BELCOUR, Arnaud; FRIOUX, Clémence; AITE, Méziane; BRETAUDEAU, Anthony; HILDEBRAND, Falk; SIEGEL, Anne

doi:10.7554/eLife.61968

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Licence d’utilisation du document

BELCOUR, Arnaud
Dynamics, Logics and Inference for biological Systems and Sequences [Dyliss]

FRIOUX, Clémence
Quadram Institute
Dynamics, Logics and Inference for biological Systems and Sequences [Dyliss]
Pleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]

AITE, Méziane
Dynamics, Logics and Inference for biological Systems and Sequences [Dyliss]

Langue

Article de revue

Ce document a été publié dans

eLife. 2020-12-29, vol. 9

eLife Sciences Publication

Résumé en anglais

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.< Réduire

Mots clés en anglais

computational biology

human

keystone species

metabolic complementarity

metabolic modelling

metagenomics

microbiota

systems biology

DOI

http://dx.doi.org/10.7554/eLife.61968

Project ANR

Biotechnologies pour la valorisation des macroalgues - ANR-10-BTBR-0004

Origine

Importé de hal

Unités de recherche

BioGeCo (Biodiversité Gènes & Communautés) - UMR 1202