Wild rodent tracking and gut microbiome data, Holly Hill, Wytham Woods, UK, 2018-2019

This data set is a combination of trapping data, tracking data, vegetation/habitat data and data on the gut microbiome composition of wild rodents caught in 4 ha study site in Holly Hill in Wytham Woods, Oxford, UK, from November 2018 to November 2019. Three species of rodents were trapped with Sherman live-traps fortnightly for 12 months: wood mouse (Apodemus sylvaticus), yellow-necked mouse (Apodemus flavicollis) and bank vole (Myodes glaerolus). Upon capture, they were measured, weighted, sexed, aged and a faecal sample was collected from all rodent individuals for microbiome analyses. All rodents were released to their location of capture. First time each individual was captured, they were injected with a permanent subcutaneous Radio-Frequency Identification(RFID)-tag (Passive Integrated Transponder-tag). The tagged rodents were subsequently tracked from February to November 2019 with a set of 120 custom-made tracking devices (loggers). Loggers recorded to time-stamped presence of any tagged individual that passed near it, producing occurrence data suitable for inferring spatiotemporal activity patterns of rodents, such as temporal niches, home ranges and social networks. Bacterial DNA extracted from faecal samples were used to profile their gut microbiome composition. The study area was surveyed for vegetation and microhabitat variation by gathering habitat data of each 10 x 10 m grid square across the 4 ha plot. Data included list of plant species (visible in late May), coverage by the main ground cover types, canopy openness and amount of dead wood in each grid square. This work was funded by a NC3Rs Fellowship to Sarah Knowles, and NERC independent Research Fellowship to Sarah Knowles (NE/L011867/1) Full details about this dataset can be found at https://doi.org/10.5285/043513e5-406c-4477-89aa-c96059acb232

Identification info

Metadata Language: English (en)

Character set: utf8

Dataset Reference Date (): 2023-11-22

Identifier: https://catalogue.ceh.ac.uk/id/043513e5-406c-4477-89aa-c96059acb232

Identifier: doi: / 10.5285/043513e5-406c-4477-89aa-c96059acb232

Other citation details: Raulo, A., Firth, J., Coulson, T., Knowles, S.C.L., Lamberth, C., English, H., Quicray, M., Dale, J. (2023). Wild rodent tracking and gut microbiome data, Holly Hill, Wytham Woods, UK, 2018-2019. NERC EDS Environmental Information Data Centre 10.5285/043513e5-406c-4477-89aa-c96059acb232

Department of Zoology - Raulo, A.

https://orcid.org/0000-0003-4860-7840

Department of Zoology - Firth, J.

https://orcid.org/0000-0001-7183-4115

Department of Zoology - Coulson, T.

https://orcid.org/0000-0001-9371-9003

Department of Zoology - Knowles, S.C.L.

https://orcid.org/0000-0002-2368-4623

Department of Zoology - Lamberth, C.

https://orcid.org/0000-0002-2851-7146

University College Dublin - English, H.

https://orcid.org/0000-0002-8854-6707

University of Liège - Quicray, M.

https://orcid.org/0000-0002-9657-0627

Department of Zoology - Dale, J.

https://orcid.org/0000-0003-2853-7152

Department of Zoology - Raulo, A.

https://orcid.org/0000-0003-4860-7840

NERC EDS Environmental Information Data Centre

University of Oxford

GEMET - INSPIRE themes, version 1.0 ()

Environmental Monitoring Facilities

Limitations on Public Access: otherRestrictions

Other constraints: no limitations

Use constraints: otherRestrictions

Other constraints: This resource is available under the terms of the Open Government Licence

Use constraints: otherRestrictions

Other constraints: If you reuse this data, you should cite: Raulo, A., Firth, J., Coulson, T., Knowles, S.C.L., Lamberth, C., English, H., Quicray, M., Dale, J. (2023). Wild rodent tracking and gut microbiome data, Holly Hill, Wytham Woods, UK, 2018-2019. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/043513e5-406c-4477-89aa-c96059acb232

Spatial representation type: textTable

Topic category

Biota

Begin date: 2018-11-01

End date: 2019-11-30

Code: OSGB 1936 / British National Grid

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Resource Locator: Supporting information
Supporting information available to assist in re-use of this dataset

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Resource Locator: Supporting information
Supporting information available to assist in re-use of this dataset

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Report

Dataset Reference Date (): 2010-12-08

Statement: Wild rodents were trapped fortnightly, tagged and continuously monitored with tracking technology for 10 months. This is a natural rodent population and no experimental manipulations were made. Upon capture, faecal samples were collected from the rodents. Faecal samples were stored without buffer in -80 C. In winter 2019-2020 DNA was extracted from the faecal samples of wood mice, yellow-necked mice and bank voles, and their gut microbiome was characterised from this by amplification and sequencing of the V4-V5 region of bacterial 16S rRNA marker gene. In May 2020 the study area was surveyed for vegetation and microhabitat variation. Details of the data generation and the cleaning process can be found from the supporting documentation.

Metadata

File identifier: 043513e5-406c-4477-89aa-c96059acb232 XML

Metadata Language: English (en)

Character set: ISO/IEC 8859-1 (also known as Latin 1)

Resource type: dataset

Hierarchy level name: dataset

Metadata Date: 2024-02-08T17:26:29

Metadata standard name: UK GEMINI

Metadata standard version: 2.3

NERC EDS Environmental Information Data Centre

Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK

https://eidc.ac.uk/

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