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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

Author

Listed:
  • Mathieu Groussin

    (Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Florent Mazel

    (Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041)

  • Jon G. Sanders

    (Organismic and Evolutionary Biology, Harvard University)

  • Chris S. Smillie

    (Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
    Massachusetts Institute of Technology
    The Broad Institute of MIT and Harvard)

  • Sébastien Lavergne

    (Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041)

  • Wilfried Thuiller

    (Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041)

  • Eric J. Alm

    (Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
    Massachusetts Institute of Technology
    The Broad Institute of MIT and Harvard)

Abstract

Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution.

Suggested Citation

  • Mathieu Groussin & Florent Mazel & Jon G. Sanders & Chris S. Smillie & Sébastien Lavergne & Wilfried Thuiller & Eric J. Alm, 2017. "Unraveling the processes shaping mammalian gut microbiomes over evolutionary time," Nature Communications, Nature, vol. 8(1), pages 1-12, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14319
    DOI: 10.1038/ncomms14319
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    Cited by:

    1. Yunpeng Liu & Xiaoting Xu & Dimitar Dimitrov & Loic Pellissier & Michael K. Borregaard & Nawal Shrestha & Xiangyan Su & Ao Luo & Niklaus E. Zimmermann & Carsten Rahbek & Zhiheng Wang, 2023. "An updated floristic map of the world," Nature Communications, Nature, vol. 14(1), pages 1-11, 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. 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.
    4. M. C. Rühlemann & C. Bang & J. F. Gogarten & B. M. Hermes & M. Groussin & S. Waschina & M. Poyet & M. Ulrich & C. Akoua-Koffi & T. Deschner & J. J. Muyembe-Tamfum & M. M. Robbins & M. Surbeck & R. M. , 2024. "Functional host-specific adaptation of the intestinal microbiome in hominids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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