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

Author

Listed:
  • Nicholas D. Youngblut

    (Max Planck Institute for Developmental Biology)

  • Georg H. Reischer

    (Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3
    ICC Interuniversity Cooperation Centre Water & Health)

  • William Walters

    (Max Planck Institute for Developmental Biology)

  • Nathalie Schuster

    (Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3)

  • Chris Walzer

    (University of Veterinary Medicine)

  • Gabrielle Stalder

    (University of Veterinary Medicine)

  • Ruth E. Ley

    (Max Planck Institute for Developmental Biology)

  • Andreas H. Farnleitner

    (Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3
    ICC Interuniversity Cooperation Centre Water & Health
    Karl Landsteiner University for Health Sciences)

Abstract

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.

Suggested Citation

  • Nicholas D. Youngblut & Georg H. Reischer & William Walters & Nathalie Schuster & Chris Walzer & Gabrielle Stalder & Ruth E. Ley & Andreas H. Farnleitner, 2019. "Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10191-3
    DOI: 10.1038/s41467-019-10191-3
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    Cited by:

    1. Itay Daybog & Oren Kolodny, 2023. "A computational framework for resolving the microbiome diversity conundrum," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Courtney M. Thomas & Elie Desmond-Le Quéméner & Simonetta Gribaldo & Guillaume Borrel, 2022. "Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Shao-Ming Gao & Han-Lan Fei & Qi Li & Li-Ying Lan & Li-Nan Huang & Peng-Fei Fan, 2024. "Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Jeremiah J. Minich & Andreas Härer & Joseph Vechinski & Benjamin W. Frable & Zachary R. Skelton & Emily Kunselman & Michael A. Shane & Daniela S. Perry & Antonio Gonzalez & Daniel McDonald & Rob Knigh, 2022. "Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species," Nature Communications, Nature, vol. 13(1), pages 1-19, December.

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