TY - JOUR
T1 - Vertebrate host phylogeny influences gut archaeal diversity
AU - Youngblut, Nicholas D
AU - Reischer, Georg H
AU - Dauser, Silke
AU - Maisch, Sophie
AU - Walzer, Chris
AU - Stalder, Gabrielle
AU - Farnleitner, Andreas H
AU - Ley, Ruth E
N1 - Funding Information:
This study was supported by the Max Planck Society and the Austrian Science Fund (FWF) research projects 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). We thank Andre Teare for providing body temperature data from the Medical Animal Records Keeping System (MedArks). We 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.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/11
Y1 - 2021/11
N2 - Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.
AB - Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.
KW - Animals
KW - Archaea/classification
KW - Biodiversity
KW - Birds/microbiology
KW - DNA, Archaeal/genetics
KW - Gastrointestinal Microbiome
KW - Host Specificity
KW - Humans
KW - Phylogeny
KW - RNA, Ribosomal, 16S/genetics
KW - Reptiles/microbiology
KW - Sequence Analysis, DNA
KW - Vertebrates/classification
UR - http://www.scopus.com/inward/record.url?scp=85118098540&partnerID=8YFLogxK
U2 - 10.1038/s41564-021-00980-2
DO - 10.1038/s41564-021-00980-2
M3 - Journal article
C2 - 34702978
VL - 6
SP - 1443
EP - 1454
JO - Nature Microbiology
JF - Nature Microbiology
SN - 2058-5276
IS - 11
ER -