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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
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
Author
  Department of Zoology - Raulo, A.
https://orcid.org/0000-0003-4860-7840
Author
  Department of Zoology - Firth, J.
https://orcid.org/0000-0001-7183-4115
Author
  Department of Zoology - Coulson, T.
https://orcid.org/0000-0001-9371-9003
Author
  Department of Zoology - Knowles, S.C.L.
https://orcid.org/0000-0002-2368-4623
Author
  Department of Zoology - Lamberth, C.
https://orcid.org/0000-0002-2851-7146
Author
  University College Dublin - English, H.
https://orcid.org/0000-0002-8854-6707
Author
  University of Liège - Quicray, M.
https://orcid.org/0000-0002-9657-0627
Author
  Department of Zoology - Dale, J.
https://orcid.org/0000-0003-2853-7152
Point of contact
  Department of Zoology - Raulo, A.
https://orcid.org/0000-0003-4860-7840
Custodian
  NERC EDS Environmental Information Data Centre
Publisher
  NERC EDS Environmental Information Data Centre
Owner
  University of Oxford
GEMET - INSPIRE themes, version 1.0
  • Environmental Monitoring Facilities
Access constraints
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Other constraints
no limitations
Use constraints
otherRestrictions Other restrictions
Other constraints
This resource is available under the terms of the Open Government Licence
Use constraints
otherRestrictions Other restrictions
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 Text, table
Metadata language
EnglishEnglish
Character set
utf8 UTF8
Topic category
  • 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
  • Comma-separated values (CSV) ()

  • .rds ()

Distributor
  NERC EDS Environmental Information Data Centre
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Supporting information

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

Hierarchy level
dataset Dataset
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dataset

Conformance result

Date (Publication)
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.
File identifier
043513e5-406c-4477-89aa-c96059acb232 XML
Metadata language
EnglishEnglish
Character set
ISO/IEC 8859-1 (also known as Latin 1) 8859 Part 1
Hierarchy level
dataset Dataset
Hierarchy level name
dataset
Date stamp
2025-11-13T16:20:43
Metadata standard name
UK GEMINI
Metadata standard version
2.3
Point of contact
  NERC EDS Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK
https://eidc.ac.uk/
 
 

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Keywords

GEMET - INSPIRE themes, version 1.0
Environmental Monitoring Facilities

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