Biology subjects

Travers, M.-A.

Publications and source records attributed to Travers, M.-A..

6 recordsLinked to original sources

bioRxiv2025

Deciphering the pangenome of the shellfish pathogen Vibrio europaeus: Evolutionary history and functional impact of core and accessory genes in aquaculture.

Vibrio europaeus is an important pathogen in shellfish aquaculture, yet its genomic diversity and adaptive potential remain poorly understood. Here, we present the first comprehensive analysis of the V. europaeus pangenome, integrating genomic data from all strains available to the date sequenced specifically for this study. Those were isolated from different aquaculture facilities (shellfish hatcheries) associated to mass mollusks mortalities from different geographical locations, years and host species. Our findings revealed an open pangenome with the 61% of the genes associated to the accessory genome that contributes to environmental and host adaptations. Phylogenomic analyses of the core-genome (39% of the pangenome size) allowed to evaluate the evolutionary history and intraspecific diversity of V. europaeus and revealed that Spanish strains displayed a much lower genetic variability than French, Chilean or American strains, probably due to a monophyletic radiation event. Functional annotation of core and accessory genes revealed the key virulence factors of the species while it also disclosed that those are located mainly into the core genes. The high number of anti-phage defense systems encoded in the accessory genome explained almost all the variability of the species. The results provide important insights into the evolutionary history and ecological versatility of V. europaeus, with potential implications for diagnostics, epidemiological surveillance, and disease management strategies in aquaculture. Impact statementThis study presents the first comprehensive pangenome analysis of Vibrio europaeus, an emergent pathogen responsible for severe economic losses in shellfish aquaculture, the second most important sector of global aquaculture. Here, we characterized for the first time the V. europaeus pangenome, integrating genomic data from all strains isolated to date, sequenced specifically for this study using NGS and/or third-generation (PacBio) technologies. This work achieved the most complete species pangenome to date and is among the first studies on aquaculture-related bacterial pathogens. Beyond a descriptive framework, the pangenome was critically examined to identify key traits, including virulence factors, secondary metabolite biosynthesis, and antimicrobial resistance genes, essential for host infection and adaptation. Moreover, the study of anti-phage defense systems was shown to account for much of the species genomic variability. The genomic resources and insights generated here substantially expand our understanding of V. europaeus biology and provide valuable information that can be applied for diagnostics, epidemiological surveillance, and sustainable management of this pathogen in aquaculture industry. Data summaryAll genome assemblies have been uploaded to the National Center for Biotechnology Information. The GenBank accession numbers for each of the 39 strains used in this study and detailed information can be found in Table S1. All bioinformatics tools used for comparative genomics have been listed in the Methods section including references, associated databases and analysis parameters.

microbiology↗

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↗

bioRxiv2024

Vibrio are a potential source of novel colistin-resistance genes in European coastal environments

Colistin is a widespread last resort antibiotic for treatment of multidrug-resistant bacteria. The recent worldwide emergence of colistin resistance (Col-R) conferred by mcr-1 in human pathogens has raised concern, but the putative sources and reservoirs of novel mcr genes in the marine environment remain underexplored. We observed a high prevalence of Col-R, particularly in Vibrio isolated from European coastal waters by using a unique stock of specific-pathogen-free (SPF) oysters as a bioaccumulator. The high sequence diversity found in the mcr/eptA gene family was geographically structured, particularly for three novel eptA gene variants, which were restricted to the Mediterranean (France, Spain) and occurred as a dgkA-eptA operon controlled by the RstA/RstB two component system. By analyzing 29427 Vibrionaceae genome assemblies, we showed that this mechanism of intrinsic resistance is prevalent and specific to the Harveyi clade, which includes strains of Vibrio parahaemolyticus and Vibrio alginolyticus causing infections in humans. The operon conferred colistin-resistance when transferred to sensitive non-Vibrio strains. While mcr-and arn-based Col-R mechanisms were also identified, the widespread presence of eptA gene variants in Vibrio suggests they play a key role in intrinsic resistance to colistin. Beyond these ancient eptA gene copies having evolved with the Vibrio lineage, we also identified mobile eptA paralogues that have been recently transferred between and within Vibrio clades. This highlights Vibrio as a potential source of Col-R mechanisms, emphasizing the need for enhanced surveillance to prevent colistin-resistant infections in coastal areas.

microbiology↗

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

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↗