TY - JOUR
T1 - Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
AU - Youngblut, Nicholas D
AU - Reischer, Georg H
AU - Walters, William
AU - Schuster, Nathalie
AU - Walzer, Chris
AU - Stalder, Gabrielle
AU - Ley, Ruth E
AU - Farnleitner, Andreas H
N1 - Funding Information:
This study was supported by the Austrian Science Fund (FWF) as part of the “Vienna Doctoral Program on Water Resource Systems” (DKplus W1219-N22) and the research project P23900 granted to A.H.F. and P22032 granted to G.H.R. Further support came from the Science Call 2015 “Resource und Lebensgrundlage Wasser“ Project SC15-016 funded by the Niederösterreichische Forschungs-und Bildungsgesellschaft (NFB). This work was supported by a David and Lucile Packard Foundation Fellowship (to R.E.L.) and the Max Planck Society. We would like to thank the following collaborators for their huge efforts in sample and data collection: Mario Baldi, School of Veterinary Medicine, Universidad Nacional de Costa Rica; Wolfgang Vogl and Frank Radon, Konrad Lorenz Institute of Ethology and Biological Station Illmitz; Endre Sós and Viktor Molnár, Budapest Zoo; Ulrike Streicher, Conservation and Wildlife Management Consultant, Vietnam; Katharina Mahr, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna and Flinders University Adelaide, South Australia; Peggy Rismiller, Pelican Lagoon Research Centre, Australia; Rob Deaville, Institute of Zoology, Zoological Society of London; Alex Lécu, Muséum National d’Histoire Naturelle and Paris Zoo; Danny Govender and Emily Lane, South African National Parks, Sanparks; Fritz Reimoser, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna; Anna Kübber-Heiss and Team, Pathology, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna; Nikolaus Eisank, Nationalpark Hohe Tauern, Kärnten; Attila Hettyey and Yoshan Moodley, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna; Mansour El-Matbouli and Oskar Schachner, Clinical Unit of Fish Medicine, University of Veterinary Medicine; Barbara Richter, Institute of Pathology and Forensic Veterinary Medicine, University of Veterinary Medicine Vienna; Hanna Vielgrader and Zoovet Team, Schönbrunn Zoo; Reinhard Pichler, Herberstein Zoo. We explicitly thank the Freek Venter of South African National Parks and the National Zoological Gardens of South Africa for granting access to their Parks for sample collection. We also thank Carolin Kolmeder and Jillian Waters for their helpful discussions on this project.
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - 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.
AB - 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.
KW - Animals
KW - Biodiversity
KW - Biological Evolution
KW - Datasets as Topic
KW - Feeding Behavior/physiology
KW - Gastrointestinal Microbiome/genetics
KW - Host Microbial Interactions/physiology
KW - Phylogeny
KW - RNA, Ribosomal, 16S/genetics
KW - Vertebrates/microbiology
UR - http://www.scopus.com/inward/record.url?scp=85065867990&partnerID=8YFLogxK
U2 - 10.1038/s41467-019-10191-3
DO - 10.1038/s41467-019-10191-3
M3 - Journal article
C2 - 31097702
SN - 2041-1723
VL - 10
SP - 2200
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 2200
ER -