Biology subjects

Degremont, L.

Publications and source records attributed to Degremont, L..

12 recordsLinked to original sources

bioRxiv2025

Multi-Omics Reprogramming Drives a Counterintuitive Reversal of Disease Susceptibility During Ageing

Ageing is a progressive and irreversible biological process characterized by the deterioration of physiological functions and increased vulnerability to mortality. Although extensively studied in vertebrates, ageing in long-lived invertebrates remains comparatively unexplored. While ageing typically leads to greater susceptibility to infectious diseases, a striking and unexpected reversal was identified in oysters: older oysters exhibit markedly increased tolerance to the Pacific Oyster Mortality Syndrome (POMS), a panzootic disease primarily driven by the OsHV-1 herpesvirus and responsible for severe losses in global aquaculture. To investigate this counterintuitive pattern, we challenged oysters aged 4, 16, and 28 months from four biparental families and conducted an integrative multi-omics analysis, including epigenomics, transcriptomics, and metabolomics on the two families showing the strongest age-related increase in survival. Our results reveal that ageing in Magallana gigas is characterized by coordinated epigenetic, transcriptional, and metabolic reprogramming that reduces host permissiveness to POMS. We show that the epigenetic remodeling of key immune regulators (e.g., Toll-like receptors, MyD88) aligns with transcriptional rewiring of NF-{kappa}B and ubiquitin pathways, producing a finely tuned innate immune state marked by enhanced antiviral activity but reduced antibacterial responsiveness. We also identify age-related repression of mTOR signaling, likely promoting autophagy and improving viral control. These regulatory changes are tightly linked to metabolic adjustments, including reduced TCA cycle flux, remodeled nitrogen metabolism, and altered glutathione dynamics, which collectively support a stress-tolerant, energy-conserving phenotype. Together, our findings reveal a fundamental evolutionary trade-off: juveniles prioritize growth at the cost of viral susceptibility, whereas adults invest in cellular maintenance and antiviral preparedness.

genomics↗

bioRxiv2025

Dynamic of the transcriptomic landscape of OsHV-1 replication in haemocytes of Pacific oyster

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. IMPORTANCEThis 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.

bioinformatics↗

bioRxiv2025

Bacteria with antibacterial activities isolated from Magallana gigas microbiota as potential probiotics against Vibrio aestuarianus infections in oyster farming

IntroductionOyster farming is a significant industry worldwide, but it is threatened by various diseases such as Pacific Oyster Mortality Syndrome or vibriosis. V. aestuarianus is a major cause 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. ResultsOur 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. ConclusionOur 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.

microbiology↗

bioRxiv2025

Experimentally mimicking 30 years of Magallana gigas infections with the OsHV-1 virus reveals evolution through positive selection

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 also been associated with mortality events in various other host species. Despite progress in understanding OsHV-1 epidemiology, important knowledge gaps remain regarding its evolutionary mechanisms and adaptation to host genetic backgrounds. This study uses experimental evolution and extensive genomic analysis to investigate the dynamics of OsHV-1 evolution in response to oyster host genetic variation. Our results show that genetic mutations, particularly transitions and transversions, play a key role in shaping viral populations, contributing to a trend toward genetic homogenization. Notably, stronger positive selection signals were observed in viral genomes isolated from oyster populations 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.

evolutionary biology↗

bioRxiv2024

Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues

2Since 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 HWM 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. 3 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.

genomics↗

bioRxiv2024

Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas

BackgroundRecently, the frequency and severity of marine diseases have increased in association with global changes, and molluscs of economic interest are particularly concerned. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. Various strategies such as genetic selection or immune priming have been developed to fight some of these infectious diseases. The microbial education, which consist 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. ResultsWe 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 the 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. We further show that the added bacteria were not maintained in the oyster microbiota after the exposure, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. ConclusionOur study reveals successful immune system education of oysters by introducing beneficial micro-organisms 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.

microbiology↗

bioRxiv2023

Antiviral protection in the Pacific oyster Crassostrea (Magallana) gigas against OsHV-1 infection using UV-inactivated virus

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.

immunology↗

bioRxiv2023

Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas) to Pacific Oyster Mortality Syndrome (POMS)

Disease emergence is accelerating in response to human activity-induced global changes. Understanding the mechanisms by which host populations can rapidly adapt to this threat will be crucial for developing future management practices. Pacific Oyster Mortality Syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations (Crassostrea gigas). Rapid adaptation to this disease may arise through both genetic and epigenetic mechanisms. In this study, we used a combination of whole exome capture of bisulfite-converted DNA, next-generation sequencing, and (epi)genome-wide association mapping, to show that natural oyster populations differentially exposed to POMS displayed signatures of selection both in their genome (single nucleotide polymorphisms) and epigenome (CG-context DNA methylation). Consistent with higher resistance to POMS, the genes targeted by genetic and epigenetic variations were mainly related to host immunity. By combining correlation analyses, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of the observed phenotypic variation was explained by interactions between the genetic sequence and epigenetic information, [~]14% by the genetic sequence, and up to 25% by the epigenome alone. Thus, as well as genetic adaptation, epigenetic mechanisms governing immune responses contribute significantly to the rapid adaptation of hosts to emerging infectious diseases.

evolutionary biology↗

bioRxiv2023

Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus

Polymicrobial diseases significantly impact the health of humans and animals but remain understudied in natural systems. We recently described the Pacific Oyster Mortality Syndrome (POMS), a polymicrobial disease that impacts oyster production and is prevalent worldwide. Analysis of POMS-infected oysters on the French North Atlantic coast revealed that the disease involves co-infection with the endemic ostreid herpesvirus 1 (OsHV-1) and virulent bacterial species such as Vibrio crassostreae. However, it is unknown whether consistent Vibrio populations are associated with POMS in different regions, how Vibrio contribute to POMS, and how they interact with the OsHV-1 virus during pathogenesis. We resolved the Vibrio population structure in oysters from a Mediterranean ecosystem and investigated their functions in POMS development. We find that Vibrio harveyi and Vibrio rotiferianus are the predominant species found in OsHV-1-diseased oysters and show that OsHV-1 is necessary to reproduce the partition of the Vibrio community observed in the field. By characterizing the interspecific interactions between OsHV-1, V. harveyi and V. rotiferianus, we find that only V. harveyi synergizes with OsHV-1. When co-infected, OsHV-1 and V. harveyi behave cooperatively by promoting mutual growth and accelerating oyster death. V. harveyi showed high virulence potential in oysters and dampened host cellular defenses, making oysters a more favorable niche for microbe colonization. We next investigated the interactions underlying the co-occurrence of diverse Vibrio species in diseased oysters. We found that V. harveyi harbors genes responsible for the biosynthesis and uptake of a key siderophore called vibrioferrin. This important resource promotes the growth of V. rotiferianus, a cheater that efficiently colonizes oysters during POMS without costly investment in host manipulation nor metabolite sharing. By connecting field-based approaches, laboratory infection assays and functional genomics, we have uncovered a web of interdependencies that shape the structure and function of the POMS pathobiota. We showed that cooperative behaviors contribute to synergy between bacterial and viral co-infecting partners. Additional cheating behaviors further shape the polymicrobial consortium. Controlling such behaviors or countering their effects opens new avenues for mitigating polymicrobial diseases.

microbiology↗

bioRxiv2022

Emergence and clonal expansion in Europe of Vibrio aestuarianus lineages pathogenic for oysters

Crassostrea gigas oysters represent a significant global food source, with 4.7 million tons harvested per year. In 2001, the bacterium V. aesturianus francensis emerged as a pathogen that causes adult oyster mortality in France and Ireland. Its impact on oyster aquaculture has increased in Europe since its reemergence in 2012. To better understand the evolutionary mechanisms leading to the emergence and persistence over time of this pathogen, we conducted a survey of mollusk diseases through national reference laboratories (NRLs) across Europe. We analyzed 54 new genomes of V. aestuarianus (Va) isolated from multiple environmental compartments since 2001, in areas with and without bivalve mortalities. We used a combination of comparative genomics and population genetics approaches to show that Va francensis lineages have undergone clonal expansion in Europe, likely after a recent selective bottleneck. Low mutation and recombination rates may have selected particular virulent genotypes. Furthermore, we identified a specific cus-cop-containing island conferring copper resistance to Va francensis whose acquisition may have favored the emergence of pathogenic lineages adapted to oysters.

microbiology↗

bioRxiv2020

A core of functionally complementary bacteria colonizes oysters in Pacific Oyster Mortality Syndrome.

BackgroundThe Pacific oyster Crassostrea gigas is one of the main cultivated invertebrate species worldwide. Since 2008, oyster juveniles have been confronted with a lethal syndrome known as the Pacific Oyster Mortality Syndrome (POMS). POMS is a polymicrobial disease initiated by a primary infection with the herpesvirus OsHV-1 Var that creates an oyster immunocompromised state and evolves towards a secondary fatal bacteremia. In the present article, we describe the implementation of an unprecedented combination of metabarcoding and metatranscriptomic approaches to show that the sequence of events in POMS pathogenesis is conserved across infectious environments. We also identified a core bacterial consortium which, together with OsHV-1 Var, forms the POMS pathobiota. This bacterial consortium is characterized by high transcriptional activities and complementary metabolic functions to exploit hosts resources. A significant metabolic specificity was highlighted at the bacterial genus level, suggesting low competition for nutrients between members of the core bacteria. Lack of metabolic competition might favor complementary colonization of host tissues and contribute to the conservation of the POMS pathobiota across distinct infectious environments.

microbiology↗

bioRxiv2018

Analysis of genome-wide differentiation between native and introduced populations of the cupped oysters Crassostrea gigas and Crassostrea angulata

The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and C. angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and morphologic similarity. In particular, whether ecological and/or intrinsic isolating mechanisms participate to species divergence remains unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation maintains under new environmental and demographic conditions. We generated a pseudo-chromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.

evolutionary biology↗