S. West, A. Griffin, and A. Gardner, Evolutionary Explanations for Cooperation, Current Biology, vol.17, issue.16, pp.661-72, 2007.
DOI : 10.1016/j.cub.2007.06.004
URL : http://doi.org/10.1016/j.cub.2007.06.004

C. Knief, N. Delmotte, and J. Vorholt, Bacterial adaptation to life in association with plants - A proteomic perspective from culture to in situ conditions, PROTEOMICS, vol.140, issue.15, pp.3086-105, 2011.
DOI : 10.1016/j.jbiotec.2008.11.006

S. Bentley and J. Parkhill, Genomic perspectives on the evolution and spread of bacterial pathogens PMID:26702036, Proc Biol Sci, vol.282, 2015.

M. Steinert, Pathogen intelligence, Frontiers in Cellular and Infection Microbiology, vol.4, issue.8, p.24551600, 2014.
DOI : 10.3389/fcimb.2014.00008
URL : http://doi.org/10.3389/fcimb.2014.00008

M. Blango and M. Mulvey, Bacterial landlines: contact-dependent signaling in bacterial populations, Current Opinion in Microbiology, vol.12, issue.2, pp.177-81, 2009.
DOI : 10.1016/j.mib.2009.01.011
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668724

J. Strassmann, O. Gilbert, and D. Queller, Kin Discrimination and Cooperation in Microbes, Annual Review of Microbiology, vol.65, issue.1, pp.349-67, 2011.
DOI : 10.1146/annurev.micro.112408.134109

D. Cornforth and K. Foster, Competition sensing: the social side of bacterial stress responses, Nature Reviews Microbiology, vol.49, issue.4, pp.285-93, 2013.
DOI : 10.1128/AAC.49.7.3087-3090.2005

W. Eisenreich, J. Heesemann, T. Rudel, and W. Goebel, Metabolic host responses to infection by intracellular bacterial pathogens, Frontiers in Cellular and Infection Microbiology, vol.3, p.2423847769, 2013.
DOI : 10.3389/fcimb.2013.00024
URL : http://doi.org/10.3389/fcimb.2013.00024

M. Juhas, Horizontal gene transfer in human pathogens, Critical Reviews in Microbiology, vol.54, issue.1, pp.101-109, 2015.
DOI : 10.1128/AAC.00185-10
URL : https://www.repository.cam.ac.uk/bitstream/1810/244728/1/Juhas%20embargo%20text.pdf

M. Ackermann, A functional perspective on phenotypic heterogeneity in microorganisms, Nature Reviews Microbiology, vol.10, issue.8, pp.497-508, 2015.
DOI : 10.1371/journal.ppat.1003987

S. Elias and E. Banin, Multi-species biofilms: living with friendly neighbors, FEMS Microbiology Reviews, vol.36, issue.5, pp.990-1004, 2012.
DOI : 10.1111/j.1574-6976.2012.00325.x

R. Marvig, L. Sommer, S. Molin, and H. Johansen, Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis, Nature Genetics, vol.176, issue.1, pp.57-64, 2015.
DOI : 10.1093/bioinformatics/btp352

R. Fern-andez-l-opez, C. Mach-on, C. Longshaw, S. Martin, S. Molin et al., Unsaturated fatty acids are inhibitors of bacterial conjugation, Microbiology, vol.151, issue.11, pp.3517-3543, 2005.
DOI : 10.1099/mic.0.28216-0

M. Getino, D. Sanabria-r-ios, F. Andez-l-opez, R. Campos-g-omez, J. Opez et al., ABSTRACT, mBio, vol.6, issue.5, pp.1032-1501032, 2015.
DOI : 10.1128/mBio.01032-15

R. Hood, P. Singh, F. Hsu, T. G?-uvener, M. Carl et al., A Type VI Secretion System of Pseudomonas aeruginosa Targets a Toxin to Bacteria, Cell Host & Microbe, vol.7, issue.1, pp.25-37, 2010.
DOI : 10.1016/j.chom.2009.12.007

Y. Brunet, L. Espinosa, S. Harchouni, T. Mignot, and E. Cascales, Imaging Type VI Secretion-Mediated Bacterial Killing, Cell Reports, vol.3, issue.1, pp.36-41, 2013.
DOI : 10.1016/j.celrep.2012.11.027
URL : https://hal.archives-ouvertes.fr/hal-01458227

Z. Ruhe, D. Low, and C. Hayes, Bacterial contact-dependent growth inhibition, Trends in Microbiology, vol.21, issue.5, pp.230-237, 2013.
DOI : 10.1016/j.tim.2013.02.003
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648609

J. Willett, G. Gucinski, J. Fatherree, D. Low, and C. Hayes, Contact-dependent growth inhibition toxins exploit multiple independent cell-entry pathways, Proceedings of the National Academy of Sciences, vol.269, issue.7, pp.11341-11347, 2015.
DOI : 10.1128/JB.00621-10
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568652

Z. Ruhe, A. Wallace, D. Low, and C. Hayes, Receptor Polymorphism Restricts Contact-Dependent Growth Inhibition to Members of the Same Species, mBio, vol.4, issue.4, pp.480-1300480, 2013.
DOI : 10.1128/mBio.00480-13

A. Zoued, Y. Brunet, E. Durand, M. Aschtgen, L. Logger et al., Architecture and assembly of the Type VI secretion system, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1843, issue.8, pp.1664-73, 2014.
DOI : 10.1016/j.bbamcr.2014.03.018
URL : https://hal.archives-ouvertes.fr/hal-01458220

F. Cianfanelli, L. Monlezun, S. Coulthurst, E. Durand, V. Nguyen et al., Aim, Load, Fire: The Type VI Secretion System, a Bacterial Nanoweapon, Trends in Microbiology, vol.24, issue.1, pp.51-62555, 2015.
DOI : 10.1016/j.tim.2015.10.005

A. Russell, A. Wexler, B. Harding, J. Whitney, A. Bohn et al., A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism, Cell Host & Microbe, vol.16, issue.2, pp.227-263, 2014.
DOI : 10.1016/j.chom.2014.07.007
URL : http://doi.org/10.1016/j.chom.2014.07.007

J. Deiwick, S. Salcedo, E. Boucrot, S. Gilliland, T. Henry et al., The Translocated Salmonella Effector Proteins SseF and SseG Interact and Are Required To Establish an Intracellular Replication Niche, Infection and Immunity, vol.74, issue.12, pp.6965-7200648, 2006.
DOI : 10.1128/IAI.00648-06
URL : https://hal.archives-ouvertes.fr/hal-00165607

M. Jong, T. Starr, M. Winter, A. Hartigh, R. Child et al., Sensing of Bacterial Type IV Secretion via the Unfolded Protein Response, mBio, vol.4, issue.1, pp.418-1200418, 2013.
DOI : 10.1128/mBio.00418-12

J. Celli and R. Tsolis, Bacteria, the endoplasmic reticulum and the unfolded protein response: friends or foes?, Nature Reviews Microbiology, vol.110, issue.2, pp.71-82, 2015.
DOI : 10.1084/jem.20101660
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447104

S. Hern-andez, I. Cota, A. Ducret, L. Aussel, and J. Casades-us, Adaptation and preadaptation of Salmonella enterica to bile, PLoS Genet, vol.8, 2012.

I. Cota, M. Romero, S. Hern-andez, M. Pucciarelli, F. Garc-ia-del-portillo et al., Epigenetic Control of Salmonella enterica O-Antigen Chain Length: A Tradeoff between Virulence and Bacteriophage Resistance, PLOS Genetics, vol.56, issue.11, 2015.
DOI : 10.1371/journal.pgen.1005667.s005

N. U~-nez-hern-andez, C. Alonso, A. Pucciarelli, M. Casades-us, J. Garc-ia-del-portillo et al., Dormant Intracellular Salmonella enterica Serovar Typhimurium Discriminates among Salmonella Pathogenicity Island 2 Effectors To Persist inside Fibroblasts, Infection and Immunity, vol.82, issue.1, pp.221-3201304, 2014.
DOI : 10.1128/IAI.01304-13

B. Vanderven, R. Fahey, W. Lee, Y. Liu, R. Abramovitch et al., Novel Inhibitors of Cholesterol Degradation in Mycobacterium tuberculosis Reveal How the Bacterium???s Metabolism Is Constrained by the Intracellular Environment, PLOS Pathogens, vol.158, issue.2, 2015.
DOI : 10.1371/journal.ppat.1004679.s005

S. Nuccio, Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut, mBio, vol.5, issue.2, pp.929-0091400929, 2014.
DOI : 10.1128/mBio.00929-14

F. Rivera-ch-avez, Metabolism in the Host Gut, Annual Review of Microbiology, vol.69, issue.1, pp.31-48, 2015.
DOI : 10.1146/annurev-micro-091014-104108

J. Viala, R. Puppo, L. My, and E. Bouveret, Posttranslational Maturation of the Invasion Acyl Carrier Protein of Salmonella enterica Serovar Typhimurium Requires an Essential Phosphopantetheinyl Transferase of the Fatty Acid Biosynthesis Pathway, Journal of Bacteriology, vol.195, issue.19, pp.4399-40500472, 2013.
DOI : 10.1128/JB.00472-13
URL : https://hal.archives-ouvertes.fr/hal-01458222

A. Wiedemann, I. Virlogeux-payant, A. Chauss-e, A. Schikora, and P. Velge, Interactions of Salmonella with animals and plants, Frontiers in Microbiology, vol.477, issue.e1004207, p.791, 2015.
DOI : 10.1038/nature10510

C. Neumann, M. Fraiture, C. Hern-andez-reyes, F. Akum, I. Virlogeux-payant et al., The Salmonella effector protein SpvC, a phosphothreonine lyase is functional in plant cells Multihost experimental evolution of the pathogen Ralstonia solanacearum unveils genes involved in adaptation to plants, Front Microbiol Mol Biol Evol, vol.5, issue.31, pp.54825368608-36, 2014.

T. Taylor, G. Mulley, A. Dills, A. Alsohim, L. Mcguffin et al., Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system, Science, vol.33, issue.7, pp.1014-1021, 2015.
DOI : 10.1093/nar/gki524

T. Arseneault, C. Goyer, and M. Filion, LBUM223 Increases Potato Yield and Reduces Common Scab Symptoms in the Field, Phytopathology, vol.105, issue.10, pp.1311-1318, 2015.
DOI : 10.1094/PHYTO-12-14-0358-R