Summary of Study ST000196
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 PR000178. The data can be accessed directly via it's Project DOI: 10.21228/M8VS3Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000196 |
| Study Title | Murine gastrointestinal bile acid profiles before and after antibiotics |
| Study Type | Bile acid analysis (colon contents/plasma) |
| Study Summary | Clostridium difficile infection (CDI) following antibiotic therapy is a major public health threat. While antibiotic disruption of the indigenous microbiota underlies the majority of cases of CDI, the early dynamics of infection in the disturbed intestinal ecosystem are poorly characterized. This study defines the dynamics of infection with C. difficile strain VPI 10463 throughout the gastrointestinal (GI) tract using a murine model of infection. After inducing susceptibility to C. difficile colonization via antibiotic administration, we followed the dynamics of spore germination, colonization, sporulation, toxin activity, and disease progression throughout the GI tract. C. difficile spores were able to germinate within 6 h postchallenge, resulting in the establishment of vegetative bacteria in the distal GI tract. Spores and cytotoxin activity were detected by 24 h postchallenge, and histopathologic colitis developed by 30 h. Within 36 h, all infected mice succumbed to infection. We correlated the establishment of infection with changes in the microbiota and bile acid profile of the small and large intestines. Antibiotic administration resulted in significant changes to the microbiota in the small and large intestines, as well as a significant shift in the abundance of primary and secondary bile acids. Ex vivo analysis suggested the small intestine as the site of spore germination. This study provides an integrated understanding of the timing and location of the events surrounding C. difficile colonization and identifies potential targets for the development of new therapeutic strategies. Research is published: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333439/ |
| Institute | University of Michigan |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@umich.edu | |
| Submit Date | 2015-06-09 |
| Num Groups | 26 |
| Total Subjects | 135 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 256 M |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-12-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000178 |
| Project DOI: | doi: 10.21228/M8VS3Q |
| Project Title: | Bile Acid Studies in Murine Gut |
| Project Summary: | Targeted bile acid analysis throughout the murine GI tract before and after antibiotics |
| Institute: | University of Michigan |
| Department: | Int Med-Infectious Diseases |
| Laboratory: | Theriot Lab |
| Last Name: | Theriot |
| First Name: | Casey |
| Address: | Ann Arbor, MI |
| Email: | caseythe@umich.edu |
| Phone: | 734-763-4133 |
Subject:
| Subject ID: | SU000215 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Recovery | Gender | Treatment |
|---|---|---|---|---|
| SA009836 | S00015979 | five week recovery | female | Cefoperazone treated |
| SA009837 | S00015978 | five week recovery | female | Cefoperazone treated |
| SA009838 | S00016046 | five week recovery | female | Cefoperazone treated |
| SA009839 | S00016048 | five week recovery | male | Cefoperazone treated |
| SA009840 | S00016047 | five week recovery | male | Cefoperazone treated |
| SA009841 | S00015981 | five week recovery | male | Cefoperazone treated |
| SA009842 | S00015980 | five week recovery | male | Cefoperazone treated |
| SA009843 | S00015975 | four week recovery | female | Cefoperazone treated |
| SA009844 | S00016044 | four week recovery | female | Cefoperazone treated |
| SA009845 | S00015974 | four week recovery | female | Cefoperazone treated |
| SA009846 | S00016043 | four week recovery | female | Cefoperazone treated |
| SA009847 | S00016045 | four week recovery | male | Cefoperazone treated |
| SA009848 | S00015977 | four week recovery | male | Cefoperazone treated |
| SA009849 | S00015976 | four week recovery | male | Cefoperazone treated |
| SA009850 | S00016081 | na | female | No antibiotics |
| SA009851 | S00016015 | na | female | No antibiotics |
| SA009852 | S00016083 | na | female | No antibiotics |
| SA009853 | S00016013 | na | female | No antibiotics |
| SA009854 | S00016082 | na | female | No antibiotics |
| SA009855 | S00016014 | na | female | No antibiotics |
| SA009856 | S00016086 | na | male | No antibiotics |
| SA009857 | S00016085 | na | male | No antibiotics |
| SA009858 | S00016016 | na | male | No antibiotics |
| SA009859 | S00016084 | na | male | No antibiotics |
| SA009860 | S00016018 | na | male | No antibiotics |
| SA009861 | S00016017 | na | male | No antibiotics |
| SA009862 | S00016020 | no recovery | female | Cefoperazone treated |
| SA009863 | S00016021 | no recovery | female | Cefoperazone treated |
| SA009864 | S00015952 | no recovery | female | Cefoperazone treated |
| SA009865 | S00016019 | no recovery | female | Cefoperazone treated |
| SA009866 | S00015953 | no recovery | female | Cefoperazone treated |
| SA009867 | S00016053 | no recovery | female | IP clindamycin |
| SA009868 | S00016054 | no recovery | female | IP clindamycin |
| SA009869 | S00015986 | no recovery | female | IP clindamycin |
| SA009870 | S00015987 | no recovery | female | IP clindamycin |
| SA009871 | S00016052 | no recovery | female | IP clindamycin |
| SA009872 | S00016078 | no recovery | female | Kanamycin treated |
| SA009873 | S00016012 | no recovery | female | Kanamycin treated |
| SA009874 | S00016080 | no recovery | female | Kanamycin treated |
| SA009875 | S00016010 | no recovery | female | Kanamycin treated |
| SA009876 | S00016079 | no recovery | female | Kanamycin treated |
| SA009877 | S00016011 | no recovery | female | Kanamycin treated |
| SA009878 | S00016007 | no recovery | female | Metronidazole treated |
| SA009879 | S00016075 | no recovery | female | Metronidazole treated |
| SA009880 | S00016073 | no recovery | female | Metronidazole treated |
| SA009881 | S00016006 | no recovery | female | Metronidazole treated |
| SA009882 | S00016074 | no recovery | female | Metronidazole treated |
| SA009883 | S00016069 | no recovery | female | Vancomycin treated |
| SA009884 | S00016002 | no recovery | female | Vancomycin treated |
| SA009885 | S00016000 | no recovery | female | Vancomycin treated |
| SA009886 | S00016001 | no recovery | female | Vancomycin treated |
| SA009887 | S00016068 | no recovery | female | Vancomycin treated |
| SA009888 | S00016067 | no recovery | female | Vancomycin treated |
| SA009889 | S00015954 | no recovery | male | Cefoperazone treated |
| SA009890 | S00015955 | no recovery | male | Cefoperazone treated |
| SA009891 | S00016023 | no recovery | male | Cefoperazone treated |
| SA009892 | S00016022 | no recovery | male | Cefoperazone treated |
| SA009893 | S00016024 | no recovery | male | Cefoperazone treated |
| SA009894 | S00016056 | no recovery | male | IP clindamycin |
| SA009895 | S00015988 | no recovery | male | IP clindamycin |
| SA009896 | S00015989 | no recovery | male | IP clindamycin |
| SA009897 | S00016057 | no recovery | male | IP clindamycin |
| SA009898 | S00015990 | no recovery | male | IP clindamycin |
| SA009899 | S00016055 | no recovery | male | IP clindamycin |
| SA009900 | S00016008 | no recovery | male | Kanamycin treated |
| SA009901 | S00016009 | no recovery | male | Kanamycin treated |
| SA009902 | S00016076 | no recovery | male | Kanamycin treated |
| SA009903 | S00016077 | no recovery | male | Kanamycin treated |
| SA009904 | S00016003 | no recovery | male | Metronidazole treated |
| SA009905 | S00016072 | no recovery | male | Metronidazole treated |
| SA009906 | S00016004 | no recovery | male | Metronidazole treated |
| SA009907 | S00016005 | no recovery | male | Metronidazole treated |
| SA009908 | S00016071 | no recovery | male | Metronidazole treated |
| SA009909 | S00016070 | no recovery | male | Metronidazole treated |
| SA009910 | S00015997 | no recovery | male | Vancomycin treated |
| SA009911 | S00016066 | no recovery | male | Vancomycin treated |
| SA009912 | S00015998 | no recovery | male | Vancomycin treated |
| SA009913 | S00015999 | no recovery | male | Vancomycin treated |
| SA009914 | S00016064 | no recovery | male | Vancomycin treated |
| SA009915 | S00016065 | no recovery | male | Vancomycin treated |
| SA009916 | S00015957 | one week recovery | female | Cefoperazone treated |
| SA009917 | S00016025 | one week recovery | female | Cefoperazone treated |
| SA009918 | S00015956 | one week recovery | female | Cefoperazone treated |
| SA009919 | S00015958 | one week recovery | female | Cefoperazone treated |
| SA009920 | S00015959 | one week recovery | female | Cefoperazone treated |
| SA009921 | S00016026 | one week recovery | female | Cefoperazone treated |
| SA009922 | S00016027 | one week recovery | female | Cefoperazone treated |
| SA009923 | S00015960 | one week recovery | male | Cefoperazone treated |
| SA009924 | S00015961 | one week recovery | male | Cefoperazone treated |
| SA009925 | S00016028 | one week recovery | male | Cefoperazone treated |
| SA009926 | S00016029 | one week recovery | male | Cefoperazone treated |
| SA009927 | S00016030 | one week recovery | male | Cefoperazone treated |
| SA009928 | S00015983 | six week recovery | female | Cefoperazone treated |
| SA009929 | S00016050 | six week recovery | female | Cefoperazone treated |
| SA009930 | S00016049 | six week recovery | female | Cefoperazone treated |
| SA009931 | S00015982 | six week recovery | female | Cefoperazone treated |
| SA009932 | S00016059 | six week recovery | female | Cefoperazone treated IP clindamycin |
| SA009933 | S00016060 | six week recovery | female | Cefoperazone treated IP clindamycin |
| SA009934 | S00015991 | six week recovery | female | Cefoperazone treated IP clindamycin |
| SA009935 | S00015992 | six week recovery | female | Cefoperazone treated IP clindamycin |
Collection:
| Collection ID: | CO000203 |
| Collection Summary: | - |
| Sample Type: | Cecum |
Treatment:
| Treatment ID: | TR000223 |
Sample Preparation:
| Sampleprep ID: | SP000217 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | Bile-acids-2015-03-11.docx |
Combined analysis:
| Analysis ID | AN000298 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | |
| Column | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ |
| Ion Mode | NEGATIVE |
| Units | µg/100mg sample weight |
Chromatography:
| Chromatography ID: | CH000219 |
| Methods ID: | AQM041 |
| Methods Filename: | 2014-07-30-Bile_acid-full-BEH-C18-h.m.zip |
| Column Name: | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000247 |
| Analysis ID: | AN000298 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Acquisition Parameters File: | 2014-07-30-Bile_acid-full-BEH-C18-h.m.zip |
| Processing Parameters File: | EX00351-Bile-Acids-Quant-method.m.zip |
