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

Abstract
Data availability
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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

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Article and author information

Author details

Arnaud Belcour

Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1170-0785
Clémence Frioux

Pleiade, Inria, Talence, France

For correspondence
clemence.frioux@inria.fr

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2114-0697
Méziane Aite

Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France

Competing interests
The authors declare that no competing interests exist.
Anthony Bretaudeau

BioInformatics Platform for Agroecosystems Arthropods (BIPAA), INRAE, UMR IGEPP, Rennes, France

Competing interests
The authors declare that no competing interests exist.
Falk Hildebrand

Quadram Institute, Norwich, United Kingdom

Competing interests
The authors declare that no competing interests exist.
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.

Copyright

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.