4f454849-0d30-4c27-ad5b-d285e461bedc English ISO/IEC 8859-1 (also known as Latin 1) dataset dataset NERC EDS Environmental Information Data Centre Lancaster Environment Centre, Library Avenue, Bailrigg Lancaster LA1 4AP UK info@eidc.ac.uk https://eidc.ac.uk/ EIDC website The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences. information pointOfContact 2025-11-13T16:18:36 UK GEMINI 2.3 OSGB 1936 / British National Grid Diet, gut microbiome and parasite data from wild rodents and diet shift data from captive rodents, 2014-2018 2024-05-10 publication https://catalogue.ceh.ac.uk/id/4f454849-0d30-4c27-ad5b-d285e461bedc 10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc doi: Marsh, K., Raulo, A., Brouard, M., Coulson, T., Knowles, S.C.L., English, H. (2024). Diet, gut microbiome and parasite data from wild rodents and diet shift data from captive rodents, 2014-2018. NERC EDS Environmental Information Data Centre 10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc 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). The 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. The 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. The 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. Samples for microbiome and diet characterization were stored without buffer at -80̊C. Samples for parasite detection were stored in 10% formalin and refrigerated at 4̊C. This work was funded by a NERC independent Research Fellowship. Full details about this dataset can be found at https://doi.org/10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc Marsh, K. University of Exeter k.j.marsh@exeter.ac.uk https://orcid.org/0000-0002-0515-9518 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Raulo, A. University of Oxford aura.raulo@zoo.ox.ac.uk https://orcid.org/0000-0003-4860-7840 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Brouard, M. University of Oxford brouard.marc@gmail.com https://orcid.org/0000-0001-7183-4115 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Coulson, T. University of Oxford tim.coulson@zoo.ox.ac.uk https://orcid.org/0000-0001-9371-9003 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Knowles, S.C.L. University of Oxford sarah.knowles@zoo.ox.ac.uk https://orcid.org/0000-0002-2368-4623 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author English, H. University College Dublin holly.english@ucdconnect.ie https://orcid.org/0000-0002-8854-6707 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Marsh, K. University of Exeter k.j.marsh@exeter.ac.uk https://orcid.org/0000-0002-0515-9518 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information pointOfContact NERC EDS Environmental Information Data Centre info@eidc.ac.uk custodian NERC EDS Environmental Information Data Centre info@eidc.ac.uk publisher University of Oxford aura.raulo@zoo.ox.ac.uk owner Environmental Monitoring Facilities theme GEMET - INSPIRE themes, version 1.0 2008-06-01 publication parasite trapping GEMET - Concepts, version 4.1.3 2019-01-28 creation Microbiome microbiota transmission gut microbiome Sherman wild mouse wood mouse Apodemus diet metabarcoding metabolite fecal flotation gut helminth otherRestrictions no limitations otherRestrictions This resource is available under the terms of the Open Government Licence otherRestrictions If you reuse this data, you should cite: Marsh, K., Raulo, A., Brouard, M., Coulson, T., Knowles, S.C.L., English, H. (2024). Diet, gut microbiome and parasite data from wild rodents and diet shift data from captive rodents, 2014-2018. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc textTable 10 English utf8 biota 2015-10-01 2018-10-31 -1.367 -1.271 51.746 51.796 Comma-separated values (CSV) .rds NERC EDS Environmental Information Data Centre info@eidc.ac.uk distributor https://data-package.ceh.ac.uk/data/4f454849-0d30-4c27-ad5b-d285e461bedc Download the data Download a copy of this data download https://data-package.ceh.ac.uk/sd/4f454849-0d30-4c27-ad5b-d285e461bedc.zip Supporting information Supporting information available to assist in re-use of this dataset information dataset dataset Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services 2010-12-08 Data and sample collection: - Wytham longitudinal study – Fortnightly for three years from October 2015-18. - Wytham dissection study – Fortnightly for one year from October 2017-18. - Diet shift experiment – Daily for one month (May 2017). Sample processing: DNA 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. Diet composition in the Wytham longitudinal study samples was determined by amplification and sequencing of the rbcL gene in winter 2019. Metabolomics 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. Parasite detection in formalin-stored faecal samples from the Wytham longitudinal study was performed using faecal flotation techniques in winter 2017. Details of the data generation and the cleaning process can be found from the documentation accompanying this data