IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-36479-z.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-36479-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-36479-z?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    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. 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.
    3. 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.
    4. 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.
    5. 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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Aaron C Ericsson & J Wade Davis & William Spollen & Nathan Bivens & Scott Givan & Catherine E Hagan & Mark McIntosh & Craig L Franklin, 2015. "Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-19, February.
    2. Duo Jiang & Thomas Sharpton & Yuan Jiang, 2021. "Microbial Interaction Network Estimation via Bias-Corrected Graphical Lasso," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(2), pages 329-350, July.
    3. Shilan Li & Jianxin Shi & Paul Albert & Hong-Bin Fang, 2022. "Dependence Structure Analysis and Its Application in Human Microbiome," Mathematics, MDPI, vol. 11(1), pages 1-14, December.
    4. William Bernard Perry & Mathew Seymour & Luisa Orsini & Ifan Bryn Jâms & Nigel Milner & François Edwards & Rachel Harvey & Mark Bruyn & Iliana Bista & Kerry Walsh & Bridget Emmett & Rosetta Blackman &, 2024. "An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Yadid M. Algavi & Elhanan Borenstein, 2023. "A data-driven approach for predicting the impact of drugs on the human microbiome," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Dawid Nosek & Tomasz Mikołajczyk & Agnieszka Cydzik-Kwiatkowska, 2023. "Anode Modification with Fe 2 O 3 Affects the Anode Microbiome and Improves Energy Generation in Microbial Fuel Cells Powered by Wastewater," IJERPH, MDPI, vol. 20(3), pages 1-21, January.
    7. Thomas A. Auchtung & Christopher J. Stewart & Daniel P. Smith & Eric W. Triplett & Daniel Agardh & William A. Hagopian & Anette G. Ziegler & Marian J. Rewers & Jin-Xiong She & Jorma Toppari & Åke Lern, 2022. "Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    8. Mendler, Isabella-Hilda & Drossel, Barbara & Hütt, Marc-Thorsten, 2024. "Microbiome abundance patterns as attractors and the implications for the inference of microbial interaction networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 639(C).
    9. Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau, 2015. "Sparse and Compositionally Robust Inference of Microbial Ecological Networks," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-25, May.
    10. Robert H. Lampe & Tyler H. Coale & Kiefer O. Forsch & Loay J. Jabre & Samuel Kekuewa & Erin M. Bertrand & Aleš Horák & Miroslav Oborník & Ariel J. Rabines & Elden Rowland & Hong Zheng & Andreas J. And, 2023. "Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    11. Chase C. James & Andrew D. Barton & Lisa Zeigler Allen & Robert H. Lampe & Ariel Rabines & Anne Schulberg & Hong Zheng & Ralf Goericke & Kelly D. Goodwin & Andrew E. Allen, 2022. "Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    12. Toby Kenney & Hong Gu & Tianshu Huang, 2021. "Poisson PCA: Poisson measurement error corrected PCA, with application to microbiome data," Biometrics, The International Biometric Society, vol. 77(4), pages 1369-1384, December.
    13. Andrea Quagliariello & Alessandra Modi & Gabriel Innocenti & Valentina Zaro & Cecilia Conati Barbaro & Annamaria Ronchitelli & Francesco Boschin & Claudio Cavazzuti & Elena Dellù & Francesca Radina & , 2022. "Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    14. Chieh Lo & Radu Marculescu, 2017. "MPLasso: Inferring microbial association networks using prior microbial knowledge," PLOS Computational Biology, Public Library of Science, vol. 13(12), pages 1-20, December.
    15. Kurtis Shuler & Samuel Verbanic & Irene A. Chen & Juhee Lee, 2021. "A Bayesian nonparametric analysis for zero‐inflated multivariate count data with application to microbiome study," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(4), pages 961-979, August.
    16. Stijn Hawinkel & J C W Rayner & Luc Bijnens & Olivier Thas, 2020. "Sequence count data are poorly fit by the negative binomial distribution," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-16, April.
    17. M. McCauley & T. L. Goulet & C. R. Jackson & S. Loesgen, 2023. "Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    18. Anna C. Peterson & Himanshu Sharma & Arvind Kumar & Bruno M. Ghersi & Scott J. Emrich & Kurt J. Vandegrift & Amit Kapoor & Michael J. Blum, 2021. "Rodent Virus Diversity and Differentiation across Post-Katrina New Orleans," Sustainability, MDPI, vol. 13(14), pages 1-18, July.
    19. Francesco Spennati & Salvatore La China & Giovanna Siracusa & Simona Di Gregorio & Alessandra Bardi & Valeria Tigini & Gualtiero Mori & David Gabriel & Giulio Munz, 2021. "Tannery Wastewater Recalcitrant Compounds Foster the Selection of Fungi in Non-Sterile Conditions: A Pilot Scale Long-Term Test," IJERPH, MDPI, vol. 18(12), pages 1-18, June.
    20. Zhirui Cao & Dejun Fan & Yang Sun & Ziyu Huang & Yue Li & Runping Su & Feng Zhang & Qing Li & Hongju Yang & Fen Zhang & Yinglei Miao & Ping Lan & Xiaojian Wu & Tao Zuo, 2024. "The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice," Nature Communications, Nature, vol. 15(1), pages 1-22, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36479-z. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.