BGS Hosted Metadata
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 glareolus). 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
Simple
- Date (Publication)
- 2023-11-22
- Citation identifier
- https://catalogue.ceh.ac.uk/id/043513e5-406c-4477-89aa-c96059acb232
- Citation identifier
- doi: / 10.5285/043513e5-406c-4477-89aa-c96059acb232
- Other citation details
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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
- Point of contact
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Organisation name Individual name Electronic mail address Role Department of Zoology Raulo, A. Author Department of Zoology Firth, J. Author Department of Zoology Coulson, T. Author Department of Zoology Knowles, S.C.L. Author Department of Zoology Lamberth, C. Author University College Dublin English, H. Author University of Liège Quicray, M. Author Department of Zoology Dale, J. Author Department of Zoology Raulo, A. Point of contact NERC EDS Environmental Information Data Centre Custodian NERC EDS Environmental Information Data Centre Publisher University of Oxford Owner
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GEMET - INSPIRE themes, version 1.0
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Environmental Monitoring Facilities
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Wikidata
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GEMET - Concepts, version 4.1.3
- Keywords
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Microbiome
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microbiota
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transmission
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gut microbiome
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trapping
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Sherman
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wild mouse
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wood mouse
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bank vole
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yellow-necked mouse
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RFID-tracking
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social network analysis
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home range analysis
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vegetation survey
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microhabitat
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- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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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
- Text, table
- Language
- English
- Character set
- UTF8
- Topic category
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- Biota
- Begin date
- 2018-11-01
- End date
- 2019-11-30
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- Unique resource identifier
- OSGB 1936 / British National Grid
- Distribution format
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Name Version Comma-separated values (CSV)
.rds
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/data/043513e5-406c-4477-89aa-c96059acb232 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/043513e5-406c-4477-89aa-c96059acb232.zip Supporting information
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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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
- Date (Publication)
- 2010-12-08
- Statement
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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
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-11-13T16:20:43
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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