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The faecal microbiome of the wild European badger Meles meles; a comparison against other wild omnivorous mammals from across the globe

James Scott-Baumann, Jessica C A Friedersdorff, Bernardo Villarreal-Ramos, Jonathan King, Beverley Hopkins, Richard Pizzey, David Rooke, Glyn Hewinson, View ORCID ProfileLuis A. J. Mur
doi: https://doi.org/10.1101/2022.03.17.484750
James Scott-Baumann
1Aberystwyth University, Institute of Biological, Environmental and Rural Science, Aberystwyth, Ceredigion, SY23 3DA, UK
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Jessica C A Friedersdorff
1Aberystwyth University, Institute of Biological, Environmental and Rural Science, Aberystwyth, Ceredigion, SY23 3DA, UK
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Bernardo Villarreal-Ramos
1Aberystwyth University, Institute of Biological, Environmental and Rural Science, Aberystwyth, Ceredigion, SY23 3DA, UK
2Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Ceredigion, SY23 3AR, UK
5Animal and Plant Health Agency, TB Research Group, New Haw, Addlestone, Surrey, KT15 3NB
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Jonathan King
3Wales Veterinary Science Centre, Y Buarth, Aberystwyth, Ceredigion, SY23 1ND, UK
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Beverley Hopkins
3Wales Veterinary Science Centre, Y Buarth, Aberystwyth, Ceredigion, SY23 1ND, UK
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Richard Pizzey
1Aberystwyth University, Institute of Biological, Environmental and Rural Science, Aberystwyth, Ceredigion, SY23 3DA, UK
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David Rooke
4ProTEM Services Ltd, West Sussex, UK
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Glyn Hewinson
1Aberystwyth University, Institute of Biological, Environmental and Rural Science, Aberystwyth, Ceredigion, SY23 3DA, UK
2Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Ceredigion, SY23 3AR, UK
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Luis A. J. Mur
1Aberystwyth University, Institute of Biological, Environmental and Rural Science, Aberystwyth, Ceredigion, SY23 3DA, UK
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  • ORCID record for Luis A. J. Mur
  • For correspondence: lum@aber.ac.uk
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Abstract

Here we investigate the faecal microbiome of wild European badgers Meles meles using samples collected at post-mortem as part of the All Wales Badger Found Dead study based on sequencing the V3-V4 region of the 16S rRNA gene. This is the first published characterisation of the badger microbiome. We initially undertook a sex-matched age comparison between the adult and cub microbiomes. Analysis used the QIIME 2 pipeline utilising DADA2 and the Silva database for taxonomy assignment. Fusobacteria appeared to be more abundant in the microbiomes of the cubs than the adults although no significant difference was seen in alpha or beta diversity between the adult and cub badger microbiomes. Comparisons were also made against other wild, omnivorous, mammals’ faecal microbiomes using publicly available data. Significant differences were seen in both alpha and beta diversity between the microbiomes from different species. As a wildlife species of interest to the disease bovine tuberculosis, knowledge of the faecal microbiome could assist in identification of infected badgers. Our work here suggests that if comparisons were made between the faeces of bTB infected and non-infected badgers, its possible age may not have a significant impact on the microbiome.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Declarations

    Data Availability:

    The nucleotide sequence data from the European badger (Meles meles) samples are available at the National Centre for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject ID: PRJNA777923 (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA777923)

  • Ethical obligations:

    The content and authorship of the submitted manuscript has been approved by all authors, and all prevailing local, national, and international regulations and conventions, and normal scientific ethical practices, have been respected. Animal tissues were collected only from dead animals found, and as part of an on-going governmental survey for tuberculosis.

  • Consent for publication:

    Not applicable

  • Funding sources:

    This work was supported by the Knowledge Economy Skills Scholarship (KESS) 2 supported by European Social Funds (ESF) through the Welsh Government. Further support was provided by Protem Services Ltd., and NFU (National Farmers’ Union) Cymru. The funding sources had no involvement in study design; in the collection, analysis and interpretation of data; in the writing of the report; or in the decision to submit the article for publication.

  • Abbreviations

    bTB
    bovine tuberculosis
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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    The faecal microbiome of the wild European badger Meles meles; a comparison against other wild omnivorous mammals from across the globe
    James Scott-Baumann, Jessica C A Friedersdorff, Bernardo Villarreal-Ramos, Jonathan King, Beverley Hopkins, Richard Pizzey, David Rooke, Glyn Hewinson, Luis A. J. Mur
    bioRxiv 2022.03.17.484750; doi: https://doi.org/10.1101/2022.03.17.484750
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    The faecal microbiome of the wild European badger Meles meles; a comparison against other wild omnivorous mammals from across the globe
    James Scott-Baumann, Jessica C A Friedersdorff, Bernardo Villarreal-Ramos, Jonathan King, Beverley Hopkins, Richard Pizzey, David Rooke, Glyn Hewinson, Luis A. J. Mur
    bioRxiv 2022.03.17.484750; doi: https://doi.org/10.1101/2022.03.17.484750

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