IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-22938-y.html
   My bibliography  Save this article

Design of synthetic human gut microbiome assembly and butyrate production

Author

Listed:
  • Ryan L. Clark

    (University of Wisconsin-Madison)

  • Bryce M. Connors

    (University of Wisconsin-Madison
    University of Wisconsin-Madison)

  • David M. Stevenson

    (University of Wisconsin-Madison)

  • Susan E. Hromada

    (University of Wisconsin-Madison
    University of Wisconsin-Madison)

  • Joshua J. Hamilton

    (University of Wisconsin-Madison)

  • Daniel Amador-Noguez

    (University of Wisconsin-Madison)

  • Ophelia S. Venturelli

    (University of Wisconsin-Madison
    University of Wisconsin-Madison
    University of Wisconsin-Madison)

Abstract

The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach to design synthetic human gut microbiomes for production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth and butyrate production separately, providing key insights into ecological mechanisms driving butyrate production. We use our model to explore a vast community design space using a design-test-learn cycle to identify high butyrate-producing communities. Our model can accurately predict community assembly and butyrate production across a wide range of species richness. Guided by the model, we identify constraints on butyrate production by high species richness and key molecular factors driving butyrate production, including hydrogen sulfide, environmental pH, and resource competition. In sum, our model-guided approach provides a flexible and generalizable framework for understanding and accurately predicting community assembly and metabolic functions.

Suggested Citation

  • Ryan L. Clark & Bryce M. Connors & David M. Stevenson & Susan E. Hromada & Joshua J. Hamilton & Daniel Amador-Noguez & Ophelia S. Venturelli, 2021. "Design of synthetic human gut microbiome assembly and butyrate production," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22938-y
    DOI: 10.1038/s41467-021-22938-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-22938-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-22938-y?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
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Lu Wu & Xu-Wen Wang & Zining Tao & Tong Wang & Wenlong Zuo & Yu Zeng & Yang-Yu Liu & Lei Dai, 2024. "Data-driven prediction of colonization outcomes for complex microbial communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Yasa Baig & Helena R. Ma & Helen Xu & Lingchong You, 2023. "Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Jordy Evan Sulaiman & Jaron Thompson & Yili Qian & Eugenio I. Vivas & Christian Diener & Sean M. Gibbons & Nasia Safdar & Ophelia S. Venturelli, 2024. "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    4. Yu-Yu Cheng & Zhengyi Chen & Xinyun Cao & Tyler D. Ross & Tanya G. Falbel & Briana M. Burton & Ophelia S. Venturelli, 2023. "Programming bacteria for multiplexed DNA detection," Nature Communications, Nature, vol. 14(1), pages 1-11, 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:12:y:2021:i:1:d:10.1038_s41467-021-22938-y. 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.

    We have no bibliographic references for this item. You can help adding them by using 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.