title: A Combinatorial Algorithm for Microbial Consortia Synthetic Design.
abstract: Synthetic biology has boomed since the early 2000s when it started being shown that it was possible to efficiently synthetize compounds of interest in a much more rapid and effective way by using other organisms than those naturally producing them. However, to thus engineer a single organism, often a microbe, to optimise one or a collection of metabolic tasks may lead to difficulties when attempting to obtain a production system that is efficient, or to avoid toxic effects for the recruited microorganism. The idea of using instead a microbial consortium has thus started being developed in the last decade. This was motivated by the fact that such consortia may perform more complicated functions than could single populations and be more robust to environmental fluctuations. Success is however not always guaranteed. In particular, establishing which consortium is best for the production of a given compound or set thereof remains a great challenge. This is the problem we address in this paper. We thus introduce an initial model and a method that enable to propose a consortium to synthetically produce compounds that are either exogenous to it, or are endogenous but where interaction among the species in the consortium could improve the production line.
authors.affiliation: Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I'Europe, 38330 Montbonnot-Saint-Martin, France.|University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Julien-Laferrière
authors.affiliation: Université Paris-Est, LIGM (UMR 8049), CNRS, UPEM, ESIEE Paris, ENPC, F-77454, Marne-la-Vallée, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Bulteau
authors.affiliation: Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I'Europe, 38330 Montbonnot-Saint-Martin, France.|University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Parrot
authors.affiliation: Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I'Europe, 38330 Montbonnot-Saint-Martin, France.|Sapienza University of Rome, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Marchetti-Spaccamela
authors.affiliation: Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I'Europe, 38330 Montbonnot-Saint-Martin, France.|VU University and CWI, Amsterdam, The Netherlands.
authors.forename: Leen
authors.initials: L
authors.lastname: Stougie
authors.affiliation: IDMEC, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.
authors.forename: Susana
authors.initials: S
authors.lastname: Vinga
authors.affiliation: Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I'Europe, 38330 Montbonnot-Saint-Martin, France.|University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Mary
authors.affiliation: Erable team, INRIA Grenoble Rhône-Alpes, 655 avenue de I'Europe, 38330 Montbonnot-Saint-Martin, France.|University Lyon 1, CNRS UMR 5558, F-69622 Villeurbanne, France.
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Sagot
mesh_terms: D000085:Acetates / Q000378:metabolism; D000465:Algorithms; D001419:Bacteria / Q000378:metabolism; D001709:Biotechnology; D005990:Glycerol / Q000378:metabolism; D059013:Microbial Consortia; D011409:Propylene Glycols / Q000378:metabolism; D058615:Synthetic Biology / Q000379:methods*
chemical_list: D000085:Acetates; D011409:Propylene Glycols; C041787:1,3-propanediol; D005990:Glycerol