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Impact of diet and host genetics on the murine intestinal mycobiome

Author

Listed:
  • Yask Gupta

    (University of Lübeck
    Columbia University Irving Medical Center)

  • Anna Lara Ernst

    (University of Lübeck)

  • Artem Vorobyev

    (University of Lübeck
    University of Lübeck)

  • Foteini Beltsiou

    (University of Lübeck)

  • Detlef Zillikens

    (University of Lübeck)

  • Katja Bieber

    (University of Lübeck)

  • Simone Sanna-Cherchi

    (Columbia University Irving Medical Center)

  • Angela M. Christiano

    (Columbia University Irving Medical Center)

  • Christian D. Sadik

    (University of Lübeck)

  • Ralf J. Ludwig

    (University of Lübeck
    University of Lübeck)

  • Tanya Sezin

    (University of Lübeck
    Columbia University Irving Medical Center)

Abstract

The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its’ interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.

Suggested Citation

  • Yask Gupta & Anna Lara Ernst & Artem Vorobyev & Foteini Beltsiou & Detlef Zillikens & Katja Bieber & Simone Sanna-Cherchi & Angela M. Christiano & Christian D. Sadik & Ralf J. Ludwig & Tanya Sezin, 2023. "Impact of diet and host genetics on the murine intestinal mycobiome," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36479-z
    DOI: 10.1038/s41467-023-36479-z
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    References listed on IDEAS

    as
    1. Artem Vorobyev & Yask Gupta & Tanya Sezin & Hiroshi Koga & Yannic C. Bartsch & Meriem Belheouane & Sven Künzel & Christian Sina & Paul Schilf & Heiko Körber-Ahrens & Foteini Beltsiou & Anna Lara Ernst, 2019. "Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    2. Fen Zhang & Tao Zuo & Yun Kit Yeoh & Frankie W. T. Cheng & Qin Liu & Whitney Tang & Kitty C. Y. Cheung & Keli Yang & Chun Pan Cheung & Chow Chung Mo & Mamie Hui & Francis K. L. Chan & Chi-Kong Li & Pa, 2021. "Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    3. Ohad Manor & Chengzhen L. Dai & Sergey A. Kornilov & Brett Smith & Nathan D. Price & Jennifer C. Lovejoy & Sean M. Gibbons & Andrew T. Magis, 2020. "Health and disease markers correlate with gut microbiome composition across thousands of people," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    4. Paul J McMurdie & Susan Holmes, 2014. "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible," PLOS Computational Biology, Public Library of Science, vol. 10(4), pages 1-12, April.
    5. Berk Aykut & Smruti Pushalkar & Ruonan Chen & Qianhao Li & Raquel Abengozar & Jacqueline I. Kim & Sorin A. Shadaloey & Dongling Wu & Pamela Preiss & Narendra Verma & Yuqi Guo & Anjana Saxena & Mridula, 2019. "The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL," Nature, Nature, vol. 574(7777), pages 264-267, October.
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