Summary of study ST001041

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 PR000697. The data can be accessed directly via it's Project DOI: 10.21228/M8B10B 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.

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Study IDST001041
Study TitleDevelopment of a weaned pig model of enterotoxigenic E.coli-induced environmental enteropathy
Study TypeAnimal Model
Study SummaryEnvironmental Enteropathy (EE) is a subclinical condition primarily effecting developing countries believed to be caused by chronic fecal-oral contamination. The condition is characterized by chronic gut inflammation, malabsorption, stunting of growth, stunted villi, and reduced efficacy of oral vaccines. Due to the similarity of the gastrointestinal tract and immune response of swine and humans, the piglet is an attractive model for studying this condition. In this present study, piglets were challenged with either a chronic or acute dose of pathogenic E.coli in an attempt to mimic the symptoms of EE over a 7 day trial period. Throughout the study a number of biological samples were collected for analysis and are presented here, including feces for untargeted metabolomics analysis.
Institute
Texas A&M University
DepartmentAnimal Science
LaboratoryGill Lab
Last NameBoeckman
First NameJustin
Address400 Bizzell Street
EmailJxboeckman@tamu.edu
Phone4084893729
Submit Date2018-08-21
Num Groups3
Total Subjects24
PublicationsIn progress
Analysis Type DetailGC-MS
Release Date2018-10-10
Release Version1
Justin Boeckman Justin Boeckman
https://dx.doi.org/10.21228/M8B10B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000697
Project DOI:doi: 10.21228/M8B10B
Project Title:Development of a weaned pig model of enterotoxigenic E.coli-induced environmental enteropathy
Project Type:Animal Model
Project Summary:Environmental Enteropathy (EE) is a subclinical condition primarily effecting developing countries believed to be caused by chronic fecal-oral contamination. The condition is characterized by chronic gut inflammation, malabsorption, stunting of growth, stunted villi, and reduced efficacy of oral vaccines. Due to the similarity of the gastrointestinal tract and immune response of swine and humans, the piglet is an attractive model for studying this condition. In this present study, piglets were challenged with either a chronic or acute dose of pathogenic E.coli in an attempt to mimic the symptoms of EE over a 7 day trial period. Throughout the study a number of biological samples were collected for analysis and are presented here, including feces for untargeted metabolomics analysis.
Institute:Texas A&M University
Department:Animal Science
Laboratory:Gill Lab
Last Name:Boeckman
First Name:Justin
Address:400 Bizzell Street, College Station, TX, 77843, USA
Email:Jxboeckman@tamu.edu
Phone:4084893729
Funding Source:Bill and Melinda Gates Foundation
Publications:In progress
Contributors:Justin Boeckman, Sarah Sprayberry, Jason Gill, Todd Callaway

Subject:

Subject ID:SU001082
Subject Type:Mammal
Subject Species:Sus scrofa
Taxonomy ID:9823
Genotype Strain:Landrace X Large White
Age Or Age Range:21 Days Old
Weight Or Weight Range:Approximately 14lbs
Gender:Male
Animal Housing:Southern Plains Agricultural Research Center in College Station, TX
Animal Light Cycle:Natural
Animal Feed:corn-soybean meal based pelleted diet (ab libitum)
Animal Water:ab libitum
Animal Inclusion Criteria:Not showing any signs preexisting illness/scours over a 2 day observation period

Factors:

Subject type: Mammal; Subject species: Sus scrofa (Factor headings shown in green)

mb_sample_id local_sample_id Day Treatment
SA070221354505-1 Acute
SA070222354507-1 Acute
SA070223354506-1 Acute
SA0702323545101 Acute
SA0702333545111 Acute
SA0702343545081 Acute
SA0702353545091 Acute
SA070224354522-1 Chronic
SA070225354552-1 Chronic
SA070226354523-1 Chronic
SA070227354521-1 Chronic
SA0702363545261 Chronic
SA0702373545251 Chronic
SA0702383545271 Chronic
SA0702393545241 Chronic
SA070228354537-1 Control
SA070229354553-1 Control
SA070230354539-1 Control
SA070231354538-1 Control
SA0702403545411 Control
SA0702413545431 Control
SA0702423545421 Control
SA0702433545401 Control
SA0702443545123 Acute
SA0702453545133 Acute
SA0702463545153 Acute
SA0702473545143 Acute
SA0702483545303 Chronic
SA0702493545313 Chronic
SA0702503545293 Chronic
SA0702513545283 Chronic
SA0702523545463 Control
SA0702533545473 Control
SA0702543545453 Control
SA0702553545443 Control
SA0702563545166 Acute
SA0702573545176 Acute
SA0702583545196 Acute
SA0702593545186 Acute
SA0702603545336 Chronic
SA0702613545326 Chronic
SA0702623545356 Chronic
SA0702633545346 Chronic
SA0702643545486 Control
SA0702653545516 Control
SA0702663545506 Control
SA0702673545496 Control
Showing results 1 to 47 of 47

Collection:

Collection ID:CO001076
Collection Summary:Swine fecal samples were collected from the pens on day -1, day 1, day 3, and day 6. Feces samples were processed and held at -80C until thawed for lyophilization.
Sample Type:Feces

Treatment:

Treatment ID:TR001096
Treatment Summary:24 Piglets were blocked into 3 different treatment groups. Acute treatment received a one time oral dose of 6mls of 10^9 CFU/ml of overnight shiga toxigenic E.coli culture. Chronic treatment received a 6ml daily dose of 1/10th dilution of overnight culture at 10^8 CFU/ml. The control group received a sham dose of PBS. At the conclusion of the trial on Day 7 piglets were euthanized and necropsied.
Treatment Compound:Pathogenic Shigatoxigenic E.coli (ATCC 23545)
Treatment Dose:One time vs Daily Dose
Treatment Dosevolume:6ml of 10^9 CFU/ml, 10^8 CFU/ml, or PBS
Treatment Vehicle:Oral Gavage

Sample Preparation:

Sampleprep ID:SP001089
Sampleprep Summary:Massed out 2mg±0.3mg of sample. Add 1ml of 3:3:2 extraction solvent (acetonitrile:isopropanol:water). Add 2 3mm grinder beads. Grind twice for 30 seconds each. Shake for 6 minutes at -4C. Centrifuge for 2 mins at 14000 rcf. Separate two 475µL aliquotes. Centrivape to dry. Add 500 µL ACN:H2O (50:50). Vortex for 10 seconds. Centrifuged for 2 minutes at 14000 rcf. Aliquoted two 475 µL samples. Dry in centrivap.

Combined analysis:

Analysis ID AN001706
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units m/z

Chromatography:

Chromatography ID:CH001204
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS001580
Analysis ID:AN001706
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC x GC-TOF
MS Type:EI
Ion Mode:POSITIVE
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