K. Alkhuder, K. L. Meibom, I. Dubail, M. Dupuis, and A. Charbit, Glutathione Provides a Source of Cysteine Essential for Intracellular Multiplication of Francisella tularensis, PLoS Pathogens, vol.205, issue.2, 2009.
DOI : 10.1371/journal.ppat.1000284.s006

R. Andrade, M. Wannagat, C. C. Klein, V. Acuña, A. Marchetti-spaccamela et al., Enumeration of minimal stoichiometric precursor sets in metabolic networks, Algorithms for Molecular Biology, vol.8, issue.1, pp.25-35, 2016.
DOI : 10.1371/journal.pone.0053957
URL : https://hal.archives-ouvertes.fr/hal-01368653

K. S. Beckham, J. P. Connolly, J. M. Ritchie, D. Wang, J. A. Gawthorne et al., ???O157:H7, Molecular Microbiology, vol.110, issue.Part 4, pp.199-211, 2014.
DOI : 10.1073/pnas.1222014110

H. Bohle, P. Henríquez, H. Grothusen, E. Navas, A. Sandoval et al., Comparative Genome Analysis of Two Isolates of the Fish Pathogen Piscirickettsia salmonis from Different Hosts Reveals Major Differences in Virulence-Associated Secretion Systems, Genome Announcements, vol.53, issue.6, pp.1219-1401219, 2014.
DOI : 10.1007/978-90-481-9078-2_6

E. Bosi, J. M. Monk, R. K. Aziz, M. Fondi, V. Nizet et al., strains identifies strain-specific metabolic capabilities linked to pathogenicity, Proceedings of the National Academy of Sciences, vol.206, issue.3, pp.3801-3809, 2016.
DOI : 10.1038/msb.2011.65
URL : http://www.pnas.org/content/113/26/E3801.full.pdf

S. Bravo, Piscirickettsiosis in freshwater, Bull. Eur. Assoc. Fish Pathol, vol.14, pp.137-138, 1994.

P. Bustos, K. Lyons, J. Jacques, and . Hower, Growing incidence of Piscirickettsia infection in fish worldwide: mechanism for prevention and control, " in Proceedings of Alltech's 22nd Annual Symposium: Nutritional Biotechnology in the Feed and Food Industries, Alltech UK), pp.23-26, 2006.

F. C. Cabello, P. Charusanti, S. Chauhan, K. Mcateer, J. A. Lerman et al., Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92, Environ. Microbiol. BMC Syst. Biol, vol.8, issue.5, pp.1137-1144163, 1186.

A. K. Chavali, K. M. Auria, E. L. Hewlett, R. D. Pearson, and J. A. And-papin, A metabolic network approach for the identification and prioritization of antimicrobial drug targets, Trends in Microbiology, vol.20, issue.3, pp.113-123, 2012.
DOI : 10.1016/j.tim.2011.12.004

A. K. Chavali, J. D. Whittemore, J. A. Eddy, K. T. Williams, and J. A. And-papin, Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major, Molecular Systems Biology, vol.60, p.15, 2008.
DOI : 10.1093/emboj/cdg584

R. R. Cusack, D. B. Groman, and S. R. Jones, Rickettsial infection in farmed Atlantic salmon in eastern Canada, Can. Vet. J, vol.43, pp.435-440, 2002.

J. D. Cvitanich, N. O. Garate, and C. E. Smith, The isolation of a rickettsia-like organism causing disease and mortality in Chilean salmonids and its confirmation by Koch's postulate, Journal of Fish Diseases, vol.7, issue.2, pp.121-145, 1991.
DOI : 10.1577/1548-8667(1989)001<0222:EOTAFA>2.3.CO;2

A. Ebrahim, J. A. Lerman, B. O. Palsson, and D. R. Hyduke, COBRApy: COnstraints-Based Reconstruction and Analysis for Python, BMC Systems Biology, vol.7, issue.1, pp.74-84, 2013.
DOI : 10.1093/bioinformatics/btr361
URL : https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-7-74?site=bmcsystbiol.biomedcentral.com

P. Fuentealba, C. Aros, Y. Latorre, I. Martínez, S. Marshall et al., Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis, Bioresource Technology, vol.223, pp.105-114, 2017.
DOI : 10.1016/j.biortech.2016.10.024

R. Gonzalez, A. Murarka, Y. Dharmadi, and S. S. Yazdani, A new model for the anaerobic fermentation of glycerol in enteric bacteria: Trunk and auxiliary pathways in Escherichia coli, Metabolic Engineering, vol.10, issue.5, pp.234-245, 2008.
DOI : 10.1016/j.ymben.2008.05.001

M. Henríquez, E. González, S. H. Marshall, V. Henríquez, F. A. Gómez et al., A Novel Liquid Medium for the Efficient Growth of the Salmonid Pathogen Piscirickettsia salmonis and Optimization of Culture Conditions, PLoS ONE, vol.72, issue.11, 2013.
DOI : 10.1371/journal.pone.0071830.t004

P. Henríquez, M. Kaiser, H. Bohle, P. Bustos, and M. Mancilla, field isolates, Journal of Fish Diseases, vol.37, issue.4, pp.441-448, 2015.
DOI : 10.1111/jfd.12144

M. A. Islam, E. A. Edwards, and R. Mahadevan, Characterizing the metabolism of Dehalococcoides with a constraint-based model, PLOS Comput. Biol, 2010.

P. D. Karp, S. Paley, P. K. Romero, J. Rozewicki, and K. D. Yamada, The pathway tools software MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Bioinformatics Brief. Bioinform, vol.18, pp.225-232, 2002.

T. Kondakova, F. D-'heygère, M. J. Feuilloley, N. Orange, H. J. Heipieper et al., Glycerophospholipid synthesis and functions in Pseudomonas, Chemistry and Physics of Lipids, vol.190, pp.27-42, 2015.
DOI : 10.1016/j.chemphyslip.2015.06.006

Y. A. Kwaik and D. Bumann, : ???Nutritional virulence??? as an emerging paradigm, Cellular Microbiology, vol.326, issue.6, pp.882-890, 2013.
DOI : 10.1126/science.1177263

A. Larhlimi, L. David, J. Selbig, and A. Bockmayr, F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks, BMC Bioinformatics, vol.13, issue.1, pp.57-67, 2012.
DOI : 10.1186/1471-2105-13-57

N. E. Lewis, H. Nagarajan, and B. O. Palsson, Constraining the metabolic genotype???phenotype relationship using a phylogeny of in silico methods, Nature Reviews Microbiology, vol.6, issue.4, pp.291-305, 1038.
DOI : 10.1371/journal.pone.0016274

Y. Liao, T. Huang, F. Chen, P. Charusanti, J. S. Hong et al., An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228, Journal of Bacteriology, vol.193, issue.7, pp.1710-1717, 1128.
DOI : 10.1128/JB.01218-10

N. Loira, A. Zhukova, and D. J. Sherman, Pantograph: A template-based method for genome-scale metabolic model reconstruction, Journal of Bioinformatics and Computational Biology, vol.83, issue.02, 2015.
DOI : 10.1006/bbrc.2001.4653
URL : https://hal.archives-ouvertes.fr/hal-01123733

D. L. Makrinos and T. J. Bowden, , in tissue culture and cell-free media, Journal of Fish Diseases, vol.66, issue.8, pp.1115-1127, 2016.
DOI : 10.1016/j.mimet.2005.12.001

D. Mandakovic, B. Glasner, J. Maldonado, P. Aravena, M. González et al., Genomic-Based Restriction Enzyme Selection for Specific Detection of Piscirickettsia salmonis by 16S rDNA PCR-RFLP, Frontiers in Microbiology, vol.97, issue.417, 2016.
DOI : 10.3354/dao02403

Ú. Mccarthy, J. E. Bron, L. Brown, F. Pourahmad, I. R. Bricknell et al., Survival and replication of Piscirickettsia salmonis in rainbow trout head kidney macrophages. Fish Shell, Immunol, vol.25, pp.477-484, 2008.

A. Mehlitz, E. Eylert, C. Huber, B. Lindner, N. Vollmuth et al., to mammalian host cells, Molecular Microbiology, vol.371, issue.6, pp.1004-1019, 2017.
DOI : 10.1016/S0140-6736(08)60836-3

R. Ménard, I. C. Schoenhofen, L. Tao, A. Aubry, P. Bouchard et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.58, issue.12, pp.7430-7440, 1128.
DOI : 10.1128/AAC.03858-14

J. M. Monk, P. Charusanti, R. K. Aziz, J. A. Lerman, N. Premyodhin et al., Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments, Proceedings of the National Academy of Sciences, vol.76, issue.13, pp.20338-20343, 2013.
DOI : 10.1128/AEM.00373-10

N. Murata and H. Wada, Acyl-lipid desaturases and their importance in the tolerance and acclimatization to cold of cyanobacteria, Biochemical Journal, vol.308, issue.1, pp.1-8, 1995.
DOI : 10.1042/bj3080001

L. N. Nguyen, A. Gacser, and J. D. Nosanchuk, ABSTRACT, Infection and Immunity, vol.79, issue.1, pp.136-14500753, 2011.
DOI : 10.1128/IAI.00753-10
URL : https://hal.archives-ouvertes.fr/inria-00100176

M. A. Oberhardt, J. Pucha?ka, K. E. Fryer, V. A. Martins-dos-santos, and J. A. And-papin, Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1, Journal of Bacteriology, vol.190, issue.8, pp.2790-2803, 1128.
DOI : 10.1128/JB.01583-07

E. J. Brien, J. M. Monk, and B. O. Palsson, Using genome-scale models to predict biological capabilities, Cell, vol.161, 2015.

J. D. Orth, T. M. Conrad, J. Na, J. A. Lerman, H. Nam et al., A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011, Molecular Systems Biology, vol.7, issue.1, p.65, 2011.
DOI : 10.1038/msb.2009.92

A. Otterlei, Ø. J. Brevik, D. Jensen, H. Duesund, I. Sommerset et al., Phenotypic and genetic characterization of Piscirickettsia salmonis from Chilean and Canadian salmonids, BMC Veterinary Research, vol.93, issue.15, p.55, 2016.
DOI : 10.1073/pnas.93.15.7979

S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi et al., Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, PLOS Computational Biology, vol.7, issue.7, 2017.
DOI : 10.1371/journal.pcbi.1005276.s005
URL : https://hal.archives-ouvertes.fr/hal-01449100

R. Pulgar, C. Hödar, D. Travisany, A. Zuñiga, C. Domínguez et al., Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system, BMC Genomics, vol.14, issue.1, pp.495-505, 2015.
DOI : 10.1093/bioinformatics/14.1.48

A. Raghunathan, S. Shin, and S. Daefler, Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis, BMC Systems Biology, vol.4, issue.1, pp.118-128, 2010.
DOI : 10.1186/1752-0509-4-118

R. Ramírez, F. A. Gómez, M. , and S. H. , The infection process of Piscirickettsia salmonis in fish macrophages is dependent upon interaction with host-cell clathrin and actin, FEMS Microbiology Letters, vol.362, issue.1, pp.1-8, 2015.
DOI : 10.1093/femsle/fnu012

O. Robinson, D. Dylus, and C. Dessimoz, : Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web, Molecular Biology and Evolution, vol.33, issue.8, pp.2163-2166, 2016.
DOI : 10.1093/molbev/msw080

L. Rohmer, D. Hocquet, and S. I. Miller, Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis, Trends in Microbiology, vol.19, issue.7, 2011.
DOI : 10.1016/j.tim.2011.04.003
URL : https://hal.archives-ouvertes.fr/hal-00668374

V. Rojas, N. Galanti, N. C. Bols, M. , and S. H. , in macrophages and monocyte-like cells from rainbow trout, a possible survival strategy, Journal of Cellular Biochemistry, vol.44, issue.3, pp.631-637, 2009.
DOI : 10.1016/j.micpath.2007.10.012

M. Rozas and R. Enríquez, in fish: a review, Journal of Fish Diseases, vol.179, issue.Suppl 4, pp.163-188, 2014.
DOI : 10.4049/jimmunol.179.12.8372

J. Saavedra, N. Hernandez, A. Osses, A. Castillo, A. Cancino et al., EM-90-like isolates, Journal of Fish Diseases, vol.28, issue.8, pp.1055-1063, 2017.
DOI : 10.1093/molbev/msr121

H. P. Schweizer and K. Choi, Pseudomonas aeruginosa aerobic fatty acid desaturase DesB is important for virulence factor production, Archives of Microbiology, vol.71, issue.3, pp.227-234, 2011.
DOI : 10.1128/IAI.71.9.5389-5393.2003

E. P. Skaar, The Battle for Iron between Bacterial Pathogens and Their Vertebrate Hosts, PLoS Pathogens, vol.100, issue.8, 2010.
DOI : 10.1371/journal.ppat.1000949.g001