1. Computational and Systems Biology
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Metage2Metabo, microbiota-scale metabolic complementarity for the identication of key species

  1. Arnaud Belcour
  2. Clémence Frioux  Is a corresponding author
  3. Méziane Aite
  4. Anthony Bretaudeau
  5. Falk Hildebrand
  6. Anne Siegel
  1. Univ Rennes, Inria, CNRS, IRISA, France
  2. Inria, France
  3. INRAE, UMR IGEPP, France
  4. Quadram Institute, United Kingdom
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Cite this article as: eLife 2020;9:e61968 doi: 10.7554/eLife.61968

Abstract

To capture the functional diversity of microbiota, one must identify metabolic functions and species of interest within hundreds or thousands of microorganisms. We present Metage2Metabo (M2M) a resource that meets the need for de-novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species with respect to metabolic cooperation. M2M comprises a flexible pipeline for the characterisation of individual metabolisms and collective metabolic complementarity. In addition, M2M identifies key species, that are meaningful members of the community for functions of interest. We demonstrate that M2M is applicable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN reconstruction with Pathway Tools, and assesses the cooperation potential between species. M2M identifies key organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses.

Data availability

Data for metabolic modelling is available in https://github.com/AuReMe/metage2metabo/tree/master/article_data .

The following previously published data sets were used

Article and author information

Author details

  1. Arnaud Belcour

    Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1170-0785
  2. Clémence Frioux

    Pleiade, Inria, Talence, France
    For correspondence
    clemence.frioux@inria.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2114-0697
  3. Méziane Aite

    Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Anthony Bretaudeau

    BioInformatics Platform for Agroecosystems Arthropods (BIPAA), INRAE, UMR IGEPP, Rennes, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Falk Hildebrand

    Quadram Institute, Norwich, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Anne Siegel

    Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
    Competing interests
    The authors declare that no competing interests exist.

Funding

BBSRC (Gut Microbes and Health BB/r012490/1,and its constituent project BBS/e/F/000Pr1035)

  • Clémence Frioux
  • Falk Hildebrand

2 (IDEALG (ANR-10-BTBR-04) Investissements d'Avenir)

  • Arnaud Belcour
  • Clémence Frioux
  • Méziane Aite

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. María Mercedes Zambrano, CorpoGen, Colombia

Publication history

  1. Received: August 10, 2020
  2. Accepted: December 25, 2020
  3. Accepted Manuscript published: December 29, 2020 (version 1)
  4. Version of Record published: February 4, 2021 (version 2)

Copyright

© 2020, Belcour et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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