D. Goulson, E. Nicholls, C. Botias, and E. L. Rotheray, Bee declines driven by combined stress from parasites, pesticides, and lack of flowers, Science, vol.347, p.1255957, 2015.

D. G. Bourne, Microbial disease and the coral holobiont, Trends Microbiol, vol.17, pp.554-562, 2009.
DOI : 10.1016/j.tim.2009.09.004

X. Guo and S. E. Ford, Infectious diseases of marine molluscs and host responses as revealed by genomic tools, Philos Trans R Soc Lond B Biol Sci, vol.371, p.20150206, 2016.
DOI : 10.1098/rstb.2015.0206
URL : http://europepmc.org/articles/pmc4760136?pdf=render

, Species Fact Sheets-Food and Agriculture Organization of the United Nations, FAO. Crassostrea gigas (Thunberg, 1793), 2014.

J. Samain and H. Mc-combie, Summer mortality of Pacific oyster Crassostrea gigas. The MOREST project, vol.400, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00667057

E. and P. A. , Oyster mortality, FASEB J, vol.13, 2015.

I. Paul-pont, N. K. Dhand, and R. J. Whittington, Influence of husbandry practices on OsHV-1 associated mortality of Pacific oysters Crassostrea gigas, Aquaculture, vol.412, pp.202-214, 2013.

V. Barbosa-solomieu, T. Renault, and M. A. Travers, Mass mortality in bivalves and the intricate case of the Pacific oyster, Crassostrea gigas, J. Invertebr. Pathol, vol.131, pp.2-10, 2015.

F. Pernet, Mass mortalities of Pacific oysters Crassostrea gigas reflect infectious diseases and vary with farming practices in the Mediterranean Thau lagoon, Aquacult Env Inter, vol.2, pp.215-237, 2012.

P. Azema, Genetic parameters of resistance to Vibrio aestuarianus, and OsHV-1 infections in the Pacific oyster, Crassostrea gigas, at three different life stages, Genet. Sel. Evol, vol.49, p.23, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01479152

F. Le-roux, K. M. Wegner, and M. F. Polz, Oysters and vibrios as a model for disease dynamics in wild animals, Trends Microbiol, vol.24, pp.568-580, 2016.

B. Petton, Crassostrea gigas mortality in France: the usual suspect, a herpes virus, may not be the killer in this polymicrobial opportunistic disease, Front. Microbiol, vol.6, p.686, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01216445

B. Petton, F. Pernet, R. Robert, and P. Boudry, Temperature influence on pathogen transmission and subsequent mortalities in juvenile Pacific oysters Crassostrea gigas, Aquacult Env Inter, vol.3, pp.257-273, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00946757

A. Segarra, Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas, in France in 2008, Virus Res, vol.153, pp.92-99, 2010.

C. Martenot, E. Oden, E. Travaille, J. P. Malas, and M. Houssin, Detection of different variants of Ostreid Herpesvirus 1 in the Pacific oyster, Crassostrea gigas between, vol.160, pp.25-31, 2008.

T. Renault, Analysis of clinical ostreid herpesvirus 1 (Malacoherpesviridae) specimens by sequencing amplified fragments from three virus genome areas, J. Virol, vol.86, pp.5942-5947, 2012.

E. J. Peeler, Investigation of mortality in Pacific oysters associated with Ostreid herpesvirus-1 muVar in the Republic of Ireland in 2009, Prev. Vet. Med, vol.105, pp.136-143, 2012.

S. A. Lynch, J. Carlsson, A. O. Reilly, E. Cotter, and S. C. Culloty, A previously undescribed ostreid herpes virus 1 (OsHV-1) genotype detected in the pacific oyster, Crassostrea gigas, Parasitology, vol.139, pp.1526-1532, 2012.

M. Abbadi, Identification of a newly described OsHV-1 microvar from the North Adriatic Sea (Italy), J. Gen. Virol, vol.99, pp.693-703, 2018.

E. A. Burioli, M. Prearo, and M. Houssin, Complete genome sequence of Ostreid herpesvirus type 1 microVar isolated during mortality events in the Pacific oyster Crassostrea gigas in France and Ireland, Virology, vol.509, pp.239-251, 2017.

A. Lemire, Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters, ISME J, vol.9, pp.1523-1531, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02083151

M. Bruto, Vibrio crassostreae, a benign oyster colonizer turned into a pathogen after plasmid acquisition, ISME J, vol.11, pp.1043-1052, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01483219

A. Lokmer, S. Kuenzel, J. Baines, and K. M. Wegner, The role of tissue-specific microbiota in initial establishment success of Pacific oysters, Environ Microbiol, vol.18, pp.970-987, 2015.

A. Lokmer and K. Mathias-wegner, Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection, ISME J, vol.9, pp.670-682, 2015.

C. C. Wendling and K. M. Wegner, Adaptation to enemy shifts: rapid resistance evolution to local Vibrio spp. in invasive Pacific oysters, Proc. Biol. Sci, vol.282, p.20142244, 2015.

A. Segarra, Ostreid herpesvirus type 1 replication and host response in adult Pacific oysters, Crassostrea gigas, Vet. Res, vol.45, p.103, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01290599

Y. He, Transcriptome analysis reveals strong and complex antiviral response in a mollusc, Fish. Shellfish. Immunol, vol.46, pp.131-144, 2015.

L. Degremont, M. Nourry, and E. Maurouard, Mass selection for survival and resistance to OsHV-1 infection in Crassostrea gigas spat in field conditions: response to selection after four generations, Aquaculture, vol.446, pp.111-121, 2015.

F. Le-roux, Diagnosis of vibriosis in the era of genomics: lessons from invertebrates, Rev. Sci. Tech, vol.35, pp.259-269, 2016.

A. J. Davison, A novel class of herpesvirus with bivalve hosts, J. Gen. Virol, vol.86, pp.41-53, 2005.

T. Renault, Genotyping of a microsatellite locus to differentiate clinical Ostreid herpesvirus 1 specimens, Vet. Res, vol.45, p.3, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01290524

T. Renault, A. L. Bouquet, J. T. Maurice, C. Lupo, and P. Blachier, Ostreid herpesvirus 1 infection among Pacific oysters, Crassostrea giga, spat: virus replication and circulation related to water temperature prior the onset of mortality, Appl Environ Microbiol, vol.80, pp.5419-5426, 2014.

E. Bachere, The new insights into the oyster antimicrobial defense: cellular, molecular and genetic view, Fish. Shellfish. Immunol, vol.46, pp.50-64, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01162911

P. Schmitt, The antimicrobial defense of the Pacific Oyster, Crassostrea gigas. How diversity may compensate for scarcity in the regulation of resident/ pathogenic microflora, Front. Microbiol, vol.3, p.160, 2012.

M. Gonzalez, Evidence in oyster of a plasma extracellular superoxide dismutase which binds LPS, Biochem. Biophys. Res. Commun, vol.338, pp.1089-1097, 2005.

M. Lafont, Long-lasting antiviral innate immune priming in the Lophotrochozoan Pacific oyster, Crassostrea gigas. Sci. Rep, vol.7, p.13143, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01632346

C. Martenot, O. Gervais, B. Chollet, M. Houssin, and T. Renault, Haemocytes collected from experimentally infected Pacific oysters, Crassostrea gigas: Detection of ostreid herpesvirus 1 DNA, RNA, and proteins in relation with inhibition of apoptosis, PLoS ONE, vol.12, p.177448, 2017.

L. Yang, HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria, AIDS, vol.30, pp.19-29, 2016.

L. K. Miller, An exegesis of IAPs: salvation and surprises from BIR motifs, Trends Cell Biol, vol.9, pp.323-328, 1999.

T. J. Green, J. L. Rolland, A. Vergnes, D. Raftos, and C. Montagnani, OsHV-1 countermeasures to the Pacific oyster's anti-viral response, Fish. Shellfish. Immunol, vol.47, pp.435-443, 2015.

F. X. Gao, Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes. BMC Genom, vol.18, p.561, 2017.

S. Alizon, F. Luciani, and R. R. Regoes, Epidemiological and clinical consequences of within-host evolution, Trends Microbiol, vol.19, pp.24-32, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01567931

D. Duneau, Stochastic variation in the initial phase of bacterial infection predicts the probability of survival in D. melanogaster, Elife, vol.6, p.28298, 2017.

M. T. Sofonea, S. Alizon, and Y. Michalakis, Exposing the diversity of multiple infection patterns, J. Theor. Biol, vol.419, pp.278-289, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01567902

B. Rico-villa, S. Pouvreau, and R. Robert, Influence of food density and temperature on ingestion, growth and settlement of Pacific oyster larvae, Crassostrea gigas, Aquaculture, vol.287, pp.395-401, 2009.

M. Gonzalez, Evidence of a bactericidal permeability increasing protein in an invertebrate, the Crassostrea gigas Cg-BPI, Proc. Natl Acad. Sci. USA, vol.104, pp.17759-17764, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00258926

M. Suquet, Anesthesia in Pacific oyster, Crassostrea gigas, Aquat. Living Resour, vol.22, pp.29-34, 2009.

D. Schikorski, Experimental infection of Pacific oyster Crassostrea gigas spat by ostreid herpesvirus 1: demonstration of oyster spat susceptibility, Vet. Res, vol.42, p.27, 2011.

J. Goecks, A. Nekrutenko, J. Taylor, and T. Galaxy, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, vol.11, p.86, 2010.

D. Blankenberg, Manipulation of FASTQ data with Galaxy, Bioinformatics, vol.26, pp.1783-1785, 2010.

G. Zhang, The oyster genome reveals stress adaptation and complexity of shell formation, Nature, vol.490, pp.49-54, 2012.

A. Dobin, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

S. Anders, P. T. Pyl, and W. Huber, HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-169, 2015.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

B. Buchfink, C. Xie, and D. H. Huson, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, vol.12, pp.59-60, 2015.

A. Conesa, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-3676, 2005.

R. M. Wright, G. V. Aglyamova, E. Meyer, and M. V. Matz, Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus, BMC Genom, vol.16, p.371, 2015.

A. I. Saeed, TM4: a free, open-source system for microarray data management and analysis, Biotechniques, vol.34, pp.374-378, 2003.

H. Li, The Sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012.

A. Klindworth, Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucleic Acids Res, vol.41, p.1, 2013.

S. Mansergh and J. P. Zehr, Vibrio diversity and dynamics in the Monterey Bay upwelling region, Front. Microbiol, vol.5, p.48, 2014.

M. W. Pfaffl, A new mathematical model for relative quantification in realtime RT-PCR, Nucleic Acids Res, vol.29, p.45, 2001.

R. Bueno, M. Perrott, M. Dunowska, C. Brosnahan, and C. Johnston, In situ hybridization and histopathological observations during ostreid herpesvirus1-associated mortalities in Pacific oysters Crassostrea gigas, Dis. Aquat. Organ, vol.122, pp.43-55, 2016.

F. Escudie, FROGS: find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, pp.1287-1294, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01886389

T. Magoc and S. L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet j, vol.17, pp.10-12, 2011.
DOI : 10.14806/ej.17.1.200

F. Mahe, T. Rognes, C. Quince, C. De-vargas, and M. Dunthorn, Swarm: robust and fast clustering method for amplicon-based studies, PeerJ, vol.2, p.593, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01245140

T. Rognes, T. Flouri, B. Nichols, C. Quince, and F. Mahe, VSEARCH: a versatile open source tool for metagenomics, PeerJ, vol.4, p.2584, 2016.
DOI : 10.7717/peerj.2584
URL : https://peerj.com/articles/2584.pdf

P. J. Mcmurdie and S. Holmes, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS ONE, vol.8, p.61217, 2013.