Summary of study ST000495

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 PR000372. The data can be accessed directly via it's Project DOI: 10.21228/M8ZP5C This work is supported by NIH grant, U2C- DK119886.

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Study IDST000495
Study TitleMetabolomic profiles along the gastrointestinal tract of the healthy dog
Study SummaryIntroduction: The fecal microbiome is relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiome and metabolome at other sites along the gastrointestinal tract remains deficient. Objective: To analyze the gastrointestinal microbiome and metabolome of healthy domestic dogs at four anatomical sites. Methods: Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods. Results: Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include amino acids, which decreased from the small to large intestine; pyruvate, which was at peak concentrations in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine. Conclusion: The microbiome and metabolome vary significantly at different sites along the canine gastrointestinal tract.
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-10-17
Num Groups4
Total Subjects24
Num Males4
Num Females2
Raw Data AvailableYes
Raw Data File Type(s).cdf
Analysis Type DetailGC-MS
Release Date2016-12-22
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8ZP5C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000372
Project DOI:doi: 10.21228/M8ZP5C
Project Title:Metabolomic profiles along the gastrointestinal tract of the healthy dog
Project Summary:Introduction: The fecal microbiome is relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiome and metabolome at other sites along the gastrointestinal tract remains deficient. Objective: To analyze the gastrointestinal microbiome and metabolome of healthy domestic dogs at four anatomical sites. Methods: Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods. Results: Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include amino acids, which decreased from the small to large intestine; pyruvate, which was at peak concentrations in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine. Conclusion: The microbiome and metabolome vary significantly at different sites along the canine gastrointestinal tract.
Institute:Texas A&M University
Department:Department of Small Animal Clinical Sciences
Laboratory:Gastrointestinal Laboratory
Last Name:Steiner
First Name:Jorg
Address:College Station, TX 77843-4474
Email:JHonneffer@cvm.tamu.edu
Phone:(979)862-2861

Subject:

Subject ID:SU000516
Subject Type:Animal
Subject Species:Canis familiaris
Taxonomy ID:9615
Genotype Strain:Hound-type
Age Or Age Range:Adult
Weight Or Weight Range:35-60 lbs
Gender:Male/Female
Animal Inclusion Criteria:no evidence of gastrointestinal illness or other disease
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Canis familiaris (Factor headings shown in green)

mb_sample_id local_sample_id Organ Sex
SA025625141217actsa05_1colon Female
SA025626141217actsa19_1colon Female
SA025627141217actsa23_1colon Male
SA025628141217actsa22_1colon Male
SA025629141217actsa10_1colon Male
SA025630141217actsa04_1colon Male
SA025631141217actsa17_1duod Female
SA025632141217actsa13_1duod Female
SA025633141217actsa24_1duod Male
SA025634141217actsa21_1duod Male
SA025635141217actsa20_1duod Male
SA025636141217actsa09_1duod Male
SA025637141217actsa18_1ileum Female
SA025638141217actsa07_1ileum Female
SA025639141217actsa02_1ileum Male
SA025640141217actsa01_1ileum Male
SA025641141217actsa15_1ileum Male
SA025642141217actsa14_1ileum Male
SA025643141217actsa06_1rectum Female
SA025644141217actsa16_1rectum Female
SA025645141217actsa03_1rectum Male
SA025646141217actsa12_1rectum Male
SA025647141217actsa11_1rectum Male
SA025648141217actsa08_1rectum Male
Showing results 1 to 24 of 24

Collection:

Collection ID:CO000510
Collection Summary:Animals were euthanized for an unrelated study. Within 1-3 hours after euthanasia, a ventral midline approach was used to access the gastrointestinal tract. A longitudinal incision was made through the serosal surface at each site sampled to expose a length of the lumen. Disposable plastic spatulae were used to collect intestinal contents from each site. Duodenal samples were collected aborally to the cranial flexure. The ileum was identified by the antimesenteric artery. The colon was identified by location in situ and samples were collected from the transverse or descending colon. Rectal contents were collected from as caudally as possible while still sampling through the abdominal incision.
Sample Type:Other (digesta/intestinal contents)
Collection Frequency:Once
Collection Duration:Once
Volumeoramount Collected:Five aliquots of 50-100mg
Storage Conditions:-80°C
Collection Vials:2 mL screw cap polypropylene vials
Storage Vials:2 mL screw cap polypropylene vials
Collection Tube Temp:room temp

Treatment:

Treatment ID:TR000530
Treatment Summary:The variable tested across the samples was the site of the GI tract, so none of the animals received any "treatment" for the purpose of comparing the effect of it to a control. The individual dogs are indicated by the letter A, C, D, E, F, and G. For each dog, we collected samples from duodenum, ileum, colon, and rectum.

Sample Preparation:

Sampleprep ID:SP000523
Sampleprep Summary:1. Weigh 50 mg tissue sample in to a 25 ml conical polypropylene centrifuge tube. 2. Add 2.5mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent. 3. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500μl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 4. Evaporate one 500μl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 5. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 6. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 7. Remove supernatant to a new Eppendorff tube. 8. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 9. Submit to derivatization.

Combined analysis:

Analysis ID AN000761
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus III GC
Column Restek Corporation Rtx-5Sil MS
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units counts

Chromatography:

Chromatography ID:CH000547
Methods Filename:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf
Instrument Name:Leco Pegasus III GC
Column Name:Restek Corporation Rtx-5Sil MS
Column Pressure:7.7 PSI
Column Temperature:50-330C
Flow Rate:1 ml/min
Injection Temperature:50 C ramped to 250 C by 12 C/s
Sample Injection:0.5 uL
Oven Temperature:50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min
Transferline Temperature:230C
Washing Buffer:Ethyl Acetate
Sample Loop Size:30 m length x 0.25 mm internal diameter
Randomization Order:Excel generated
Chromatography Type:GC

MS:

MS ID:MS000673
Analysis ID:AN000761
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Ion Source Temperature:250 C
Ionization Energy:70 eV
Mass Accuracy:Nominal
Source Temperature:250 C
Scan Range Moverz:85-500 Da
Scanning Cycle:17 Hz
Scanning Range:85-500 Da
Skimmer Voltage:1850 V
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