{"accessLimitation":{"value":"noLimitations","availability":"Available","description":"Access to the resource is not subject to any access limitations and is available to all users without restriction.","uri":"http://vocab.nerc.ac.uk/collection/N07/current/UNRS/"},"authors":[{"familyName":"Marsh","givenName":"K.","organisationName":"University of Exeter","organisationIdentifier":"https://ror.org/03yghzc09","role":"author","email":"k.j.marsh@exeter.ac.uk","nameIdentifier":"https://orcid.org/0000-0002-0515-9518","fullName":"Marsh, K."},{"familyName":"Raulo","givenName":"A.","organisationName":"University of Oxford","organisationIdentifier":"https://ror.org/052gg0110","role":"author","email":"aura.raulo@zoo.ox.ac.uk","nameIdentifier":"https://orcid.org/0000-0003-4860-7840","fullName":"Raulo, A."},{"familyName":"Brouard","givenName":"M.","organisationName":"University of Oxford","organisationIdentifier":"https://ror.org/052gg0110","role":"author","email":"brouard.marc@gmail.com","nameIdentifier":"https://orcid.org/0000-0001-7183-4115","fullName":"Brouard, M."},{"familyName":"Coulson","givenName":"T.","organisationName":"University of Oxford","organisationIdentifier":"https://ror.org/052gg0110","role":"author","email":"tim.coulson@zoo.ox.ac.uk","nameIdentifier":"https://orcid.org/0000-0001-9371-9003","fullName":"Coulson, T."},{"familyName":"Knowles","givenName":"S.C.L.","organisationName":"University of Oxford","organisationIdentifier":"https://ror.org/052gg0110","role":"author","email":"sarah.knowles@zoo.ox.ac.uk","nameIdentifier":"https://orcid.org/0000-0002-2368-4623","fullName":"Knowles, S.C.L."},{"familyName":"English","givenName":"H.","organisationName":"University College Dublin","organisationIdentifier":"https://ror.org/05m7pjf47","role":"author","email":"holly.english@ucdconnect.ie","nameIdentifier":"https://orcid.org/0000-0002-8854-6707","fullName":"English, H."}],"availability":"Available","boundingBoxes":[{"westBoundLongitude":-1.367,"eastBoundLongitude":-1.271,"southBoundLatitude":51.746,"northBoundLatitude":51.796,"bounds":"{\"type\": \"Feature\",      \"properties\": {},      \"geometry\": {        \"type\": \"Polygon\",        \"coordinates\": [[[-1.367, 51.746], [-1.367, 51.796], [-1.271, 51.796], [-1.271, 51.746], [-1.367, 51.746]]]      }}","coordinates":"[[[-1.367, 51.746], [-1.367, 51.796], [-1.271, 51.796], [-1.271, 51.746], [-1.367, 51.746]]]"}],"citation":{"authors":["Marsh, K.","Raulo, A.","Brouard, M.","Coulson, T.","Knowles, S.C.L.","English, H."],"bibtex":"https://catalogue.ceh.ac.uk/documents/4f454849-0d30-4c27-ad5b-d285e461bedc/citation?format=bib","day":10,"doi":"10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc","month":5,"publisher":"NERC EDS Environmental Information Data Centre","resourceTypeGeneral":"dataset","ris":"https://catalogue.ceh.ac.uk/documents/4f454849-0d30-4c27-ad5b-d285e461bedc/citation?format=ris","title":"Diet, gut microbiome and parasite data from wild rodents and diet shift data from captive rodents, 2014-2018","url":"https://doi.org/10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc","year":2024},"custodians":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"custodian","email":"info@eidc.ac.uk"}],"datasetReferenceDate":{"publicationDate":"2024-05-10"},"description":"This dataset is a combination of data obtained from a longitudinal live trapping study of wild rodents in Wytham Woods, Oxford (51.796 N,-1.367 W); October 2015-18), a dissection study of rodents caught in the same woodland (October 2017-18), and a diet shift experiment on a captive colony of wood mice housed at the University of Edinburgh (May 2017).\n\nThe longitudinal live trapping study dataset contains trapping data and data on the gut microbiome composition, diet and gut parasite infection of individually-identifiable rodents. Three species of rodents were trapped with Sherman live-traps fortnightly for 3 years: wood mice (Apodemus sylvaticus), yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glaerolus). Upon capture, they were injected with a passive integrated transponder (PIT) tag, measured, weighted, sexed, aged and a faecal sample was collected from individuals for microbiome, diet and parasite analyses. All rodents were released to their location of capture. \n\nThe dissection study contains trapping data, gut microbiome and parasite infection data. Wood mice were trapped fortnightly for one year with Sherman live-traps at least 300m away from the longitudinal sampling grid. Individuals that had been captured and marked with a PIT tag as part of the longitudinal study were released along with other rodents species and juvenile or pregnant individuals (only non-marked adult wood mice were sampled). Wood mice were euthanized (with ethical approval) and their gastrointestinal tract dissected for counts of gut helminths. Samples from along the gastrointestinal tract were taken for gut microbiome analysis. \n\nThe diet shift experiment dataset contains data on experimental diet treatments and gut microbiome composition of wood mice captively bred in a facility at the University of Edinburgh.  Wood mice were given diets varying in the ratio of food supplementation (dried mealworm and/or peanut) and faecal samples taken periodically over 30 days to measure changes in gut microbiome composition and function.\n\nSamples for microbiome and diet characterization were stored without buffer at -80̊C. Samples for parasite detection were stored in 10% formalin and refrigerated at 4̊C.\n\nThis work was funded by a NERC independent Research Fellowship.","distributionFormats":[{"name":"Comma-separated values (CSV)","type":"text/csv","version":"unknown"},{"name":".rds","type":"text/csv","version":"unknown"}],"distributorContacts":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"distributor","email":"info@eidc.ac.uk"}],"funding":[{"funderName":"Natural Environment Research Council","funderIdentifier":"https://ror.org/02b5d8509","awardNumber":"NE/L011867/1","orcid":false,"ror":true}],"id":"4f454849-0d30-4c27-ad5b-d285e461bedc","incomingCitationCount":0,"infoLinks":[{"url":"https://data-package.ceh.ac.uk/sd/4f454849-0d30-4c27-ad5b-d285e461bedc.zip","name":"Supporting information","description":"Supporting information available to assist in re-use of this dataset","function":"information","type":"OTHER"}],"inspireThemes":[{"theme":"Environmental Monitoring Facilities","uri":"http://inspire.ec.europa.eu/theme/ef"}],"keywordsOther":[{"value":"Microbiome"},{"value":"microbiota"},{"value":"transmission"},{"value":"gut microbiome"},{"value":"Sherman"},{"value":"wild mouse"},{"value":"wood mouse"},{"value":" Apodemus"},{"value":"diet"},{"value":"metabarcoding"},{"value":"metabolite"},{"value":"fecal flotation"},{"value":"gut helminth"},{"value":"parasite","uri":"http://www.eionet.europa.eu/gemet/concept/6035"},{"value":"trapping","uri":"http://www.eionet.europa.eu/gemet/concept/8655"}],"licences":[{"value":"This resource is available under the terms of the Open Government Licence","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"}],"lineage":"Data and sample collection:\n - Wytham longitudinal study – Fortnightly for three years from October 2015-18.\n - Wytham dissection study – Fortnightly for one year from October 2017-18.\n - Diet shift experiment – Daily for one month (May 2017).\n\nSample processing:\nDNA from the first year of the Wytham longitudinal study plus diet shift experiment faecal samples was extracted and sequenced in winter 2017 for microbiome composition using the V4-V5 region of bacterial 16S rRNA marker gene. DNA from the last two years of the Wytham longitudinal study and the dissection study samples was extracted and sequenced in early 2019 for microbiome composition.\n\nDiet composition in the Wytham longitudinal study samples was determined by amplification and sequencing of the rbcL gene in winter 2019.\n\nMetabolomics analysis of frozen faecal samples from the Wytham longitudinal and diet shift experiment studies was done in winter 2019 using Gas Chromatography- Mass Spectrometry methods to provide data on microbiome function.\n\nParasite detection in formalin-stored faecal samples from the Wytham longitudinal study was performed using faecal flotation techniques in winter 2017.\n\nDetails of the data generation and the cleaning process can be found from the documentation accompanying this data","metadataDate":"2026-06-29T16:29:09","notGEMINI":false,"onlineResources":[{"url":"https://data-package.ceh.ac.uk/data/4f454849-0d30-4c27-ad5b-d285e461bedc","name":"Download the 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Oxford","organisationIdentifier":"https://ror.org/052gg0110","role":"rightsHolder","email":"aura.raulo@zoo.ox.ac.uk"}],"rightsHolders":[{"organisationName":"University of Oxford","organisationIdentifier":"https://ror.org/052gg0110","role":"rightsHolder","email":"aura.raulo@zoo.ox.ac.uk"}],"spatialReferenceSystems":[{"code":"http://www.opengis.net/def/crs/EPSG/0/27700","title":"OSGB 1936 / British National Grid"}],"spatialRepresentationTypes":["textTable"],"spatialResolutions":[{"distance":"10","uom":"urn:ogc:def:uom:EPSG::9001"}],"supplemental":[{"name":"Synchronous seasonality in the gut microbiota of wild mouse populations.","url":"https://doi.org/10.3389/fmicb.2022.809735","function":"relatedArticle"},{"name":"The wild mammalian microbiome: host-microbe interactions in a natural mouse model","description":"Marsh, K.J (2020). 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