IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37429-5.html
   My bibliography  Save this article

Functional comparison of metabolic networks across species

Author

Listed:
  • Charlotte Ramon

    (Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich
    Life Science Zurich Graduate School)

  • Jörg Stelling

    (Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich)

Abstract

Metabolic phenotypes are pivotal for many areas, but disentangling how evolutionary history and environmental adaptation shape these phenotypes is an open problem. Especially for microbes, which are metabolically diverse and often interact in complex communities, few phenotypes can be determined directly. Instead, potential phenotypes are commonly inferred from genomic information, and rarely were model-predicted phenotypes employed beyond the species level. Here, we propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and thereby link genotype and environment to phenotype. We show that these correlations provide a consistent functional complement to genomic information by capturing how network context shapes gene function. This enables, for example, phylogenetic inference across all domains of life at the organism level. For 245 bacterial species, we identify conserved and variable metabolic functions, elucidate the quantitative impact of evolutionary history and ecological niche on these functions, and generate hypotheses on associated metabolic phenotypes. We expect our framework for the joint interpretation of metabolic phenotypes, evolution, and environment to help guide future empirical studies.

Suggested Citation

  • Charlotte Ramon & Jörg Stelling, 2023. "Functional comparison of metabolic networks across species," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37429-5
    DOI: 10.1038/s41467-023-37429-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37429-5
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-37429-5?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. Germán Plata & Christopher S. Henry & Dennis Vitkup, 2015. "Long-term phenotypic evolution of bacteria," Nature, Nature, vol. 517(7534), pages 369-372, January.
    2. Elizabeth L. Johnson & Stacey L. Heaver & Jillian L. Waters & Benjamin I. Kim & Alexis Bretin & Andrew L. Goodman & Andrew T. Gewirtz & Tilla S. Worgall & Ruth E. Ley, 2020. "Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    3. Akshit Goyal, 2018. "Metabolic adaptations underlying genome flexibility in prokaryotes," PLOS Genetics, Public Library of Science, vol. 14(10), pages 1-15, October.
    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. Xiaomei Sun & Yanhong Wang & Fei Yuan & Yanan Zhang & Xun Kang & Jian Sun & Pengcheng Wang & Tengfei Lu & Fanny Sae Wang & Jinbao Gu & Jinglin Wang & Qianfeng Xia & Aihua Zheng & Zhen Zou, 2024. "Gut symbiont-derived sphingosine modulates vector competence in Aedes mosquitoes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Rabindra K. Mandal & Anita Mandal & Joshua E. Denny & Ruth Namazii & Chandy C. John & Nathan W. Schmidt, 2023. "Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Isaac G. Crusoe & Ian C. Chiwaya & Tasnim I. Habib, 2024. "Immune Control of Gut Microbiota Prevents Obesity and the Effect of Antibiotic on Microbial Population," International Journal of Research and Scientific Innovation, International Journal of Research and Scientific Innovation (IJRSI), vol. 11(5), pages 1-9, May.
    4. Jennifer T. Wolstenholme & Justin M. Saunders & Maren Smith & Jason D. Kang & Phillip B. Hylemon & Javier González-Maeso & Andrew Fagan & Derrick Zhao & Masoumeh Sikaroodi & Jeremy Herzog & Amirhossei, 2022. "Reduced alcohol preference and intake after fecal transplant in patients with alcohol use disorder is transmissible to germ-free mice," Nature Communications, Nature, vol. 13(1), pages 1-14, 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_s41467-023-37429-5. 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.