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Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes

The gut microbiome plays a vital role in health and wellbeing of animals, and an increasing number of studies are investigating microbiome changes in wild and managed populations to improve conservation and welfare. The short-beaked echidna (Tachyglossus aculeatus) is an iconic Australian species, t...

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Autores principales: Perry, Tahlia, West, Ella, Eisenhofer, Raphael, Stenhouse, Alan, Wilson, Isabella, Laming, Belinda, Rismiller, Peggy, Shaw, Michelle, Grützner, Frank
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279566/
https://www.ncbi.nlm.nih.gov/pubmed/35847103
http://dx.doi.org/10.3389/fmicb.2022.687115
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author Perry, Tahlia
West, Ella
Eisenhofer, Raphael
Stenhouse, Alan
Wilson, Isabella
Laming, Belinda
Rismiller, Peggy
Shaw, Michelle
Grützner, Frank
author_facet Perry, Tahlia
West, Ella
Eisenhofer, Raphael
Stenhouse, Alan
Wilson, Isabella
Laming, Belinda
Rismiller, Peggy
Shaw, Michelle
Grützner, Frank
author_sort Perry, Tahlia
collection PubMed
description The gut microbiome plays a vital role in health and wellbeing of animals, and an increasing number of studies are investigating microbiome changes in wild and managed populations to improve conservation and welfare. The short-beaked echidna (Tachyglossus aculeatus) is an iconic Australian species, the most widespread native mammal, and commonly held in zoos. Echidnas are cryptic animals, and much is still unknown about many aspects of their biology. Furthermore, some wild echidna populations are under threat, while echidnas held in captivity can have severe gastric health problems. Here, we used citizen science and zoos to collect echidna scats from across Australia to perform the largest gut microbiome study on any native Australian animal. Using 16S rRNA gene metabarcoding of scat samples, we characterised and compared the gut microbiomes of echidnas in wild (n = 159) and managed (n = 44) populations, which were fed four different diets. Wild echidna samples were highly variable, yet commonly dominated by soil and plant-fermenting bacteria, while echidnas in captivity were dominated by gut commensals and plant-fermenting bacteria, suggesting plant matter may play a significant role in echidna diet. This work demonstrates significant differences between zoo held and wild echidnas, as well as managed animals on different diets, revealing that diet is important in shaping the gut microbiomes in echidnas. This first analysis of echidna gut microbiome highlights extensive microbial diversity in wild echidnas and changes in microbiome composition in managed populations. This is a first step towards using microbiome analysis to better understand diet, gastrointestinal biology, and improve management in these iconic animals.
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spelling pubmed-92795662022-07-15 Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes Perry, Tahlia West, Ella Eisenhofer, Raphael Stenhouse, Alan Wilson, Isabella Laming, Belinda Rismiller, Peggy Shaw, Michelle Grützner, Frank Front Microbiol Microbiology The gut microbiome plays a vital role in health and wellbeing of animals, and an increasing number of studies are investigating microbiome changes in wild and managed populations to improve conservation and welfare. The short-beaked echidna (Tachyglossus aculeatus) is an iconic Australian species, the most widespread native mammal, and commonly held in zoos. Echidnas are cryptic animals, and much is still unknown about many aspects of their biology. Furthermore, some wild echidna populations are under threat, while echidnas held in captivity can have severe gastric health problems. Here, we used citizen science and zoos to collect echidna scats from across Australia to perform the largest gut microbiome study on any native Australian animal. Using 16S rRNA gene metabarcoding of scat samples, we characterised and compared the gut microbiomes of echidnas in wild (n = 159) and managed (n = 44) populations, which were fed four different diets. Wild echidna samples were highly variable, yet commonly dominated by soil and plant-fermenting bacteria, while echidnas in captivity were dominated by gut commensals and plant-fermenting bacteria, suggesting plant matter may play a significant role in echidna diet. This work demonstrates significant differences between zoo held and wild echidnas, as well as managed animals on different diets, revealing that diet is important in shaping the gut microbiomes in echidnas. This first analysis of echidna gut microbiome highlights extensive microbial diversity in wild echidnas and changes in microbiome composition in managed populations. This is a first step towards using microbiome analysis to better understand diet, gastrointestinal biology, and improve management in these iconic animals. Frontiers Media S.A. 2022-06-30 /pmc/articles/PMC9279566/ /pubmed/35847103 http://dx.doi.org/10.3389/fmicb.2022.687115 Text en Copyright © 2022 Perry, West, Eisenhofer, Stenhouse, Wilson, Laming, Rismiller, Shaw and Grützner. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Perry, Tahlia
West, Ella
Eisenhofer, Raphael
Stenhouse, Alan
Wilson, Isabella
Laming, Belinda
Rismiller, Peggy
Shaw, Michelle
Grützner, Frank
Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes
title Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes
title_full Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes
title_fullStr Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes
title_full_unstemmed Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes
title_short Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes
title_sort characterising the gut microbiomes in wild and captive short-beaked echidnas reveals diet-associated changes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279566/
https://www.ncbi.nlm.nih.gov/pubmed/35847103
http://dx.doi.org/10.3389/fmicb.2022.687115
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