ml SK, b) 1.5 ml SK + 20 µM 6-mercaptopurine, and c) 1.5 ml SK + 20 µM 6-azathioprine. Additionally, sterile SK was prepared in an identical fashion to serve as a control for the experiment. Cells were incubated in a plate reader (4 wells/treatment) with low shaking and 37ºC for about ~5 h, and when the OD600 reached 0.4 cells were collected. For collection, 700 µl of the suspensions were centrifuged at 21,000 g for 2 min, and 400 µl of the supernatant harvested and stored at -20 ºC for analysis. Preparation of thiopurine drugs: 20 mM solutions were prepared using 4.25 mg of 6-mercaptopurine (Sigma 852678) or 6.9 mg of azathioprine (Sigma A4638) dissolved in 1 ml of DMSO. The drugs were prepared and used the same day. |
| Sample Type: | Culture Media |
