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

Nicholas D. Youngblut, Georg H. Reischer, William Walters, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Ruth E. Ley, Andreas H. Farnleitner
doi: https://doi.org/10.1101/484006
Nicholas D. Youngblut
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Georg H. Reischer
2Technische Universität Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics, Vienna, Austria
4Interuniversity Cooperation Centre for Water & Health, Vienna, Austria
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William Walters
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Nathalie Schuster
2Technische Universität Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics, Vienna, Austria
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Chris Walzer
3Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
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Gabrielle Stalder
3Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
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Ruth E. Ley
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Andreas H. Farnleitner
2Technische Universität Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics, Vienna, Austria
4Interuniversity Cooperation Centre for Water & Health, Vienna, Austria
5Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, Krems, Austria
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Abstract

Multiple factors modulate microbial community assembly in the gut, but the magnitude of each can vary substantially across studies. This may be in part due to a heavy reliance on captive animals, which can have very different gut microbiomes versus their wild counterparts. In order to better resolve the influence of evolution and diet on gut microbiome diversity, we generated a large and highly diverse animal distal gut 16S rRNA microbiome dataset, which comprises 80 % wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decoupled the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor explains different aspects of diversity. Moreover, we resolved particular microbial taxa associated with host phylogeny or diet, and we show that Mammalia have a stronger signal of cophylogeny versus non-mammalian hosts. Additionally, our results from ecophylogenetics and co-occurrence analyses suggest 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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 03, 2018.
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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
Nicholas D. Youngblut, Georg H. Reischer, William Walters, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Ruth E. Ley, Andreas H. Farnleitner
bioRxiv 484006; doi: https://doi.org/10.1101/484006
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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
Nicholas D. Youngblut, Georg H. Reischer, William Walters, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Ruth E. Ley, Andreas H. Farnleitner
bioRxiv 484006; doi: https://doi.org/10.1101/484006

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