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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we...

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Autores principales: Youngblut, Nicholas D., Reischer, Georg H., Walters, William, Schuster, Nathalie, Walzer, Chris, Stalder, Gabrielle, Ley, Ruth E., Farnleitner, Andreas H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522487/
https://www.ncbi.nlm.nih.gov/pubmed/31097702
http://dx.doi.org/10.1038/s41467-019-10191-3
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author Youngblut, Nicholas D.
Reischer, Georg H.
Walters, William
Schuster, Nathalie
Walzer, Chris
Stalder, Gabrielle
Ley, Ruth E.
Farnleitner, Andreas H.
author_facet Youngblut, Nicholas D.
Reischer, Georg H.
Walters, William
Schuster, Nathalie
Walzer, Chris
Stalder, Gabrielle
Ley, Ruth E.
Farnleitner, Andreas H.
author_sort Youngblut, Nicholas D.
collection PubMed
description Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
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spelling pubmed-65224872019-05-20 Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades Youngblut, Nicholas D. Reischer, Georg H. Walters, William Schuster, Nathalie Walzer, Chris Stalder, Gabrielle Ley, Ruth E. Farnleitner, Andreas H. Nat Commun Article Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine. Nature Publishing Group UK 2019-05-16 /pmc/articles/PMC6522487/ /pubmed/31097702 http://dx.doi.org/10.1038/s41467-019-10191-3 Text en © The Author(s) 2019 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Youngblut, Nicholas D.
Reischer, Georg H.
Walters, William
Schuster, Nathalie
Walzer, Chris
Stalder, Gabrielle
Ley, Ruth E.
Farnleitner, Andreas H.
Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
title Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
title_full Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
title_fullStr Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
title_full_unstemmed Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
title_short Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
title_sort host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522487/
https://www.ncbi.nlm.nih.gov/pubmed/31097702
http://dx.doi.org/10.1038/s41467-019-10191-3
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