DS0504 - Enjeux de santé

Deciphering multifactorial diseases: insight into oyster mortalities – DECIPHER

Deciphering multifactorial diseases: insight into oyster mortalities

<br />Mass and recurrent mortality events of complex etiology have increasingly affected oysters over the past years, To open a way out of this unprecedented crisis and find solutions for a sustainable oyster aquaculture, it is necessary to decipher this complex pathosystem. This is the aim of the DECIPHER project.

The objectives of the DECIPHER project is to contribute to our understanding of the multi-factorial dimension of oyster pathologies.

The objectives of the DECIPHER project is to contribute to our understanding of the multi-factorial dimension (infectious agents, microbiota, genetics) of the “summer mortality” disease affecting oysters and to propose adequate and effective control strategies. To achieve these ambitious objectives, the DECIPHER project proposes a collaborative framework and a set of experiments able to tackle the main scientific and technical issues remaining unsolved. The main obstacle encountered so far towards understanding oyster mortalities was the complexity of this pathosystem and the lack of an experimental model permitting to unravel the factors involved. This is why until recently only correlative studies using a limited number of arbitrarily chosen factors were possible, making the interaction between all factors difficult to investigate. Only an integrative research program using an experimental model of infection able to reproduce the pathogenesis in controlled conditions could address this difficult challenge. The recent development (2013) of such an experimental model of pathogenesis (EMP) by partner 3 will allow us for the first time (i) to break those conceptual and technical limitations and (ii) to move towards an integrative and dynamic view of the pathosystem in which all the parameters can be controlled. <br />In addition, DECIPHER will benefit from the recent emergence and constant progress done in Next Generation Sequencing (NGS) and associated analytical methods. It is now possible to monitor the holobiont dynamics and the functional response of each partners of the interaction (oyster, microbiota, pathogens) during the whole process from the beginning of the protocol until the pathogenesis. Combined together, EMP and NGS give us today the unique opportunity to study and quantify the respective influence of the genetic status of the oyster, the microbiota and the history of microbial challenge (during life or ontogenesis) on the emergence of the pathology.

TASK 0 will be dedicated to the management, the coordination of the project and reports.

TASK 1 will be dedicated to the production of oyster families and to implement an experimental model of pathogenesis (EMP). In subtask 1.1., full-sib families of diploid oysters with different genetic backgrounds will be produced using wild broodstock from different farming areas (i) displaying different environmental conditions (the Bay of Brest, cold and oceanic open sea zone - and the Thau lagoon, warm and lagoon coastal site) and (ii) being differentially impacted by summer mortalities.

TASK 2 will be dedicated to the characterization of the oyster holobiont dynamics throughout the development of pathogenesis in the different samples collected during the first task.

TASK 3 will be dedicated to (i) the handling and treatment of the large sets of data generated in task 2 and (ii) their statistical analysis to disentangle the relative importance of each factor (oyster genetic background, microbial environment, oyster associated microbiota and history of interactions) on the breakdown of oyster homeostasis and pathogenesis.

TASK 4 will be dedicated to the validation of the indicators identified in task 3 as biomarkers useful to monitor the oyster health status in farming conditions.

In progress

DECIPHER will generate knowledge on unexplored questions in mollusks related to the structure and function of bivalve microbiota and its contribution to homeostasis and disease resistance in bivalves. It will thus open prospects for scientific knowledge advancement on a complex multifactorial disease but also decision-making tools and applied innovations in view of the sustainable and integrated management of oyster aquaculture in France. We expect DECIPHER to have important socio-economic implications. We want to mention that the project DECIPHER will also be a first step leading to a deeper analysis the relative importance of genetic vs. epigenetic mechanisms in the heritability of the trait susceptibility/resistance to “summer mortalities”. This will be achieved through the development of a following project which will use F2 and F3 generations of the oyster full-sib families prepared in the present project and by studying (i) the transcriptomic response of the F1, F2 and F3 generation as well as (ii) their genomic and epigenomic features.

Finally, DECIPHER will be committed to a rapid and effective dissemination of advances, knowledge and their exploitation. This will be assumed by all DECIPHER partners at all levels of society including scientific dissemination, higher education, professional associations, SMEs (small and medium-sized enterprises) and general public. For that, the partners will develop the means for constructive and effective communication between researchers and professionals through a dedicated website and a specific committee in charge of dissemination. Thanks to this communication plan, all actors and stakeholders concerned at the local, national, and even European scale will be informed of the DECIPHER advances and exploitation potentials.


Mass and recurrent mortality events of complex etiology have increasingly affected invertebrates of ecological and/or economical interest such as honeybees, corals and oysters over the past years. The main oyster species exploited in France and worldwide, Crassostrea gigas, is no exception to this rule. It suffers from devastating summer mortality outbreaks, whose severity has dramatically increased since 2008. It particularly affects juvenile stages throughout France decimating up to 90 % of spats in some farms, resulting in significant economic losses. This phenomenon is due to a combination of direct and indirect factors. Among indirect factors, the intensification of the production, worldwide transport of animals, anthropogenic impacts or climate change in coastal areas have been suspected to weaken the animals and increase the frequency of outbreaks thus contributing to the emergence of the phenomenon. In addition, a series of research projects have evidenced several factors involved the expression of the disease and have underscored the complexity of the pathosystem brought into play: (i) the disease depends on the temperature of the seawater potentially modifying both host physiology (reproductive capacities, health) and composition/function of its associated microbiota (including pathogen virulence); (ii) the susceptibility of oysters to potential pathogens (herpes viruses, bacteria such as Vibrio splendidus, V. aestuarianus, …) depends on the genetics of oysters; (iii) a species/strain of a single microorganism is not sufficient to cause disease suggesting that microorganisms cooperate to initiate pathogenesis; (iv) different dynamics of oyster mortalities are observed according to the production sites. All these data taken together suggest that abiotic factors, human activities, oyster genetics, their life history, their immune status and of course, the pathogens are involved and might influence each other. However, the relative weight of these factors, their interaction patterns, their dynamics during pathogenesis are largely unknown, which makes the disease difficult to understand, predict and control.
To open a way out of this unprecedented crisis and find solutions for a sustainable oyster aquaculture, it is necessary to decipher this complex pathosystem. This is the aim of the DECIPHER project. To achieve this ambitious goal, DECIPHER proposes an integrated multidisciplinary research program in an attempt to link together different levels of understanding of the disease. It will focus on the dynamic study of the "oyster holobiont" (oyster and associated microbiota, including pathogens) and will integrate in a global picture the genetic background of the host, changes in the environment and the history of interactions between the protagonists of this pathosystem and the emergence of the disease.
This ambitious goal is now feasible thanks to recent scientific and technical breakthroughs that the consortium of scientists gathered in this project proposes to use and implement. DECIPHER should bring (i) a clear answer to the question of summer mortalities affecting oyster and (ii) solutions to improve the eco-efficiency of oyster culture and contribute to the sustainability of this industry.

Project coordinator

Monsieur Guillaume Mitta (Ecologie et évolution des interactions)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


UMR 6539 Laboratoire des sciences de l'environnement marin
UMR 8621 Institut de Génétique et Microbiologie
UMR5244 Ecologie et évolution des interactions
UMR 5119 Ecologie des systémes marins cotiers

Help of the ANR 793,891 euros
Beginning and duration of the scientific project: October 2014 - 48 Months

Useful links

Explorez notre base de projets financés



ANR makes available its datasets on funded projects, click here to find more.

Sign up for the latest news:
Subscribe to our newsletter