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Functional comparison of metabolic networks across species

Author

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  • 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
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    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)

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