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Discrete patterns of microbiome variability across timescales in a wild rodent population

Fenn, Jonathan; Taylor, Christopher; Goertz, Sarah; Wanelik, Klara M.; Paterson, Steve; Begon, Mike; Jackson, Joe; Bradley, Jan

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Jonathan Fenn

Sarah Goertz

Klara M. Wanelik

Steve Paterson

Mike Begon

Jan Bradley


Mammalian gastrointestinal microbiomes are highly variable, both within individuals and across populations, with changes linked to time and ageing being widely reported. Discerning patterns of change in wild mammal populations can therefore prove challenging. We used high-throughput community sequencing methods to characterise the microbiome of wild field voles (Microtus agrestis) from faecal samples collected across 12 live-trapping field sessions, and then at cull. Changes in α- and β-diversity were modelled over three timescales. Short-term differences (following 1–2 days captivity) were analysed between capture and cull, to ascertain the degree to which the microbiome can change following a rapid change in environment. Medium-term changes were measured between successive trapping sessions (12–16 days apart), and long-term changes between the first and final capture of an individual (from 24 to 129 days). The short period between capture and cull was characterised by a marked loss of species richness, while over medium and long-term in the field, richness slightly increased. Changes across both short and long timescales indicated shifts from a Firmicutes-dominant to a Bacteroidetes-dominant microbiome. Dramatic changes following captivity indicate that changes in microbiome diversity can be rapid, following a change of environment (food sources, temperature, lighting etc.). Medium- and long-term patterns of change indicate an accrual of gut bacteria associated with ageing, with these new bacteria being predominately represented by Bacteroidetes. While the patterns of change observed are unlikely to be universal to wild mammal populations, the potential for analogous shifts across timescales should be considered whenever studying wild animal microbiomes. This is especially true if studies involve animal captivity, as there are potential ramifications both for animal health, and the validity of the data itself as a reflection of a ‘natural’ state of an animal.


Fenn, J., Taylor, C., Goertz, S., Wanelik, K. M., Paterson, S., Begon, M., …Bradley, J. (2023). Discrete patterns of microbiome variability across timescales in a wild rodent population. BMC Microbiology, 23, Article 87.

Journal Article Type Article
Acceptance Date Mar 15, 2023
Online Publication Date Mar 30, 2023
Publication Date Mar 30, 2023
Deposit Date Jun 1, 2023
Publicly Available Date Jun 2, 2023
Journal BMC Microbiology
Electronic ISSN 1471-2180
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 23
Article Number 87
Keywords Microbiome, Aging, Wild Populations, Captivity, Alpha Diversity, Beta Diversity
Public URL
Publisher URL
Additional Information Received: 22 August 2022; Accepted: 15 March 2023; First Online: 30 March 2023; : ; : All procedures were performed with approval from the University of Liverpool Animal Welfare Committee, under a UK Home Office license (PPL 40/3235 to MB), and according to all related welfare guidelines and regulations. Where relevant, all procedures and reporting are in line with ARRIVE guidelines for the reporting of animal experiments.; : Not applicable.; : The authors declare no competing interests.


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