D. Ro, Production of the antimalarial drug precursor artemisinic acid in engineered yeast, Nature, vol.272, issue.7086, pp.940-943, 2006.
DOI : 10.1038/nature04640

H. C. Bernstein, S. D. Paulson, and R. P. Carlson, Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity, Journal of Biotechnology, vol.157, issue.1, pp.159-166, 2012.
DOI : 10.1016/j.jbiotec.2011.10.001

K. Brenner, L. You, and F. Arnold, Engineering microbial consortia: a new frontier in synthetic biology, Trends in Biotechnology, vol.26, issue.9, pp.483-489, 2008.
DOI : 10.1016/j.tibtech.2008.05.004

B. Momeni, C. Chen, K. L. Hillesland, A. Waite, and W. Shou, Using artificial systems to explore the ecology and evolution of symbioses, Cellular and Molecular Life Sciences, vol.100, issue.8, pp.1353-1368, 2011.
DOI : 10.1007/s00018-011-0649-y

W. Sabra, D. Dietz, D. Tjahjasari, and A. Zeng, Biosystems analysis and engineering of microbial consortia for industrial biotechnology, Engineering in Life Sciences, vol.9, issue.5, pp.407-421, 2010.
DOI : 10.1002/elsc.201000111

N. Bourdakos, E. Marsili, and R. Mahadevan, in a membrane-less microbial fuel cell, Biotechnology and Bioengineering, vol.5, issue.4, pp.709-781, 2014.
DOI : 10.1002/bit.25137

I. Mnif, Biodegradation of diesel oil by a novel microbial consortium: comparison between co-inoculation with biosurfactant-producing strain and exogenously added biosurfactants, Environmental Science and Pollution Research, vol.164, issue.8, pp.14852-14861, 2015.
DOI : 10.1007/s11356-015-4488-5

N. M. Oliveira, R. Niehus, and K. R. Foster, Evolutionary limits to cooperation in microbial communities, Proceedings of the National Academy of Sciences, vol.111, issue.50, pp.17941-17946, 2014.
DOI : 10.1073/pnas.1412673111

M. Bizukojc, D. Dietz, J. Sun, and A. P. Zeng, Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions, Bioprocess and Biosystems Engineering, vol.142, issue.4, pp.507-523, 2010.
DOI : 10.1007/s00449-009-0359-0

A. R. Zomorrodi, M. M. Islam, and C. D. Maranas, d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities, ACS Synthetic Biology, vol.3, issue.4, pp.247-257, 2014.
DOI : 10.1021/sb4001307

A. R. Zomorrodi and C. D. Maranas, OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities, PLoS Computational Biology, vol.6, issue.2, 2012.
DOI : 10.1371/journal.pcbi.1002363.s002

A. Eng and E. Borenstein, An algorithm for designing minimal microbial communities with desired metabolic capacities, Bioinformatics, vol.32, issue.13, 2016.
DOI : 10.1093/bioinformatics/btw107

M. Fellows and F. Rosamond, The complexity ecology of parameters: an illustration using bounded max leaf number, Computation And Logic In The Real World, pp.268-277, 2007.

M. Fellows, The Complexity Ecology of Parameters: An Illustration Using Bounded Max Leaf Number, Theory of Computing Systems, vol.92, issue.4, pp.822-848, 2009.
DOI : 10.1007/s00224-009-9167-9

M. R. Garey and D. S. Johnson, Computers And Intractability: A Guide To The Theory Of NP-Completeness, 1979.

M. Kanehisa, S. Goto, and . Kegg, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000.
DOI : 10.1093/nar/28.1.27

L. Cottret, MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks, Nucleic Acids Research, vol.38, issue.Web Server, pp.132-137, 2010.
DOI : 10.1093/nar/gkq312

URL : https://hal.archives-ouvertes.fr/hal-00690651

L. Katz and R. H. Baltz, Natural product discovery: past, present, and future, Journal of Industrial Microbiology & Biotechnology, vol.42, issue.2-3, pp.155-176, 2016.
DOI : 10.1007/s10295-015-1723-5

L. R. Lynd, P. J. Weimer, W. H. Vanzyl, and I. S. Pretorius, Microbial Cellulose Utilization: Fundamentals and Biotechnology, Microbiology and Molecular Biology Reviews, vol.66, issue.3, pp.506-577, 2002.
DOI : 10.1128/MMBR.66.3.506-577.2002

P. A. Jose, S. Robinson, and D. Jebakumar, Non-streptomycete actinomycetes nourish the current microbial antibiotic drug discovery, Frontiers in Microbiology, vol.4, 2008.
DOI : 10.3389/fmicb.2013.00240

R. Saxena, P. Anand, S. Saran, and J. Isar, Microbial production of 1,3-propanediol: Recent developments and emerging opportunities, Biotechnology Advances, vol.27, issue.6, pp.895-913, 2009.
DOI : 10.1016/j.biotechadv.2009.07.003

D. Silva, G. P. Mack, M. Contiero, and J. , Glycerol: A promising and abundant carbon source for industrial microbiology, Biotechnology Advances, vol.27, issue.1, pp.30-39, 2009.
DOI : 10.1016/j.biotechadv.2008.07.006

M. Jung, Improvement of 2,3-Butanediol Yield in Klebsiella pneumoniae by Deletion of the Pyruvate Formate-Lyase Gene, Applied and Environmental Microbiology, vol.80, issue.19, pp.6195-203, 2014.
DOI : 10.1128/AEM.02069-14

K. K. Cheng, H. J. Liu, and D. H. Liu, Multiple growth inhibition of Klebsiella pneumoniae in 1,3-propanediol fermentation, Biotechnology Letters, vol.44, issue.1, pp.19-22, 2005.
DOI : 10.1007/s10529-004-6308-8

W. E. Balch, G. E. Fox, L. J. Magrum, C. R. Woese, and R. S. Wolfe, Methanogens: reevaluation of a unique biological group, Microbiol. Rev, vol.43, pp.260-296, 1979.

A. Bock, A. Prieger-kraft, and P. Schönheit, Pyruvate?a novel substrate for growth and methane formation in Methanosarcina barkeri, Arch. Microbiol, vol.161, pp.33-46, 1994.

I. Getsin, Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor, BMC Microbiology, vol.13, issue.1, p.279, 2013.
DOI : 10.1007/s00203-003-0561-4

G. Fiermonte, Identification of the Human Mitochondrial Oxodicarboxylate Carrier: BACTERIAL EXPRESSION, RECONSTITUTION, FUNCTIONAL CHARACTERIZATION, TISSUE DISTRIBUTION, AND CHROMOSOMAL LOCATION, Journal of Biological Chemistry, vol.276, issue.11, pp.8225-8230, 2001.
DOI : 10.1074/jbc.M009607200

L. Palmieri, Identification in Saccharomyces cerevisiae of Two Isoforms of a Novel Mitochondrial Transporter for 2-Oxoadipate and 2-Oxoglutarate, Journal of Biological Chemistry, vol.276, issue.3, pp.1916-1922, 2001.
DOI : 10.1074/jbc.M004332200

K. Chater, M. Bibb, and . Chapter, Regulation of bacterial antibiotic production: products of secondary metabolism, pp.57-105, 1997.

D. C. Alexander and S. E. Jensen, Investigation of the Streptomyces clavuligerus cephamycin C gene cluster and its regulation by the CcaR protein, J. Bacteriol, vol.180, pp.4068-4079, 1998.

L. Nuñez, C. Méndez, A. Brãna, G. Blanco, and J. A. Salas, The Biosynthetic Gene Cluster for the ??-Lactam Carbapenem Thienamycin in Streptomyces cattleya, Chemistry & Biology, vol.10, issue.4, pp.301-311, 2003.
DOI : 10.1016/S1074-5521(03)00069-3

J. Field, A. J. Stams, M. Kato, and G. Schraa, Enhanced biodegradation of aromatic pollutants in cocultures of anaerobic and aerobic bacterial consortia, Antonie van Leeuwenhoek, vol.27, issue.5, pp.47-77, 1995.
DOI : 10.1007/BF00872195

E. Gunnigle, A Functional Approach To Uncover the Low-Temperature Adaptation Strategies of the Archaeon Methanosarcina barkeri, Applied and Environmental Microbiology, vol.79, issue.14, pp.4210-4219, 2013.
DOI : 10.1128/AEM.03787-12

W. Chen and Z. Qin, Development of a gene cloning system in a fast-growing and moderately thermophilic Streptomyces species and heterologous expression of Streptomyces antibiotic biosynthetic gene clusters, BMC Microbiology, vol.11, issue.1, p.243, 2011.
DOI : 10.1016/S0378-1119(01)00723-5

N. Koesnandar, N. Kuroda, K. Nagai, and S. , Methanogenesis of glucose by defined thermophilic coculture of Clostridium thermoaceticum and Methanosarcina sp., Journal of Fermentation and Bioengineering, vol.70, issue.6, pp.398-403, 1990.
DOI : 10.1016/0922-338X(90)90121-C

H. Friedmann and A. Zeng, Process and apparatus for the microbial production of a specific product and methane (2013), US Patent, vol.8426, p.162

P. Carbonell, A. Planson, D. Fichera, and J. Faulon, A retrosynthetic biology approach to metabolic pathway design for therapeutic production, BMC Systems Biology, vol.5, issue.1, p.122, 2011.
DOI : 10.1016/j.ymben.2011.01.006

J. D. Orth, I. Thiele, and B. Palsson, What is flux balance analysis?, Nature Biotechnology, vol.19, issue.3, pp.245-248, 2010.
DOI : 10.1038/nbt.1614

D. Segrè, D. Vitkup, and G. M. Church, 29182 | DOI: 10.1038/srep29182 43 Analysis of optimality in natural and perturbed metabolic networks, Proc. Natl. Acad. Sci. USA 99, pp.15112-15117, 2002.

A. Chowdhury, A. R. Zomorrodi, and C. D. Maranas, Bilevel optimization techniques in computational strain design, Computers & Chemical Engineering, vol.72, pp.363-372, 2014.
DOI : 10.1016/j.compchemeng.2014.06.007

P. Pharkya and C. D. Maranas, An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems, Metabolic Engineering, vol.8, issue.1, pp.1-13, 2006.
DOI : 10.1016/j.ymben.2005.08.003

N. Tepper and T. Shlomi, Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways, Bioinformatics, vol.26, issue.4, pp.536-543, 2009.
DOI : 10.1093/bioinformatics/btp704

S. Koch, D. Benndorf, K. Fronk, U. Reichl, and S. Klamt, Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process, Biotechnology for Biofuels, vol.135, issue.2, pp.1-16, 2016.
DOI : 10.1186/s13068-016-0429-x

N. Jagmann and B. Philipp, Design of synthetic microbial communities for biotechnological production processes, Journal of Biotechnology, vol.184, pp.209-218, 2014.
DOI : 10.1016/j.jbiotec.2014.05.019

W. Shou, S. Ram, and J. M. Vilar, Synthetic cooperation in engineered yeast populations, Proc. Natl. Acad. Sci. USA, pp.1877-82, 2007.
DOI : 10.1073/pnas.0610575104

K. Hosoda, Cooperative Adaptation to Establishment of a Synthetic Bacterial Mutualism, PLoS ONE, vol.256, issue.2, pp.1-9, 2011.
DOI : 10.1371/journal.pone.0017105.s006