Summary of Study ST003141
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 PR001952. The data can be accessed directly via it's Project DOI: 10.21228/M8DD95 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 | ST003141 |
| Study Title | untargeted metabolomic analysis of whole blood from AMX-treated and untreated mice |
| Study Summary | untargeted metabolomic analysis of whole blood from AMX-treated and untreated mice |
| Institute | Brown University |
| Last Name | Beekman |
| First Name | Chapman |
| Address | 171 Meeting Street, Providence, Rhode Island, 02912, USA |
| Chapman_Beekman@brown.edu | |
| Phone | 4012071832 |
| Submit Date | 2024-01-17 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001952 |
| Project DOI: | doi: 10.21228/M8DD95 |
| Project Title: | Spatial analysis of murine GI reveals role of small intestinal bile acid metabolism in amoxicillin-induced dysbiosis |
| Project Summary: | Antibiotics cause collateral damage to resident microbes that is associated with various health risks. To-date, studies have largely focused on impacts of antibiotics on large intestinal and fecal microbiota. Here, we employ a GI-wide integrated multiomic approach to reveal that amoxicillin (AMX) treatment reduces overall bacterial abundance, bile salt hydrolase activity and unconjugated bile acids in the small intestine (SI). An accompanying loss of fatty acids and increase in acyl-carnitines in the large intestine corresponded with spatially-distinct expansions of proteobacteria. Parasutterella excrementihominis utilized fatty acid biosynthesis, becoming dominant in the SI while multiple Klebsiella species employed fatty acid oxidation during expansion in the large intestine. Depletion of bile acids and lipids may contribute to AMX-induced dysbiosis in the lower GI. To test this, we demonstrate that restoration of unconjugated bile acids can mitigate losses of commensals in the large intestine while also inhibiting the expansion of Proteobacteria during AMX treatment. |
| Institute: | Brown University |
| Department: | MMI |
| Laboratory: | MMI, Belenky Lab |
| Last Name: | Beekman |
| First Name: | Chapman |
| Address: | BMC 613, 171 Meeting Street, Providence RI 02912 |
| Email: | Chapman_Beekman@brown.edu |
| Phone: | 4012071832 |
Subject:
| Subject ID: | SU003258 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA340606 | CB80 | Amox |
| SA340607 | CB81 | Amox |
| SA340608 | CB73 | Amox |
| SA340609 | CB79 | Amox |
| SA340610 | CB74 | Amox |
| SA340611 | CB75 | Amox |
| SA340612 | CB84 | Control |
| SA340613 | CB77 | Control |
| SA340614 | CB83 | Control |
| SA340615 | CB82 | Control |
| SA340616 | CB78 | Control |
| SA340617 | CB76 | Control |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003251 |
| Collection Summary: | Lumenal contents collected from multiple GI sites and immediately flash frozen |
| Sample Type: | Blood (whole) |
Treatment:
| Treatment ID: | TR003267 |
| Treatment Summary: | Mice were treated for 24h with amoxicillin/vehicle in drinking water |
| Treatment Compound: | Amoxicillin |
| Treatment Route: | oral |
Sample Preparation:
| Sampleprep ID: | SP003265 |
| Sampleprep Summary: | Frozen GI contents were lyophilized and 10mg of dry contents were extracted twice in 300µL in (2:1) acetone and isopropanol. Samples were maintained on dry ice during extraction steps. Extracts were diluted 1:10 in a solution of 80% methanol in water. All solvents were LC-MS grade purchased from Fisher Scientific. |
Combined analysis:
| Analysis ID | AN005154 |
|---|---|
| Analysis type | MS |
| Chromatography type | None (Direct infusion) |
| Chromatography system | none |
| Column | none |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6550 QTOF |
| Ion Mode | NEGATIVE |
| Units | ion counts |
Chromatography:
| Chromatography ID: | CH003902 |
| Instrument Name: | none |
| Column Name: | none |
| Column Temperature: | na |
| Flow Gradient: | none |
| Flow Rate: | na |
| Solvent A: | none |
| Solvent B: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS004890 |
| Analysis ID: | AN005154 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | A pooled study sample (pSS) was prepared by combining 5 µL of each sample. The pSS was injected every ten samples during data acquisition. Instrumental Analysis Metabolome profiles of the sample extracts were acquired using flow-injection mass spectrometry. The method described here is adapted from Fuhrer et al 2011. The instrumentation consisted of an Agilent 6550 iFunnel LC-MS Q-TOF mass spectrometer in tandem with an MPS3 autosampler (Gerstel) and an Agilent 1260 Infinity II quaternary pump. The running buffer was 60% isopropanol in water (v/v) with 1 mM ammonium fluoride. Hexakis (1H, 1H, 3H-tetrafluoropropoxy)-phosphazene) (Agilent) and 3-amino-1-propanesulfonic acid (HOT) (Sigma Aldrich) were added to the running buffer to serve as lockmasses. The isocratic flow rate was set to 0.150 mL/min. The instrument was run in 4GHz High Resolution, negative ionization mode. Mass spectra between 50 and 1,000 m/z were collected in profile mode. 5 µL of each sample were injected twice, consecutively, within 0.96 minutes to serve as technical replicates. The pooled study sample was injected periodically throughout the batch. Data Processing & Annotation Raw profile data were centroided, merged, and recalibrated using MATLAB software described by Fuhrer et al(doi/10.1021/ac201267k). |
| Ion Mode: | NEGATIVE |
