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Discrete patterns of microbiome variability across timescales in a wild rodent population
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 sequen...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061908/ https://www.ncbi.nlm.nih.gov/pubmed/36997846 http://dx.doi.org/10.1186/s12866-023-02824-x |
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author | Fenn, Jonathan Taylor, Christopher Goertz, Sarah Wanelik, Klara M. Paterson, Steve Begon, Mike Jackson, Joe Bradley, Jan |
author_facet | Fenn, Jonathan Taylor, Christopher Goertz, Sarah Wanelik, Klara M. Paterson, Steve Begon, Mike Jackson, Joe Bradley, Jan |
author_sort | Fenn, Jonathan |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-023-02824-x. |
format | Online Article Text |
id | pubmed-10061908 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-100619082023-03-31 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 BMC Microbiol Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-023-02824-x. BioMed Central 2023-03-30 /pmc/articles/PMC10061908/ /pubmed/36997846 http://dx.doi.org/10.1186/s12866-023-02824-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Fenn, Jonathan Taylor, Christopher Goertz, Sarah Wanelik, Klara M. Paterson, Steve Begon, Mike Jackson, Joe Bradley, Jan Discrete patterns of microbiome variability across timescales in a wild rodent population |
title | Discrete patterns of microbiome variability across timescales in a wild rodent population |
title_full | Discrete patterns of microbiome variability across timescales in a wild rodent population |
title_fullStr | Discrete patterns of microbiome variability across timescales in a wild rodent population |
title_full_unstemmed | Discrete patterns of microbiome variability across timescales in a wild rodent population |
title_short | Discrete patterns of microbiome variability across timescales in a wild rodent population |
title_sort | discrete patterns of microbiome variability across timescales in a wild rodent population |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061908/ https://www.ncbi.nlm.nih.gov/pubmed/36997846 http://dx.doi.org/10.1186/s12866-023-02824-x |
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