S. Bhatt, P. W. Gething, O. J. Brady, J. P. Messina, A. W. Farlow et al., The global distribution and burden of dengue, Nature, vol.496, issue.7446, pp.504-511, 2013.

A. Wilder-smith, D. J. Gubler, S. C. Weaver, T. P. Monath, D. L. Heymann et al., Epidemic arboviral diseases: priorities for research and public health, Lancet Infect Dis, vol.17, issue.3, pp.101-107, 2017.

E. A. Mcgraw, O. Neill, and S. L. , Beyond insecticides: new thinking on an ancient problem, Nat Rev Microbiol, vol.11, issue.3, pp.181-93, 2013.

L. Lambrechts, N. M. Ferguson, E. Harris, E. C. Holmes, E. A. Mcgraw et al., Assessing the epidemiological effect of Wolbachia for dengue control, Lancet Infect Dis, vol.15, issue.7, pp.862-868, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01176423

L. Lambrechts, T. B. Knox, J. Wong, K. A. Liebman, R. G. Albright et al., Shifting priorities in vector biology to improve control of vector-borne disease, Trop Med Int Health, vol.14, issue.12, pp.1505-1519, 2009.

C. F. Bosio, R. E. Fulton, M. L. Salasek, B. J. Beaty, and W. C. Black, Quantitative trait loci that control vector competence for dengue-2 virus in the mosquito Aedes aegypti, Genetics, vol.156, issue.2, pp.687-98, 2000.

K. E. Bennett, D. Flick, K. H. Fleming, R. Jochim, B. J. Beaty et al., Quantitative trait loci that control dengue-2 virus dissemination in the mosquito Aedes aegypti, Genetics, vol.170, issue.1, pp.185-94, 2005.

T. Fansiri, A. Fontaine, L. Diancourt, V. Caro, B. Thaisomboonsuk et al., Genetic mapping of specific interactions between Aedes aegypti mosquitoes and dengue viruses, PLoS Genet, vol.9, issue.8, p.1003621, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00854586

L. B. Dickson, D. Jiolle, G. Minard, I. Moltini-conclois, S. Volant et al., Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector, Sci Adv, vol.3, issue.8, p.1700585, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01580399

L. Lambrechts, K. P. Paaijmans, T. Fansiri, L. B. Carrington, L. D. Kramer et al., Impact of daily temperature fluctuations on dengue virus transmission by Aedes aegypti, Proc Natl Acad Sci USA, vol.108, issue.18, pp.7460-7465, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00587940

C. J. Westbrook, M. H. Reiskind, K. N. Pesko, K. E. Greene, and L. P. Lounibos, Larval environmental temperature and the susceptibility of Aedes albopictus Skuse (Diptera: Culicidae) to chikungunya virus, Vector Borne Zoonotic Dis, vol.10, issue.3, pp.241-248, 2010.

B. W. Alto, L. P. Lounibos, S. Higgs, and S. A. Juliano, Larval competition differentially affects arbovirus infection in Aedes mosquitoes, Ecology, vol.86, issue.12, pp.3279-88, 2005.

G. Minard, P. Mavingui, and C. V. Moro, Diversity and function of bacterial microbiota in the mosquito holobiont, Parasit Vectors, vol.6, p.146, 2013.

S. Hegde, J. L. Rasgon, and G. L. Hughes, The microbiome modulates arbovirus transmission in mosquitoes, Curr Opin Virol, vol.15, pp.97-102, 2015.
DOI : 10.1016/j.coviro.2015.08.011
URL : http://europepmc.org/articles/pmc5731638?pdf=render

C. M. Cirimotich, J. L. Ramirez, and G. Dimopoulos, Native microbiota shape insect vector competence for human pathogens, Cell Host Microbe, vol.10, issue.4, pp.307-317, 2011.
DOI : 10.1016/j.chom.2011.09.006
URL : https://doi.org/10.1016/j.chom.2011.09.006

J. L. Ramirez, S. M. Short, A. C. Bahia, R. G. Saraiva, Y. Dong et al., Chromobacterium Csp_P reduces malaria and dengue infection in vector mosquitoes and has entomopathogenic and in vitro anti-pathogen activities, PLoS Pathog, vol.10, issue.10, p.1004398, 2014.
DOI : 10.1371/journal.ppat.1004398
URL : https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1004398&type=printable

J. L. Ramirez, J. Souza-neto, T. Cosme, R. Rovira, J. Ortiz et al., Reciprocal tripartite interactions between the Aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence, PLoS Negl Trop Dis, vol.6, issue.3, p.1561, 2012.
DOI : 10.1371/journal.pntd.0001561
URL : https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0001561&type=printable

A. Apte-deshpande, M. Paingankar, M. D. Gokhale, and D. N. Deobagkar, Serratia odorifera a midgut inhabitant of Aedes aegypti mosquito enhances its susceptibility to dengue-2 virus, PLoS One, vol.7, issue.7, p.40401, 2012.

A. D. Apte-deshpande, M. S. Paingankar, M. D. Gokhale, and D. N. Deobagkar, Serratia odorifera mediated enhancement in susceptibility of Aedes aegypti for chikungunya virus, Indian J Med Res, vol.139, issue.5, pp.762-770, 2014.

K. Zouache, F. N. Raharimalala, V. Raquin, V. Tran-van, L. H. Raveloson et al., Bacterial diversity of field-caught mosquitoes, Aedes albopictus and Aedes aegypti, from different geographic regions of Madagascar, FEMS Microbiol Ecol, vol.75, issue.3, pp.377-89, 2011.
URL : https://hal.archives-ouvertes.fr/halsde-00724643

K. L. Coon, M. R. Brown, and M. R. Strand, Mosquitoes host communities of bacteria that are essential for development but vary greatly between local habitats, Mol Ecol, vol.25, issue.22, pp.5806-5832, 2016.

J. Osei-poku, C. M. Mbogo, W. J. Palmer, and F. M. Jiggins, Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from Kenya, Mol Ecol, vol.21, issue.20, pp.5138-50, 2012.

M. Buck, L. K. Nilsson, C. Brunius, R. K. Dabire, R. Hopkins et al., Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes, Sci Rep, vol.6, p.22806, 2016.

G. Gimonneau, M. T. Tchioffo, L. Abate, A. Boissiere, P. H. Awono-ambene et al., Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages, Infect Genet Evol, vol.28, pp.715-739, 2014.
DOI : 10.1016/j.meegid.2014.09.029
URL : https://hal.archives-ouvertes.fr/hal-01546167

K. L. Coon, K. J. Vogel, M. R. Brown, and M. R. Strand, Mosquitoes rely on their gut microbiota for development, Mol Ecol, vol.23, issue.11, pp.2727-2766, 2014.
DOI : 10.1111/mec.12771
URL : http://europepmc.org/articles/pmc4083365?pdf=render

Y. Wang, . Gilbreath-tm-3rd, P. Kukutla, G. Yan, and J. Xu, Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya, PLoS One, vol.6, issue.9, p.24767, 2011.

A. Pike, Y. Dong, N. B. Dizaji, A. Gacita, E. F. Mongodin et al., Changes in the microbiota cause genetically modified Anopheles to spread in a population, Science, vol.357, issue.6358, pp.1396-1405, 2017.

K. M. Oliver, N. A. Moran, and M. S. Hunter, Variation in resistance to parasitism in aphids is due to symbionts not host genotype, Proc Natl Acad Sci USA, vol.102, issue.36, pp.12795-800, 2005.

C. Sandrock, A. Gouskov, and C. Vorburger, Ample genetic variation but no evidence for genotype specificity in an all-parthenogenetic host-parasitoid interaction, J Evol Biol, vol.23, issue.3, pp.578-85, 2010.

C. Vorburger, C. Sandrock, A. Gouskov, L. E. Castaneda, and J. Ferrari, Genotypic variation and the role of defensive endosymbionts in an allparthenogenetic host-parasitoid interaction, Evolution, vol.63, issue.6, pp.1439-50, 2009.

H. Koch and P. Schmid-hempel, Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system, Ecol Lett, vol.15, issue.10, pp.1095-103, 2012.

S. S. Charan, K. D. Pawar, D. W. Severson, M. S. Patole, and Y. S. Shouche, Comparative analysis of midgut bacterial communities of Aedes aegypti mosquito strains varying in vector competence to dengue virus, Parasitol Res, vol.112, issue.7, pp.2627-2664, 2013.

S. M. Short, E. F. Mongodin, H. J. Macleod, O. Talyuli, and G. Dimopoulos, Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability, PLoS Negl Trop Dis, vol.11, issue.7, p.5677, 2017.
DOI : 10.1371/journal.pntd.0005677
URL : https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0005677&type=printable

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, issue.4, pp.357-366, 2012.
DOI : 10.1038/nmeth.1923
URL : http://europepmc.org/articles/pmc3322381?pdf=render

J. J. Quereda, O. Dussurget, M. A. Nahori, A. Ghozlane, S. Volant et al., Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection, Proc Natl Acad Sci USA, vol.113, issue.20, pp.5706-5717, 2016.
DOI : 10.1073/pnas.1523899113
URL : https://hal.archives-ouvertes.fr/hal-01533881

Y. Hochberg and Y. Benjamini, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J Roy Stat Soc B, vol.57, issue.1, pp.289-300, 1995.

G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath et al., Multiple comparative metagenomics using multiset k-mer counting, PeerJ Comput Sci, vol.2, p.94, 2016.
DOI : 10.7717/peerj-cs.94
URL : https://hal.archives-ouvertes.fr/hal-01397150

P. Engel and N. A. Moran, The gut microbiota of insects-diversity in structure and function, FEMS Microbiol Rev, vol.37, issue.5, pp.699-735, 2013.

R. J. Dillon and V. M. Dillon, The gut bacteria of insects: nonpathogenic interactions, Annu Rev Entomol, vol.49, pp.71-92, 2004.

W. J. Tabachnick and J. R. Powell, A world-wide survey of genetic variation in the yellow fever mosquito, Aedes aegypti, Genet Res, vol.34, issue.3, pp.215-244, 1979.

L. B. Dickson, C. L. Campbell, P. Juneja, F. M. Jiggins, M. Sylla et al., Exon-enriched libraries reveal large genic differences between Aedes aegypti from Senegal, West Africa, and populations outside, Africa. G3, vol.7, issue.2, pp.571-82, 2017.
DOI : 10.1534/g3.116.036053
URL : https://www.g3journal.org/content/ggg/7/2/571.full.pdf

J. E. Brown, B. R. Evans, W. Zheng, V. Obas, L. Barrera-martinez et al., Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito, Evolution, vol.68, issue.2, pp.514-539, 2014.

J. E. Brown, C. S. Mcbride, P. Johnson, S. Ritchie, C. Paupy et al., Worldwide patterns of genetic differentiation imply multiple 'domestications' of Aedes aegypti, a major vector of human diseases, Proc Biol Sci, vol.278, pp.2446-54, 1717.

J. E. Crawford, J. M. Alves, W. J. Palmer, J. P. Day, M. Sylla et al., Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector, BMC Biol, vol.15, issue.1, p.16, 2017.

A. Gloria-soria, D. Ayala, A. Bheecarry, O. Calderon-arguedas, D. D. Chadee et al., Global genetic diversity of Aedes aegypti, Mol Ecol, vol.25, issue.21, pp.5377-95, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02065022

C. F. Bosio, L. C. Harrington, J. W. Jones, R. Sithiprasasna, D. E. Norris et al., Genetic structure of Aedes aegypti populations in Thailand using mitochondrial DNA, Am J Trop Med Hyg, vol.72, issue.4, pp.434-476, 2005.

F. Garcia-franco, M. Mde, L. Lozano-fuentes, S. Fernandez-salas, I. Garciarejon et al., Large genetic distances among Aedes aegypti populations along the South Pacific coast of Mexico, Am J Trop Med Hyg, vol.66, issue.5, pp.594-602, 2002.

M. U. Kraemer, M. E. Sinka, K. A. Duda, A. Q. Mylne, F. M. Shearer et al., The global distribution of the arbovirus vectors Aedes aegypti and Ae, albopictus. Elife, vol.4, p.8347, 2015.

M. U. Kraemer, M. E. Sinka, K. A. Duda, A. Mylne, F. M. Shearer et al., The global compendium of Aedes aegypti and Ae. albopictus occurrence, Sci Data, vol.2, p.150035, 2015.