Coinfection by multiple pathogens is common in aquaculture. Since 2012, Pacific oysters in Europe have been affected by two main pathogens, with additive or cooperative pathogenicity: the ostreid herpes virus type 1 (OsHV-1) and bacterium Vibrio aestuarianus. In oysters, genetic improvement by selective breeding is effective in mitigating diseases caused by single pathogens, but little is known about resistance to coinfections. This study aimed to investigate the genetic parameters and genomic architecture of disease resistance in C. gigas by comparing experimental infections made with each of the two pathogens, as well as coinfection with both. One hundred families were produced using parents from three origins: two wild populations experiencing different pathogen pressures and oysters experimentally selected for their higher resistance to OsHV-1 and V. aestuarianus infections. The experimental infections were carried out on 7-month old juveniles, leading to survival rates of 52%, 55% and 43%, for the bacterial, the viral and dual infection, respectively. Individuals were genotyped using a 57 k SNP array. Survival varied widely among families and parental origins. Heritability estimates for survival ranged from 0.20 to 0.50 for the three infections, and genetic correlations were low between V. aestuarianus and the two other experimental infections, but very high between OsHV-1 and coinfection. Genome-wide association study revealed a polygenic architecture for all traits. However, five quantitative trait loci (QTLs) were detected in the OsHV-1 treatment as well as for coinfection with one specific genomic region on linkage group 6 being related to higher survival. Prediction accuracy was higher using a genomic model than a pedigree-based model, particularly for OsHV-1 and coinfection, for which larger numbers of individuals were genotyped. Our results suggest that (1) geographic origin of oysters should be considered when establishing a breeding program for improved survival; (2) use of genomic selection (GS) and QTL mapping may lead to more efficient selection and faster genetic gain; and (3) the coinfection challenge used in this study, which is likely to be closer to field conditions than the other treatments, is practical and may be suitable for breeding programs. Our findings represent a significant step towards using genomic information to improve disease resistance in selective breeding programs for the Pacific oyster, and possibly other aquaculture species.

The ostreid herpesvirus type 1 (OsHV-1) is a major pathogen of the Pacific oyster (Magallana gigas), causing recurrent episodes of spat mortality worldwide. While OsHV-1 replication and associated outbreaks occur at moderate seawater temperatures (16–22 °C), the virus becomes largely undetectable during colder months, raising the question of how it persists between epidemic episodes. In this study, we investigated the potential of Pacific oyster spat to act as reservoirs of OsHV-1. Our approach combined two-year field monitoring in a major French production area (Marennes-Oléron Bay, France) with controlled cohabitation assays, molecular detection by qPCR and ultra-deep DNA/RNA sequencing. Our results show that OsHV-1 can persist in asymptomatic spat at seawater temperatures below 13°C, and that a transition to a lytic phase is observed once temperatures rise and remain above 16°C. Sequencing analyses confirmed the presence of viral genomic fragments but revealed extremely limited transcriptional activity. These findings support the hypothesis that OsHV-1 adopts a latent-like state in Pacific oyster spat, characterized by the persistence of a non-integrated viral genome, although definitive evidence remains lacking. They further suggest that early cohorts may play a key role in this process. They also emphasise the necessity of targeted molecular approaches to fully elucidate the mechanisms underlying herpesvirus persistence in marine invertebrates.

Aging is a progressive and irreversible biological process that typically increases susceptibility to infectious diseases. However, unexpectedly, the opposite outcome was observed in oysters: older oysters exhibit increased tolerance to Pacific oyster mortality syndrome (POMS), a panzootic disease responsible for severe losses worldwide. We investigated this pattern by challenging four biparental families of oysters aged 4, 16, and 28 months. We conducted an integrative multiomics analysis, which included epigenomics, transcriptomics, and metabolomics, on the two families that exhibited the greatest age-related increase in survival. Our results reveal that aging is characterized by coordinated epigenetic, transcriptional, and metabolic reprogramming that reduces host permissiveness to POMS. We show that the epigenetic remodeling of immune regulators (e.g., toll-like receptors and myeloid differentiation primary response 88; MyD88) aligns with the transcriptional rewiring of the nuclear factor-kappa B (NF-κB) and ubiquitin pathways, producing a tuned state with enhanced antiviral activity. We also identify age-related repression of mechanistic target of rapamycin (mTOR) signaling, which likely promotes autophagy and enhances viral control. These changes are tightly linked to metabolic adjustments, including reduced activity of the tricarboxylic acid cycle (TCA), altered nitrogen metabolism, and altered glutathione dynamics, supporting a stress-tolerant, energy-conserving phenotype. Together, our findings reveal juveniles prioritize growth at the cost of viral susceptibility, whereas adults invest in cellular maintenance and antiviral preparedness.

Over the past few years, methodological advances have driven major progress in epidemiological modelling tools, improving our ability to understand pathogen dynamics and inform management strategies. However, these powerful approaches remain underused in marine mollusc health, despite their well-recognized potential to assess the impact of pathogens that threaten the long-term viability of the industry. This is notably the case for Ostreid herpesvirus type 1 (OsHV-1), a virus associated with recurrent mass mortalities of Pacific oyster spat worldwide. These recurring outbreaks underscore important gaps in our understanding of its transmission dynamics and the strategies required to mitigate epizootic events. To bridge this gap, we developed a stochastic compartmental epidemiological model that extends the classical SEIR framework by incorporating an environmental viral compartment and distinguishing between oysters that survive infection and those that succumb to it. Model parameters were estimated using targeted experimental data and integrated into stochastic simulations, enabling the model to reproduce the overall dynamics of the observed mortality kinetics and thereby supporting its validity. Remaining discrepancies were then addressed using an Approximate Bayesian Computation approach to refine parameter estimates and improve model accuracy. Additionally, sensitivity analysis identified viral shedding rates as the main drivers of epidemic dynamics. Through this integrative framework, we provide new insights into OsHV-1 transmission patterns and establish a foundation for future spatial modelling aimed at supporting disease management in oyster farming.

Abstract The order Herpesvirales comprises double-stranded DNA viruses characterized by substantial genomic plasticity, including recombination, structural variation, gene gain and loss, and lineage turnover. These processes can obscure phylogenetic relationships and complicate the reconstruction of viral evolutionary histories. Within this order, Ostreid herpesvirus 1 (OsHV-1) is a major pathogen of the Pacific oyster Magallana gigas and is responsible for recurrent mortality events affecting global aquaculture. Early molecular investigations based on partial genomic regions identified several viral lineages, including the “var” and “µVar” lineages, but provided limited resolution for genome-wide evolutionary inference. The subsequent availability of complete genomes revealed extensive structural variation, such as insertions, deletions, and genomic rearrangements, highlighting the high genomic plasticity of OsHV-1. Although phylogenomic analyses have estimated evolutionary rates compatible with other large double-stranded DNA viruses, current inferences remain based on geographically restricted datasets, leaving the global evolutionary dynamics of OsHV-1 within its principal host insufficiently resolved. Here, we present 275 newly sequenced OsHV-1 genomes collected from infected M. gigas oysters between 1994 and 2022 across major oyster-producing regions worldwide. Using de novo genome assembly combined with comparative genomics, population genetic analyses, and time-scaled phylogenetic reconstruction, we investigate global genomic diversity and the spatio-temporal dynamics of viral diversification. Our results reveal long-standing viral diversity in East Asia, the emergence of structurally distinct Pacific and microvariants lineages, and ongoing diversification shaped by recombination, structural genome plasticity, and anthropogenic oyster movements. By integrating three decades of whole-genome data, this study provides a phylogenomic framework for understanding the diversity, evolution, and dispersal of OsHV-1 in modern aquaculture systems.

Since the 1990s, the Pacific oyster Magallana gigas has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole-genome analysis. Identification of the best method for extraction of high molecular weight (HMW) DNA and development of accurate bioinformatic pipelines for its characterization are now required. To this end, we evaluated and compared six HMW methods and one conventional DNA extraction kit for their ability to extract OsHV-1 DNA from M. gigas-infected tissues. We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole-genome and "adaptive sampling" (AS) sequencing approaches. Finally, we evaluated the efficiency of bioinformatics tools for de novo assembly and consensus calling to generate accurate OsHV-1 genomes. The HMW DNA extraction kit coupled with ONT sequencing and dedicated bioinformatics tools allowed us to produce accurate OsHV-1 genomes compared to those assembled using Illumina technology. The AS approach allowed up to 60% enrichment for viral data, and the long reads generated by ONT allowed the characterization of OsHV-1 isomers. Together with its portability, this sequencing shows great promise as a diagnostic tool for the characterization of unculturable aquatic viruses directly from host tissues.IMPORTANCEMany aquatic viruses threaten commercially valuable species and cause significant economic losses during outbreaks. To improve our understanding of the origin, transmission patterns and spread of these viruses, additional genomic data are essential. However, genomic characterization of unculturable large DNA viruses is a major challenge. In the present study, we have successfully evaluated the ability of ONT sequencing and adaptive sequencing (AS) to sequence and assemble the complete OsHV-1 genome. Our results show that it is now possible to sequence the whole genome of large DNA viruses directly from infected host tissue, without the need for prior in vitro propagation or prior laboratory steps for virus enrichment.

Pacific oysters face recurring outbreaks of Pacific Oyster Mortality Syndrome (POMS), a polymicrobial multifactorial disease. Although this interaction is increasingly understood, the role of epigenetics (e.g., DNA methylation) appears to be of fundamental importance because of its ability to shape oyster resistance/susceptibility and respond to environmental triggers, including infections. In this context, we comprehensively characterized basal (no infection) and POMS-induced changes in the methylome of resistant and susceptible oysters, focusing on the gills and mantle. Our analysis identified differentially methylated regions (DMRs) that revealed distinct methylation patterns uniquely associated with the susceptible or resistant phenotypes in each tissue. Enrichment analysis of genes bearing DMRs highlighted that these epigenetic changes were specifically linked to immunity, signaling, metabolism, and transport. Notably, 31 genes with well-known immune functions were differentially methylated after POMS, with contrasting methylation patterns between the phenotypes. Based on the methylome differences between phenotypes, we identified a set of candidate epibiomarkers that could characterize whether an oyster is resistant or susceptible (1998 candidates) and whether a site has been exposed to POMS (164 candidates). Overall, the findings provide a deeper understanding of the molecular interactions between oysters and POMS infection, opening new questions about the broader implications of epigenetic mechanisms in host-pathogen dynamics and offering promising strategies for mitigating the impacts of this devastating disease. Beyond its biological aspects, this study provides insights into potential epigenetic biomarkers for POMS disease management and targets for enhancing oyster health and productivity.

Climate change and rising temperatures are frequently cited as key factors in the emergence of diseases. While the increase in temperature can alter host immunity, influence pathogen virulence, and change the geographic distribution of vectors and their associated pathogens, few studies have investigated the impact of temperature variations on the molecular mechanisms controlling disease permissiveness. The present study addresses this question on a panzootic and polymicrobial disease, the Pacific Oyster Mortality Syndrome (POMS). POMS, initiated by the herpesvirus OsHV-1 μVar, affects juveniles of Magallana gigas, which is the most widely cultured oyster species in the world. In our study, two full-sib families were exposed to the disease under permissive (23 °C) and non-permissive (30 °C) conditions. Using an integrative multi-omics approach, we demonstrate that high temperature has a dual effect on oysters (1) inducing a metabolic reprogramming, creating a sub-optimal metabolic environment for viral infection and thereby limiting POMS development, and (2) enhancing the host's antiviral immune capabilities, both at a baseline level and in response to infection. Overall, these responses triggered at elevated temperature improve oyster survival against POMS. Our study showed that temperature exerts complex effects on host-pathogen interactions; and molecular-level mechanistic approaches are crucial to thoroughly understand and accurately assess how temperature changes can influence epidemiological risk.

Herpesviruses are double-stranded DNA viruses with distinct morphological features and are among the largest and most complex viruses. According to the International Committee on Taxonomy of Viruses (ICTV), in 2022, there were 133 herpesviruses classified into three families: Orthoherpesviridae, infecting mammals and birds; Malacoherpesviridae infecting marine molluscs; and Alloherpesviridae infecting fish and amphibians. Herpesviruses have a complex genomic architecture, characterised by unique regions flanked by repeated and inverted sequences. Unique regions can undergo rearrangements leading to the formation of genomic isomers, which could have important implications for the life cycle of the virus. Herpesviruses life cycle consists of two main phases: the lytic phase, during which viral genes are expressed and translated into viral proteins that regulate DNA replication, capsid formation and the production of new particles; and the persistence phase, in which the virus persists in the host without being eliminated by the immune system. This review offers an updated and comprehensive overview of the Herpesvirales order, detailing their morphological characteristics, providing an in-depth taxonomic classification, examining their genomic architecture and isomers, and describing their life cycle.

Introduction: Oyster farming is a significant industry worldwide, but it is threatened by various diseases such as Pacific Oyster Mortality Syndrome and vibriosis. V. aestuarianus is one of the major causes of mortality for market-size oysters, resulting in significant economic losses for oyster farmers. Among the various control methods developed, probiotics appear to be a promising approach. More specifically, the use of the antibacterial activity of bacteria from the natural microbiota of the oyster Magallana gigas appears to be a sustainable solution against V. aestuarianus infections. Results: Our study investigated the probiotic potential of bacteria isolated from the microbiota of M. gigas oysters. We screened a collection of 334 bacteria against eight target pathogens, including V. aestuarianus, and identified 78 bacteria with antibacterial activity for which eight retained this activity in their culture supernatants. Five strains were selected for further testing and exposed to oysters prior to V. aestuarianus infection. Our results show that four strains significantly reduced oyster mortality, with a maximum reduction of 70 %. In addition, changes in oyster microbiota composition were observed following exposure, but the administered bacteria were not detected in the microbiota. Conclusion: Our findings demonstrate the potential of oyster microbiota-derived bacteria as probiotics for disease control in oyster farming. This approach could provide a sustainable and environmentally friendly solution for the oyster farming industry. Further research is needed to understand the underlying mechanisms and to develop effective probiotic-based strategies for preventing V. aestuarianus infection.

The role of microbiota in health and disease is most often expressed by structural shifts of the taxonomic composition of prokaryote communities in infected and healthy individuals. In cultured aquatic animals with open circulatory systems, such as mollusks, microbiota also harbor a wide range of protists, which are unicellular eukaryotes that could also play an important role during infections. To evaluate the effectiveness of eukaryotic vs. prokaryotic microbiota in characterizing infection states, we examined both microbial compartments under natural conditions in two commercially important oyster species, the flat oyster Ostrea edulis and the Pacific oyster Magallana (Crassostrea) gigas. With O. edulis being infected by two protist parasites, Marteilia refringens and Bonamia ostreae, and M. gigas being infected by the ostreid herpes virus OsHV-1, we chose iconic diseases responsible for substantial mortalities and economic damage within the two species. We analyzed and compared the structural and compositional differences between healthy and infected oysters and used random forest machine learning to classify infection states and identify indicator taxa that distinguish healthy from infected individuals. Both at the structural and compositional levels, bacterial microbiota proved to be better predictors of infection states. By eliminating noisy taxa through variable selection in the random forest models, we enhanced the compositional differences between infection states. In all host-pathogen combinations, only a few taxa (<31) were required to achieve optimal separation. While the identity of indicator taxa will partly reflect the specific environmental conditions at the time of sampling, we recovered several previously described indicator taxa, such as Mycoplasma, Vibrio, Photobacterium, and Arcobacter. Next to these we also discovered new taxa like Motiliproteus that exhibited the potential to differentiate between infection states of the investigated O. edulis specimen. The simultaneous characterization of prokaryotic and eukaryotic microbiota suggests that only few prokaryotic indicator species might be needed to reliably differentiate between infected from healthy individuals and monitor infection risks.

Sequencing technologies continue to evolve, providing novel opportunities for disease surveillance and control. These advancements are crucial for diagnosing diseases and identifying genetically distinct variants with diverse host reservoir species and geographical distributions. Recent progress in sequencing-based analyses of marine mollusc diseases has been significant, yet challenges remain in data management due to a lack of dedicated tools and databases. To address this, we present MoPSeq-DB (Mollusc Pathogen Sequences DataBase), an open-source web application for managing curated genomic data on mollusc pathogens. Designed for accessibility to non-bioinformaticians, MoPSeq-DB features interactive data visualization and integrated analysis tools. Built with the Python Django framework, it automates common bioinformatics workflows, enabling rapid exploration of sequencing data. The application has minimal hardware requirements, and is easy to install, host, and update. MoPSeq-DB facilitates systematic storage and flexible management of genomic data and metadata, improving data organization for mollusc pathogen research. Although developed with a focus on mollusc pathogens, the platform's adaptable design makes it a valuable resource for studying a wide range of pathogens. Database URL: https://mopseq-db.ifremer.fr.

Understanding how pathogens adapt to new hosts is critical to elucidating the evolutionary mechanisms driving disease emergence. This study investigates the evolutionary dynamics of Ostreid herpesvirus 1 (OsHV-1) in two host species-the Pacific oyster Magallana gigas and the European flat oyster Ostrea edulis-to address the question of host specificity and cross-species transmission. While OsHV-1 is primarily associated with mortality in M. gigas, its detection in O. edulis raises concerns about its potential host range and evolutionary trajectory. We aimed to determine whether viral populations in these two hosts show genetic differentiation and to identify the evolutionary forces shaping this divergence. Using high-throughput sequencing, we assembled 40 OsHV-1 genomes from both oyster species and applied comparative genomics, population genetics, and phylodynamic approaches. Our results show that host species significantly influence viral genetic structure, with two distinct lineages emerging after a cross-species transmission event likely following the introduction of M. gigas into Europe. Selection signals were detected in viral genes related to host interaction, replication, and membrane-associated functions, suggesting host-driven adaptation. These findings underscore the importance of host-specific evolutionary pressures in shaping viral diversity and provide a framework for future studies on host-virus coevolution in marine ecosystems.

Variation in food availability can shape host susceptibility and pathogen virulence, thereby impacting disease outcomes. An ad libitum diet may enhance host physiology and immunity but it can also favor pathogen proliferation. Here, we investigated how food availability (ad libitum vs. starvation) affects interactions between the oyster Magallana gigas and the herpesvirus OsHV-1 μVar initiating the panzootic Pacific Oyster Mortality Syndrome (POMS). We found that starvation reduced oyster susceptibility to POMS. Through a comparative integrative-omics approach, we showed that (1) starvation induces metabolic rate depression, which may limit viral replication by reducing the availability of cellular energy that viruses can hijack, and (2) enhances autophagy and antiviral responses, thereby improving viral control. These results underscore the importance of nutritional status in shaping viral disease outcomes and may inform management strategies in aquaculture systems.

Since the 1990s, the Pacific oyster ( Magallana gigas ) has experienced repeated mortality events associated with Ostreid herpesvirus 1 (OsHV-1). Although the virus has been genomically characterised, its replication cycle and its interactions with the oyster immune system are still not well understood. In particular, little is known about the dynamics of OsHV-1 gene expression and the immune responses of haemocytes from oysters with varying susceptibility to the virus. While some studies have focused on the expression of specific viral and host genes on whole oysters, none have provided a comprehensive analysis of genomes-wide expression across multiple post-infection time points in haemocytes. The lack of oyster cell lines makes studying virus-host interactions in vitro challenging. However, haemocytes, the key immune cells circulating in hemolymph, can be maintained in vitro in the short term and represent a relevant model for analyzing infection dynamics. In this study, haemocytes from two M. gigas families, one highly susceptible and one less susceptible to OsHV-1, were infected in vitro . We tracked the viral and host transcriptomes over a 24-hour period post-infection using high-throughput dual transcriptomics. Our results provide a detailed overview of the OsHV-1 transcriptomic landscape in haemocytes from high and low susceptible M. gigas over time. In addition, WGCNA analysis of host genes expression provided insights into the haemocytes response to infection, and highlighted family-specific immune responses. This comprehensive transcriptomic study is the first to describe virus-host interactions across multiple stages of infection in haemocytes from Pacific oysters showing contrasted survival when exposed to OsHV-1. IMPORTANCE This study provides valuable insights into the interaction between M. gigas and OsHV-1 by analyzing viral expression and host immune response at the cellular level. By focusing on haemocytes, the key immune cells in Pacific oysters, the results reveal a link between host genotype and viral transcriptomic activity, providing new perspectives on molecular basis of natural susceptibility levels to OsHV-1 infection depending of the genetic background. Overall, our findings deepen the understanding of OsHV-1 gene expression dynamics and antiviral defense mechanisms in key species cultivated worldwide.

Since the 1990s, the Pacific oyster (Magallana gigas) has experienced repeated mortality events associated with Ostreid herpesvirus 1 (OsHV-1). Although the virus has been genomically characterised, its replication cycle and its interactions with the oyster immune system are still not well understood. In particular, little is known about the dynamics of OsHV-1 gene expression and the immune responses of haemocytes from oysters with varying susceptibility to the virus. While some studies have focused on the expression of specific viral and host genes in whole oysters, none have provided a comprehensive analysis of genome-wide expression across multiple post-infection time points in haemocytes.The lack of oyster cell lines makes studying virus-host interactions in vitro challenging. However, haemocytes, the key immune cells circulating in haemolymph, can be maintained in vitro in the short term and represent a relevant model for analysing infection dynamics. In this study, haemocytes from two M. gigas batches, one highly susceptible and one less susceptible to OsHV-1, were infected in vitro. We tracked the viral and host transcriptomes over a 24-h period post-infection using high-throughput dual transcriptomics.Our results provide a detailed overview of the OsHV-1 transcriptomic landscape in haemocytes from high- and low-susceptible M. gigas over time. In addition, weighted correlation network analysis of host gene expression provided insights into the haemocytes' response to infection and highlighted batch-specific immune responses. This comprehensive transcriptomic study is the first to describe virus-host interactions across multiple stages of infection in haemocytes from Pacific oysters, showing contrasted survival when exposed to OsHV-1.

Ostreid herpesvirus 1 (OsHV-1) poses a significant threat to the global oyster farming industry, causing substantial economic losses due to mortality outbreaks. While OsHV-1 primarily affects the Pacific oyster Magallana gigas, it has been linked to mortality events in various host species. Despite advancements in understanding OsHV-1 epidemiology, knowledge gaps persist regarding its evolutionary mechanisms and adaptation to host genetic backgrounds. This study employs experimental evolution and extensive genomic analysis to unravel the dynamics of OsHV-1 evolution in response to oyster host genetic variation. Our results show that genetic mutations, particularly transitions and transversions, played a significant role in shaping the viral population, leading to a trend toward genetic homogenization. Stronger positive selection signals were observed in the oyster population with higher susceptibility, suggesting adaptation of viral genotypes to specific host genetic backgrounds. These findings shed light on the complex evolutionary dynamics of OsHV-1 and its interactions with oyster hosts. Understanding how this virus adapts to host genetic diversity is crucial for developing strategies to mitigate its impact on the oyster farming industry and provides valuable insights into the broader mechanisms of viral evolution in response to host variation. ### Competing Interest Statement The authors have declared no competing interest.

The increase of the frequency and severity of marine diseases affecting farmed marine mollusks are currently threatening the sustainability of this aquaculture sector, with few available prophylactic or therapeutic solutions. Recent advances have shown that the innate immune system of invertebrates can develop memory mechanisms allowing for efficient protection against pathogens. These properties have been called innate immune memory, immune priming or trained immunity. Previous results demonstrated the possibility to elicit antiviral immune priming to protect Pacific oysters against the ostreid herpes virus 1 (OsHV-1), currently plaguing M. gigas production worldwide. Here, we demonstrate that UV-inactivated OsHV-1 is also a potent elicitor of immune priming. Previous exposure to the inactivated virus was able to efficiently protect oysters against OsHV-1, significantly increasing oyster survival. We demonstrate that this exposure blocked viral replication and was able to induce antiviral gene expression potentially involved in controlling the infection. Finally, we show that this phenomenon can persist for at least 3 months, suggesting the induction of innate immune memory mechanisms. This study unravels new ways to train the Pacific oyster immune system that could represent an opportunity to develop new prophylactic strategies to improve health and to sustain the development of marine mollusk aquaculture.

The holobiont theory expands the notion of individual multicellular organisms as a community composed of a host and all its associated microorganisms. This concept has been extensively studied in the field of aquaculture, where increasing evidence has highlighted the importance of the host associated microorganisms in species fitness. Here, we focus our review on mollusc and crustacean species in which microbiota dysbiosis has recently been described in the context of various diseases, resulting in significant economic losses. Influencing the holobiont structure through the use of probiotics is a potential strategy that could improve the fitness or the robustness of cultivated species. We discuss here the possibility of developing microbiome targeted prophylactic approaches by promoting (1) methods to identify host microbial community that fosters good health status and (2) early life microbial education to favour long-term resistance to stress or disease. This review aims to inform the aquaculture industry about potential strategies in rearing practices to mitigate diseases and economic losses. Microbial education during the early life stages enhances the robustness of cultivated species and favour a long term disease resistance. image

The increase in marine diseases, particularly in economically important mollusks, is a growing concern. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases, such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. The microbial education, which consists of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. We demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. Furthermore, the added bacteria were not maintained into the oyster microbiota, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. Our study reveals successful immune system education of oysters by introducing beneficial microorganisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture.