Summary of Study ST001287
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 PR000869. The data can be accessed directly via it's Project DOI: 10.21228/M8C40P This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001287 |
| Study Title | Luminal succinate in UC-HMA (human microbiota-associated) mice. |
| Study Type | MS analysis |
| Study Summary | Patients with ulcerative colitis (UC) are known to be at higher risk for Clostridium difficile (C. difficile) infection (CDI), and CDI in UC patients is recognized as a major clinical problem because it worsens UC outcome. In order to assess the role of gut dysbiosis, seen in UC patients, we have established a human microbiota-associated mouse model in which germ-free mice are colonized with gut microbiota from UC patients. Utilizing this model, we found that UC microbiota colonized HMA mice (UC-HMA mice) were susceptible to CDI. To address the mechanism by which UC-HMA mice are unable to acquire the colonization resistance against C. difficile, we analyzed the luminal metabolites in UC-HMA mice, especially in succinate which is a crucial metabolite doe the growth of C. difficile. |
| Institute | University of Michigan |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | Ann Arbor, MI |
| mkachman@med.umich.edu | |
| Phone | 734-232-0842 |
| Submit Date | 2019-12-11 |
| Num Groups | 63 |
| Total Subjects | 3 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-01-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000869 |
| Project DOI: | doi: 10.21228/M8C40P |
| Project Title: | Association of luminal succinate in UC-Mb mice and succinate consuming bacteria |
| Project Type: | MS analysis |
| Project Summary: | Measure the levels of luminal succinate in UC-Mb mice (UC-Mb colonized human gnotobiotic mise) and succinate consuming bacteria inoculated UC-Mb mice to elucidate the association between the increased abundance of succinate consuming bacteira and decreased amounts of luminal succinate in CDI-susceptible UC-Mb mice. |
| Institute: | University of Michigan |
| Department: | Internal Medicine-Gastroenterology |
| Laboratory: | Kamada Lab |
| Last Name: | Kamada |
| First Name: | Nobuhiko |
| Address: | Ann Arbor, MI |
| Email: | nkamada@umich.edu |
| Phone: | 734-763-2142 |
Subject:
| Subject ID: | SU001365 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | UC-hGB |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Replication | Treatment |
|---|---|---|---|
| SA093870 | S00034622 | #1 | Ctrl |
| SA093871 | S00034623 | #1 | Ctrl |
| SA093872 | S00034624 | #1 | Ctrl |
| SA093873 | S00034625 | #1 | SuccinateConsumingBacteria |
| SA093874 | S00034626 | #1 | SuccinateConsumingBacteria |
| SA093875 | S00034630 | #2 | Ctrl |
| SA093876 | S00034631 | #2 | Ctrl |
| SA093877 | S00034628 | #2 | Ctrl |
| SA093878 | S00034627 | #2 | Ctrl |
| SA093879 | S00034629 | #2 | Ctrl |
| SA093880 | S00034636 | #2 | SuccinateConsumingBacteria |
| SA093881 | S00034635 | #2 | SuccinateConsumingBacteria |
| SA093882 | S00034634 | #2 | SuccinateConsumingBacteria |
| SA093883 | S00034632 | #2 | SuccinateConsumingBacteria |
| SA093884 | S00034633 | #2 | SuccinateConsumingBacteria |
| SA093885 | S00034642 | #3 | Ctrl |
| SA093886 | S00034641 | #3 | Ctrl |
| SA093887 | S00034643 | #3 | Ctrl |
| SA093888 | S00034637 | #3 | Ctrl |
| SA093889 | S00034640 | #3 | Ctrl |
| SA093890 | S00034638 | #3 | Ctrl |
| SA093891 | S00034639 | #3 | Ctrl |
| SA093892 | S00034650 | #3 | SuccinateConsumingBacteria |
| SA093893 | S00034651 | #3 | SuccinateConsumingBacteria |
| SA093894 | S00034649 | #3 | SuccinateConsumingBacteria |
| SA093895 | S00034647 | #3 | SuccinateConsumingBacteria |
| SA093896 | S00034644 | #3 | SuccinateConsumingBacteria |
| SA093897 | S00034645 | #3 | SuccinateConsumingBacteria |
| SA093898 | S00034646 | #3 | SuccinateConsumingBacteria |
| SA093899 | S00034648 | #3 | SuccinateConsumingBacteria |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO001360 |
| Collection Summary: | Mouse feces |
| Sample Type: | Feces |
Treatment:
| Treatment ID: | TR001380 |
| Treatment Summary: | None |
Sample Preparation:
| Sampleprep ID: | SP001373 |
| Sampleprep Protocol Filename: | 2018-4-20_Succinate_fecal_EX00837.docx |
Combined analysis:
| Analysis ID | AN002147 | AN002148 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Agilent Q-TOF 6520 | Agilent Q-TOF 6520 |
| Column | Phenomenex Luna NH2,1mm ID | Phenomenex Luna NH2,1mm ID |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6520 QTOF | Agilent 6520 QTOF |
| Ion Mode | NEGATIVE | NEGATIVE |
| Units | pmol/mg | Peak area normalized |
Chromatography:
| Chromatography ID: | CH001571 |
| Methods Filename: | 002-HILIC-27min-1mm-flatInsert_-_A2B2.m.zip |
| Instrument Name: | Agilent Q-TOF 6520 |
| Column Name: | Phenomenex Luna NH2,1mm ID |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001998 |
| Analysis ID: | AN002147 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Agilent Quant V8 was used for data analysis |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001999 |
| Analysis ID: | AN002148 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Agilent Quant V8 was used for data analysis |
| Ion Mode: | NEGATIVE |
