Summary of Study ST001248

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 PR000835. The data can be accessed directly via it's Project DOI: 10.21228/M8RH65 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 IDST001248
Study TitleThe cecal and fecal metabolomes of horses before and after metronidazole administration
Study SummaryMetronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration. The metabolome was characterized by mass spectrometry-based methods. Fecal, but not cecal metabolites were affected by metronidazole. The fecal metabolites affected represented diverse metabolic pathways such as nucleic acid metabolism, secondary bile metabolism, fatty acid synthesis/degradation/elongation or metabolism and sugar metabolism.
Institute
Texas A&M University
DepartmentDepartment of Small Animal Clinical Sciences
LaboratoryGastrointestinal Laboratory
Last NameArnold
First NameCarolyn
Address4474 TAMU
Emailcarnold@cvm.tamu.edu
Phone979 845 3541
Submit Date2019-09-04
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailMALDI-MS
Release Date2020-03-03
Release Version1
Carolyn Arnold Carolyn Arnold
https://dx.doi.org/10.21228/M8RH65
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000835
Project DOI:doi: 10.21228/M8RH65
Project Title:The cecal and fecal microbiomes and metabolomes of horses before and after metronidazole administration
Project Summary:Metronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration. DNA was extracted from the cecal and fecal samples, and 16S rRNA genes were sequenced. The bacterial diversity and composition of each sample was determined. Richness and evenness indices were significantly decreased by metronidazole administration in both cecal and fecal samples, but overall composition was only significantly changed in fecal samples on Day 3 (ANOSIM, p=0.008). The most dominant phyla were Bacteroidetes and Firmicutes in all groups examined. In fecal samples, significant changes at the phyla Actinobacteria, Spirochaetes, Lentisphaerae and Verrucomicrobia occurred on Day 3, which correlated with clinical signs of gastrointestinal disease. Analysis of the predicted microbial functions using PICRUSt indicated changes associated with metronidazole in fecal samples. The metabolome was characterized by mass spectrometry-based methods. Fecal, but not cecal metabolites were affected by metronidazole. The fecal metabolites affected represented diverse metabolic pathways such as nucleic acid metabolism, secondary bile metabolism, fatty acid synthesis/degradation/elongation or metabolism and sugar metabolism.
Institute:Texas A&M University
Department:Department of Small Animal Clinical Sciences
Laboratory:Gastrointestinal Laboratory
Last Name:Arnold
First Name:Carolyn
Address:4474 TAMU
Email:carnold@cvm.tamu.edu
Phone:979 845 3541

Subject:

Subject ID:SU001316
Subject Type:Mammal
Subject Species:Equus caballus
Taxonomy ID:9796

Factors:

Subject type: Mammal; Subject species: Equus caballus (Factor headings shown in green)

mb_sample_id local_sample_id organ Day Treatment
SA090893AlvinD0_058cecal D0 No
SA090894FrankD0_037cecal D0 No
SA090895SteveD0_042cecal D0 No
SA090896ErnieD0_053cecal D0 Yes
SA090897BillyD0_047cecal D0 Yes
SA090884AlvinD-14_057cecal D-14 No
SA090885FrankD-14_036cecal D-14 No
SA090886ErnieD-14_052cecal D-14 No
SA090887SteveD-14_041cecal D-14 No
SA090888BillyD-14_046cecal D-14 No
SA090898BillyD14_049cecal D14 Yes
SA090899AlvinD14_060cecal D14 Yes
SA090900FrankD14_039cecal D14 Yes
SA090901SteveD14_043cecal D14 Yes
SA090902ErnieD14_055cecal D14 Yes
SA090889ErnieD-28_051cecal D-28 No
SA090890BillyD-28_045cecal D-28 No
SA090891AlvinD-28_056cecal D-28 No
SA090892FrankD-28_035cecal D-28 No
SA090903SteveD28_044cecal D28 No
SA090904FrankD28_040cecal D28 Yes
SA090905BillyD28_050cecal D28 Yes
SA090906AlvinD28_061cecal D28 Yes
SA090907SteveD7_062cecal D7 Yes
SA090908BillyD7_048cecal D7 Yes
SA090909ErnieD7_054cecal D7 Yes
SA090910FrankD7_038cecal D7 Yes
SA090911AlvinD7_059cecal D7 Yes
SA090920AlvinD0_033fecal D0 No
SA090921AlvinD0_032fecal D0 No
SA090922SteveD0_010fecal D0 No
SA090923ErnieD0_024fecal D0 No
SA090924AlvinD0_031fecal D0 No
SA090925FrankD0_003fecal D0 No
SA090926BillyD0_017fecal D0 No
SA090927AlvinD0_030fecal D0 No
SA090912BillyD-14_016fecal D-14 No
SA090913SteveD-14_009fecal D-14 No
SA090914ErnieD-14_023fecal D-14 No
SA090915FrankD-14_002fecal D-14 No
SA090928SteveD14_013fecal D14 Yes
SA090929BillyD14_020fecal D14 Yes
SA090930ErnieD14_027fecal D14 Yes
SA090931FrankD14_006fecal D14 Yes
SA090916ErnieD-28_022fecal D-28 No
SA090917FrankD-28_001fecal D-28 No
SA090918SteveD-28_008fecal D-28 No
SA090919BillyD-28_015fecal D-28 No
SA090932SteveD28_014fecal D28 Yes
SA090933FrankD28_007fecal D28 Yes
SA090934AlvinD28_034fecal D28 Yes
SA090935BillyD28_021fecal D28 Yes
SA090936AlvinD3_031fecal D3 Yes
SA090937BillyD3_018fecal D3 Yes
SA090938ErnieD3_025fecal D3 Yes
SA090939SteveD3_011fecal D3 Yes
SA090940FrankD3_004fecal D3 Yes
SA090941BillyD7_019fecal D7 Yes
SA090942FrankD7_005fecal D7 Yes
SA090943AlvinD7_032fecal D7 Yes
SA090944SteveD7_012fecal D7 Yes
SA090945ErnieD7_026fecal D7 Yes
Showing results 1 to 62 of 62

Collection:

Collection ID:CO001310
Collection Summary:Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration.
Sample Type:Feces

Treatment:

Treatment ID:TR001331
Treatment Summary:Metronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to severe adverse gastrointestinal effects.

Sample Preparation:

Sampleprep ID:SP001324
Sampleprep Summary:Samples were stored at −80 °C until shipped on dry ice to the West Coast Metabolomics Core (University of California, Davis, CA, USA) using an untargeted approach.(20) Samples were homogenized and extracted. Following resuspension in methanol/chloroform, samples were derivatized by methoxyamine hydrochloride in pyridine and subsequently by N-methyl-N-trimethylsilyltrifluoroacetamide for trimethylsilylation of acidic protons.

Combined analysis:

Analysis ID AN002072
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type MALDI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units peak intensity

Chromatography:

Chromatography ID:CH001509
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC

MS:

MS ID:MS001923
Analysis ID:AN002072
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:MALDI
MS Comments:Raw data files are preprocessed directly after data acquisition and stored as ChromaTOF-specific *.peg files, as generic *.txt result files and additionally as generic ANDI MS *.cdf files. ChromaTOF vs. 2.32 is used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported for use in the BinBase algorithm. Result *.txt files are exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database.
Ion Mode:POSITIVE
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