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Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Arnaud Belcour 1 Clémence Frioux 2, 1, 3, * Méziane Aite 1 Anthony Bretaudeau 4, 5 Falk Hildebrand 2, 6 Anne Siegel 1
* Corresponding author
1 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
3 PLEIADE - from patterns to models in computational biodiversity and biotechnology
LaBRI - Laboratoire Bordelais de Recherche en Informatique, Inria Bordeaux - Sud-Ouest, BioGeCo - Biodiversité, Gènes & Communautés
4 Plateforme bioinformatique GenOuest [Rennes]
UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
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.
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https://hal.inria.fr/hal-02395024
Contributor : Belcour Arnaud <>
Submitted on : Thursday, January 7, 2021 - 5:59:40 PM
Last modification on : Thursday, January 14, 2021 - 11:37:47 AM

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Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife, eLife Sciences Publication, 2020, 9, ⟨10.1101/803056⟩. ⟨hal-02395024v2⟩

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