Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

Author:

Song Se Jin1ORCID,Sanders Jon G.1ORCID,Delsuc Frédéric2,Metcalf Jessica3,Amato Katherine4,Taylor Michael W.5,Mazel Florent6ORCID,Lutz Holly L.17ORCID,Winker Kevin8,Graves Gary R.910,Humphrey Gregory1,Gilbert Jack A.1,Hackett Shannon J.7,White Kevin P.11,Skeen Heather R.712,Kurtis Sarah M.13,Withrow Jack8,Braile Thomas8,Miller Matthew814,McCracken Kevin G.815161718,Maley James M.19,Ezenwa Vanessa O.2021,Williams Allison20,Blanton Jessica M.22,McKenzie Valerie J.23,Knight Rob12425

Affiliation:

1. Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA

2. Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France

3. Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA

4. Department of Anthropology, Northwestern University, Evanston, Illinois, USA

5. School of Biological Sciences, University of Auckland, Auckland, New Zealand

6. Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada

7. Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA

8. University of Alaska Museum, Fairbanks, Alaska, USA

9. Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA

10. Center for Macroecology, Evolution and Climate National Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

11. Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA

12. Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA

13. Department of Biology, University of Florida, Gainesville, Florida, USA

14. Sam Noble Oklahoma Museum of Natural History, Department of Biology, University of Oklahoma, Norman, Oklahoma, USA

15. Department of Biology, University of Miami, Coral Gables, Florida, USA

16. Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, USA

17. Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA

18. Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, Alaska, USA

19. Moore Laboratory of Zoology, Occidental College, Los Angeles, California, USA

20. Odum School of Ecology, University of Georgia, Athens, Georgia, USA

21. Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA

22. Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA

23. Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA

24. Department of Computer Science & Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA

25. Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA

Abstract

In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.

Funder

European Research Council

Centre National de la Recherche Scientifique

CEBA

Banting Postdoctoral Fellowship

National Science Foundation Postdoctoral Research Fellowships in Biology

the late Dr. John DuPont

the Eurasian Pacific Wildlife Conservation Foundation

National Science Foundation

U.S. Department of Agriculture

John Templeton Foundation

W. M. Keck Foundation

Friends of Ornithology

Davee Foundation

Dr. Ralph and Marian Falk Medical Research Trust

Publisher

American Society for Microbiology

Subject

Virology,Microbiology

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