Analysis of fecal volatiles in skunks and raccoons subjected to rabies immunization and infection

Metadata:
Identification_Information:
Citation:
Citation_Information:
Originator: Kimball, Bruce A.
Originator: Volker, Steven F.
Originator: Griffin, Doreen L.
Originator: Johnson, Shylo R.
Originator: Gilbert, Amy T.
Publication_Date: 2019
Title:
Analysis of fecal volatiles in skunks and raccoons subjected to rabies immunization and infection
Geospatial_Data_Presentation_Form: spreadsheet and tabular digital data
Series_Information:
Series_Name: Research Dataset Series
Publication_Information:
Publication_Place: Fort Collins, CO
Publisher: USDA, APHIS, WS National Wildlife Research Center
Online_Linkage: https://doi.org/10.2737/NWRC-RDS-2019-001
Description:
Abstract:
Chromatographic peak data and rabies antibody data were collected from raccoon and skunk subjects that were subjected to rabies vaccination and/or challenge with rabies virus. Feces were collected from captive animals held in USDA facilities in Fort Collins, CO USA during the period 10 July 2014 to 28 September 2015. Fecal samples were subjected to chemical analyses during the period of 12 August 2015 to 11 February 2016. This data publication includes all chromatograms (gas chromatography/mass spectrometry data files as .cdf files) and a summary of chromatographic peak responses and measured serum antibody responses.
Purpose:
The study, arising from opportunistic sampling of feces from two well-replicated vaccination and challenge studies, was designed to uncover volatile signatures associated with oral immunization using a live recombinant rabies vaccine and lethal RABV infection in two key North American reservoir hosts for this pathogen.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 201407
Ending_Date: 201903
Currentness_Reference:
Ground condition
Status:
Progress: Complete
Maintenance_and_Update_Frequency: As Needed
Spatial_Domain:
Description_of_Geographic_Extent:
Animals were purchased from commercial breeders and housed in Fort Collins, Colorado. Data could represent entire United States.
Bounding_Coordinates:
West_Bounding_Coordinate: -125
East_Bounding_Coordinate: -65
North_Bounding_Coordinate: 50
South_Bounding_Coordinate: 25
Keywords:
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: health
Theme:
Theme_Keyword_Thesaurus: National Research & Development Taxonomy
Theme_Keyword: Ecology, Ecosystems, & Environment
Theme_Keyword: Wildlife (or Fauna)
Theme_Keyword: Mammals
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: disease
Theme_Keyword: rabies
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: United States
Place_Keyword: Colorado
Access_Constraints: None
Use_Constraints:
These data were collected using funding from the U.S. Government and can be used without additional permissions or fees. If you use these data in a publication, presentation, or other research product please use the following citation:

Kimball, Bruce A.; Volker, Steven F.; Griffin, Doreen L.; Johnson, Shylo R.; Gilbert, Amy T. 2019. Analysis of fecal volatiles in skunks and raccoons subjected to rabies immunization and infection. Research Dataset Series. USDA, APHIS, WS National Wildlife Research Center. Ft. Collins, Colorado. https://doi.org/10.2737/NWRC-RDS-2019-001
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Bruce A. Kimball
Contact_Organization: USDA, APHIS, WS National Wildlife Research Center
Contact_Position: Research Chemist
Contact_Address:
Address_Type: mailing and physical
Address: 3500 Market Street
City: Philadelphia
State_or_Province: PA
Postal_Code: 19104
Country: USA
Contact_Voice_Telephone: 267-519-4930
Contact_Electronic_Mail_Address: bruce.a.kimball@usda.gov
Data_Set_Credit:
This project was funded by USDA, APHIS, Wildlife Services National Wildlife Research Center.
Analytical_Tool:
Analytical_Tool_Description:
ProteoWizard software is a tool that helps facilitate proteomics data analysis.
Tool_Access_Information:
Online_Linkage: http://proteowizard.sourceforge.net/
Tool_Access_Instructions:
See website for more information.
Tool_Citation:
Citation_Information:
Originator: Chambers, M.C.
Originator: MacLean, B.
Originator: Burke, R.
Originator: Amode, D.
Originator: Ruderman, D.L.
Originator: Neumann, S.
Originator: Gatto, L.
Originator: Fischer, B.
Originator: Pratt, B.
Originator: Egertson, J.
Originator: Hoff, K.
Originator: Kessner, D.
Originator: Tasman, N.
Originator: Shulman, N.
Originator: Frewen, B.
Originator: Baker, T.A.
Originator: Brusniak, M.-Y.
Originator: Paulse, C.
Originator: Creasy, D.
Originator: Flashner, L.
Originator: Kani, K.
Originator: Moulding, C.
Originator: Seymour, S.L.
Originator: Nuwaysir, L.M.
Originator: Lefebvre, B.
Originator: Kuhlmann, F.
Originator: Roark, J.
Originator: Rainer, P.
Originator: Detlev, S.
Originator: Hemenway, T.
Originator: Huhmer, A.
Originator: Langridge, J.
Originator: Connolly, B.
Originator: Chadick, T.
Originator: Holly, K.
Originator: Eckels, J.
Originator: Deutsch, E.W.
Originator: Moritz, R.L.
Originator: Katz, J.E.
Originator: Agus, D.B.
Originator: MacCoss, M.
Originator: Tabb, D.L.
Originator: Mallick, P.
Publication_Date: 2012
Title:
A cross-platform toolkit for mass spectrometry and proteomics
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Nature Biotechnology
Issue_Identification: 30: 918-920
Online_Linkage: http://www.nature.com/nbt/journal/v30/n10/full/nbt.2377.html
Analytical_Tool:
Analytical_Tool_Description:
MetAlign is a software programme for the pre-processing and comparison of full scan nominal or accurate mass LC-MS and GC-MS data.
Tool_Access_Information:
Online_Linkage: https://www.wur.nl/en/show/MetAlign-1.htm
Tool_Access_Instructions:
See website for more information.
Tool_Citation:
Citation_Information:
Originator: Lommen, Arjen
Publication_Date: 2009
Title:
MetAlign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Analytical Chemistry
Issue_Identification: 81(8): 3079–3086
Online_Linkage: https://doi.org/10.1021/ac900036d
Analytical_Tool:
Analytical_Tool_Description:
MSClust is a A Matlab package for Clustering 16S rRNA sequences into OTUs.
Tool_Access_Information:
Online_Linkage: https://bio.tools/MSClust
Tool_Access_Instructions:
See website for more information.
Tool_Citation:
Citation_Information:
Originator: Tikunov, Y. M.
Originator: Laptenok, S.
Originator: Hall, R. D.
Originator: Bovy, A.
Originator: De Vos, R. C. H.
Publication_Date: 2012
Title:
MSClust: A tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Metabolomics
Issue_Identification: 8(4):714-718
Online_Linkage: https://doi.org/10.1007/s11306-011-0368-2
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Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
For these data we merely used the carvone response (peak _37) in "carvone" samples and actual samples to determine if the instrument was operating properly (watching for dramatic changes in the carvone response). We also tried to identify peaks that had nothing to do with the samples by examining their abundances in "blank" samples and comparing them with actual samples. We identified 48 peaks in blank vials samples that were determined to be related to the system and excluded from the summary data spreadsheet (see \Supplements\Example_chromatograms.pdf).
Completeness_Report:
No data are missing or intentionally withheld.
Lineage:
Methodology:
Methodology_Type: Lab
Methodology_Description:
STUDY DESIGN
Animals were purchased from commercial breeders and maintained in captivity at USDA-APHIS-WS-NWRC facilities located in Fort Collins, CO. Animal enclosures were routinely cleaned of all feces at least weekly and additionally the day immediately prior to a planned fecal sample collection. Fecal samples of individual animals were collected directly from the pen floor, cage catch pan, or den box cob material. Sample collection occurred while the animal was locked in the associated enclosure den box or otherwise had been temporarily removed from the enclosure for blood sample collection. Samples were collected prior to study treatments (e.g. vaccination or infection), and then at pre-determined intervals post-vaccination (pv) and post-infection (pi). On a given collection day, animal enclosures were examined for fresh feces and the freshest appearing were preferentially collected. Approximately 2-5 grams were collected directly into a whirl-pak specimen bag. Samples were kept cool on ice packs for up to 6 hours and then stored at -80° Celsius until analysis. For a visual representation of the sample collection schedule see \Supplements\Sample_collection_schedule.pdf.

DATA COLLECTION
Fecal samples were collected at multiple time points from raccoons and striped skunks subjected to oral treatment with rabies vaccine (or sham) as well as challenge with a lethal rabies virus. In addition to fecal samples, blood was collected at various time points to permit quantitative assessment of rabies antibody responses arising from immunization and/or infection.
Methodology_Citation:
Citation_Information:
Originator: Kimball, Bruce A.
Originator: Volker, Steven F.
Originator: Griffin, Doreen L.
Originator: Johnson, Shylo R.
Originator: Gilbert, Amy T.
Publication_Date: 2019
Title:
Volatile metabolomic signatures of rabies immunization and infection in two mesocarnivore species
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: PloS Neglected Tropical Diseases
Issue_Identification: 13(12): e0007911
Online_Linkage: https://doi.org/10.1371/journal.pntd.0007911
Methodology:
Methodology_Type: Lab
Methodolgy_Identifier:
Methodolgy_Keyword_Thesaurus:
None
Methodology_Keyword: headspace
Methodology_Keyword: gas chromatography
Methodology_Keyword: mass spectrometry
Methodology_Description:
SAMPLE PREP
One gram of feces (raccoon or skunk) was individually placed in 20-milliliters (mL) glass headspace vials, capped, and refrigerated until analysis. Immediately prior to analysis, vials and contents were warmed to room temperature and the internal standard (0.010 mL of 70 parts per million [ppm] (S)-carvone prepared in water) was added using a syringe. Headspace extraction was performed with a PAL autosampler (Agilent Technologies, Santa Clara, CA) equipped with a SPME fiber assembly (DVB/CAR/PDMS). The sample was pre-incubated for 10 minutes (min) at 37° Celsius (C) with pulsed agitation (250 revolutions per minute [RPM] for 5 seconds [s], off for 2 s) and the SPME needle was inserted into the vial for 40 min headspace collection. Collected volatiles were desorbed from the SPME fiber at 270° C for 1 min in the injection port of an Agilent 7890B gas chromatograph (Agilent Technologies, Santa Clara, CA) equipped with an ultra-inert straight liner and 23 gauge. Merlin Microseal™ septum (Merlin Instrument Co., Newark, DE). Chromatographic separation was achieved using a 30 meter (m) x 0.25 millimeter (mm) ID Stabilwax®-DA (0.25 micrometer [µm] film thickness) capillary column (Restek Corp., Bellefonte, PA) with helium carrier gas in constant flow mode (1.0 mL/min). The oven temperature was held at 35° C for 2.5 min, increased at 6.0° C/min to 260° C, and then held for 5 min. The gas chromatograph was coupled to an Agilent 5977A mass selective detector (MSD) for collection of electron impact (EI) spectra over the range of 50 to 500 m/z (mass/charge).

ANALYSIS
Feces were analyzed by headspace gas chromatography with mass spectrometric detection and the chromatographic responses were subjected to linear discriminant analyses (LDA) to classify health status and multiple regression to predict quantitative immune responses.
Methodology_Citation:
Citation_Information:
Originator: Kimball, Bruce A.
Originator: Volker, Steven F.
Originator: Griffin, Doreen L.
Originator: Johnson, Shylo R.
Originator: Gilbert, Amy T.
Publication_Date: 2019
Title:
Volatile metabolomic signatures of rabies immunization and infection in two mesocarnivore species
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: PloS Neglected Tropical Diseases
Issue_Identification: 13(12): e0007911
Online_Linkage: https://doi.org/10.1371/journal.pntd.0007911
Process_Step:
Process_Description:
Chromatographic data were exported to mzData format using Proteowizard software followed by baseline correction, noise elimination, and peak alignment using Metalign software. The processed data (consisting of all mass spectrometric responses exceeding a defined threshold at each scan event) were subjected to unsupervised peak identification and integration using the MSClust tool. Data files provided here may be imported directly into the Metalign software, viewed with a CDF player, or converted to raw files using a chromatographic software. For example, Xcalibur software (Thermo Fisher).
Process_Date: 201809
Process_Step:
Process_Description:
In addition to fecal samples, quality control samples were subjected to headspace analyses. Each chromatographic run consisted of approximately 16 fecal samples, two sample vials containing only the internal standard (carvone), and one empty vial (blank). The first sample of each run was a “conditioning” sample designed to bake the SPME fiber.
Process_Date: 2019
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Entity_and_Attribute_Information:
Overview_Description:
Entity_and_Attribute_Overview:
Below you will find the data available in this data publication and a short description of its contents.

1). \Data\Peak_IDs.csv: Comma-delimited ASCII text file containing peak retention time, m/z value of selected ion monitoring (SIM) mass, and tentative compound identification.
Variables include:

PEAK = peak number (e.g., _1, _2, ..., _52)

RET(umin) = Chromatographic retention time in microminutes. Note: umin is a convention of the Metalign software

SCAN = Chromatographic scan number (detector)

MASS = M/Z (mass/charge) of selected ion used for peak height determination

ID = Tentative compound identification based on spectral library match (NIST Standard Reference Database)


2). \Data\Quality_Control.csv: Comma-delimited ASCII text file containing selected ion monitoring (SIM) peak heights for quality control samples.
Variables include:

FILE = name of associated CDF file

SAMPLE = Identity of quality control sample (Blank=empty vial, Condition = no sample - SPME fiber condition, and Carvone=no sample - vial fortified with carvone standard solution)

_1 to _52 = Chromatographic peak height for each peak number


3). \Data\Raccoon.csv: Comma-delimited ASCII text file containing animal subject, sample collection, and experimental treatment information, serum antibody results, and selected ion monitoring (SIM) peak heights for fecal samples collected from raccoons.
4). \Data\Skunk.csv: Comma-delimited ASCII text file containing animal subject, sample collection, and experimental treatment information, serum antibody results, and selected ion monitoring (SIM) peak heights for fecal samples collected from skunks.
Variables included in both data files:

FILE = name of associated CDF file

AVID = animal subject ID number

SEX = Sex of subject (F=female, M=male)

DATE = Date of sample collection (mm/dd/yyyy where mm=month, dd=day, and yyyy=year)

MASS = Mass of sample analyzed (grams)

EXP = Experiment ID (1 or 2)

DOSE = Vaccine dose (only available in \Data\Skunk.csv)

TRT = Treatment group (Control_and_infect=no vaccination and rabies infection, Vacc_and_infect=vaccination and rabies infection, Infect_only=infection only, and Vacc_and_died=vaccination and died)

EXP_DAY = Experiment day. Vaccination date is day 0.

COMMENT = comments

rVNA = Rabies virus neutralization antibody response (International units per millilitre [IU/mL])

rVBA = Rabies virus binding antibody response (Skunk = %blocking; Raccoon = IU/mL)

_1 to _52 = Chromatographic peak number


5). \Data\AABBCC_DDD.cdf: CDF files (620) containing mass spectrometric data required to reconstruct selected ion monitoring (SIM) and total ion chromatograms (TIC) for each fecal and quality control sample. Note: The filename represents the date of the GC/MS analysis: AA=year; BB=month; CC=day; DDD=run number (sequence of the order the samples were analyzed that day).


6). \Supplements\Example_chromatograms.pdf: Adobe Acrobat PDF/a file containing example chromatograms obtained from the analysis of a blank vial and skunk feces.


7). \Supplements\Sample_collection_schedule.pdf: Adobe Acrobat PDF/a file containing a visual representation of the sample collection schedule at post-vaccination (pv) and post-infection (pi) time points for subjects in challenge cohorts.
Entity_and_Attribute_Detail_Citation:
none provided
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Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: USDA Forest Service, Research and Development
Contact_Position: Research Data Archivist
Contact_Address:
Address_Type: mailing and physical
Address: 240 West Prospect Road
City: Fort Collins
State_or_Province: CO
Postal_Code: 80526
Country: USA
Contact_Voice_Telephone: see Contact Instructions
Contact Instructions: This contact information was current as of March 2020. For current information see Contact Us page on: https://doi.org/10.2737/RDS.
Resource_Description: NWRC-RDS-2019-001
Distribution_Liability:
Metadata documents have been reviewed for accuracy and completeness. Unless otherwise stated, all data and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. However, neither the author, the Archive, nor any part of the federal government can assure the reliability or suitability of these data for a particular purpose. The act of distribution shall not constitute any such warranty, and no responsibility is assumed for a user's application of these data or related materials.

The metadata, data, or related materials may be updated without notification. If a user believes errors are present in the metadata, data or related materials, please use the information in (1) Identification Information: Point of Contact, (2) Metadata Reference: Metadata Contact, or (3) Distribution Information: Distributor to notify the author or the Archive of the issues.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: ASCII
Format_Version_Number: see Format Specification
Format_Specification:
Comma-delimited ASCII text files (CSV)
File_Decompression_Technique: Files zipped with 7-Zip 19.0
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: https://doi.org/10.2737/NWRC-RDS-2019-001
Digital_Form:
Digital_Transfer_Information:
Format_Name: CDF
Format_Version_Number: see Format Specification
Format_Specification:
Computable Document Format (CDF)
File_Decompression_Technique: Files zipped with 7-Zip 19.0
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: https://doi.org/10.2737/NWRC-RDS-2019-001
Fees: None
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Metadata_Reference_Information:
Metadata_Date: 20200325
Metadata_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Bruce A. Kimball
Contact_Organization: USDA, APHIS, WS National Wildlife Research Center
Contact_Position: Research Chemist
Contact_Address:
Address_Type: mailing and physical
Address: 3500 Market Street
City: Philadelphia
State_or_Province: PA
Postal_Code: 19104
Country: USA
Contact_Voice_Telephone: 267-519-4930
Contact_Electronic_Mail_Address: bruce.a.kimball@usda.gov
Metadata_Standard_Name: FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001.1-1999
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