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Aquatic animals, such as fish and shellfish, provide important economic and nutritional benefits for human society. Due to overexploitation of natural fish sources through traditional wild-caught fisheries, aquaculture (generally described as fish farming or culturing) has grown into an economically important industry. A major focus area for the aquaculture field is related to sustainability by ensuring the health and welfare of the aquatic animals. Communities of microorganisms inhabiting the various niches of a given host comprise its microbiome and provide several key health benefits. The microbiome impacts nutrient acquisition, gut homeostasis, protection against pathogens, and immune system modulation. Therefore, much attention has been placed on studying how various culturing conditions and host factors impact the microbiomes of aquatic animals. Here, multiple studies were conducted to elucidate the impacts of various parameters on the microbiomes of rainbow trout, steelhead trout, and Nile tilapia, including dietary supplementation, administration of probiotics and animal age. Though there is a significant correlation between the diet fed to fish and their microbiome communities, small dietary changes such as the inclusion of a dried and lysed yeast product, acting as a protein source alternative to unsustainable fishmeal did not significantly alter the intestinal adherent microbiome of rainbow trout. Moreover, an optimal percentage of yeast replacement that did not negatively impact weight gain for the aquaculture-raised fish was identified, suggesting its efficacy for the industry. Similarly, the intestinal adherent microbiomes of steelhead trout were not significantly altered by diet supplementation with a Bacillus subtilis probiotic. The total microbiome of steelhead trout (mucosa combined with digesta) was instead significantly changed when they were only fed the probiotic additive at an early stage of intestinal development. This change in the microbiome of steelhead trout correlated with a significant increase in weight gain compared to fish only fed the probiotic during later stages of intestinal development. These findings also corroborate previous observations wherein the intestinal microbiome of fish varies during their developmental stages but then stabilizes over time. Determining the core set of bacteria present in fish microbiomes, independent of treatment variables, is another important factor when considering attempts to manipulate the microbiome. To that end, a literature review was conducted in which the phyla Firmicutes, Proteobacteria and, to a lesser extent, Actinobacteria, Bacteroides, and Tenericutes were identified as likely members of the rainbow trout core microbiome. Bacterial families identified as part of the core phyla included Lactobacilliaceae that are commonly used as probiotics and Mycoplasmataceae that lack cell walls. Preventing dysbiosis of the rainbow trout microbiomes will be crucial to ensuring the health of the fish hosts and increasing longevity and profitability of the aquaculture industry. Another important aquaculture-raised species is the Eastern oyster. This animal is critical for the ecological health of the Chesapeake Bay, and it is also an important source of revenue. A significant portion of the revenue flow is the harvest and sale of live oysters for consumption. Unfortunately, consumption of raw or undercooked oysters is the most common route of infection by the human pathogen Vibrio parahaemolyticus (VP) as oysters are a natural reservoir for VP. This bacterium is responsible for a debilitating acute gastroenteritis with potential to cause fatal septicemia. Despite efforts to mitigate infection by this CDC-reportable pathogen, cases continue to increase. The understudied host-microbe relationship between the Eastern oyster and VP has been implicated as a path to research for potential future therapeutics. A novel culturing system for oysters was created using fermentation jars within a BSL-2 ready biosafety cabinet. Using this system, the effect of harvest season was tested against the inoculation efficiency of VP. It was found that higher native Vibrio levels within the oysters were present during the summer compared to the winter. Moreover, addition of the bacteriostatic antibiotic chloramphenicol (Cm) enabled a higher inoculation efficiency by VP during both the summer and winter compared to oysters not exposed to the antibiotic. During the winter, exposure to Cm led to the highest inoculation efficiency (~100%). These findings confirm the importance of the existing microbial communities against exogenous inoculation. Therefore, a year-long study was conducted to investigate the microbiome of oysters during each season. This pan-microbiome study identified a significant impact of harvest season on the microbiome structure. An increased diversity, including higher levels of Cyanobacteriaceae, was observed during the summer. Whereas an increase in Arcobacteriaceae was observed during the winter. Bacteria that persisted throughout the year included Mycoplamataceae and Spirochaeteacae; these families may represent potential members of the Eastern oyster core microbiome. Further work is needed to study the localization patterns of VP within oysters. Such work includes further optimization of immunohistochemistry (IHC) and intracellular colonization assay methods under development here. Collectively, studies of the oyster-microbe interactions will help improve aquaculture methods and identify mitigation targets to reduce VP-related clinical infections. / Doctor of Philosophy / Fish and shellfish provide important economic and nutritional benefits for human society across the globe. Unfortunately, over-fishing of traditional sources of fish and shellfish has led to a reduced supply for world markets, even as the human population increases. Aquaculture, or fish farming, has been around for centuries, but its role in society has significantly increased in the past 50 years. It currently provides about half of fish and other aquatic products on the market today. To better maintain and increase the sustainability and profitability of this industry, more focus is being placed on the health of the fish. The microbiome is the collection of communities of microorganisms, including bacteria, fungi, and archaea, that inhabit various environments including animal hosts. The majority of this dissertation focuses on the impact of factors like diet and age on the microbiomes of aquaculture-raised animals, especially fish. Dietary changes such as the addition of dried yeast-products had a significant impact on fish health but not on the microbiome communities. However, a common probiotic, Bacillus subtilis, did significantly increase not only the growth rate of trout but it also significantly altered the total intestinal microbiome found in the feces and the intestinal mucosal layer. Moreover, it was found that early exposure of the animals to the probiotic had enhanced benefits even though the microbiome appeared to stabilize over time as the fish developed. Maintaining or improving the microbiomes of fish, paying close attention to the microbes that exist as part of a core group of bacteria always present, is vital to ensuring fish health and understanding vertebrate host-microbe relationships. Thus, an analysis of the core microbiome of trout was performed. The final set of projects within this dissertation focused on the relationship between the Eastern oyster, a mollusk native to the Chesapeake Bay, and the bacterial human pathogen Vibrio parahaemolyticus (VP). VP is the leading cause of seafood-borne acute gastroenteritis worldwide, and efforts are needed to mitigate the increasing rate of human infections. Therefore, a simple system using fermentation jars within the laboratory biosafety cabinet was designed to enable safe culture of oysters that were exposed to VP under experimentally controlled conditions. Oysters harvested during the summer naturally harbored higher amounts of native Vibrio organisms in contrast to the winter oysters that harbored much lower levels. A separate microbiome analysis revealed large shifts in the oyster microbiome between summer and winter, although some microbes were continually present. The lower levels of existing Vibrio species detected in winter oysters may have allowed for the higher efficiency of inoculation of winter animals by VP. In fact, these winter animals had Vibrio microbiomes that were completely dominated by the inoculated strain which will enable future work to observe the pattern by which VP localizes, or colonizes, the oysters. Ultimately, these efforts may lead to the development of future disease mitigation strategies against VP.

Little is known about the microbiome composition associated with peri-implantitis in developing countries. A recent study found a high prevalence of peri-implantitis in a group of Moroccan patients. We hypothesized that a distinct microbiome may be associated with this disease in Moroccan subjects, and the aim of this study was to investigate the composition of the microbiome in peri-implantitis sites and sites without peri-implantitis. The study material consisted of 35 dental patients with dental implants: 22 of these had peri-implantitis, and 13 were without peri-implantitis. Among these subjects, dental plaque samples were collected from 50 peri-implant sites as follows: in the peri-implantitis subjects, 22 samples were from peri-implantitis sites (peri-implantitis patient diseased sites) and 15 samples from sites without peri-implantitis (peri-implantitis patient control sites); and 13 samples from implants from subjects without peri-implantitis (non-peri-implantitis patient control sites). The samples were sequenced for the V1-V3 region of the 16S rRNA gene, and the resultant sequences were classified at the species level using a previously described Blastn-based algorithm. Downstream analysis of the data was performed with Phyloseq, Microbiome, Vegan and MaAsLin packages in R, using a false discovery rate (FDR) cutoff of 0.25. Fifty-six species and 30 genera were identified per sample on average. No significant differences were found between the groups in terms of species richness and alpha diversity. However, beta diversity analysis by PERMANOVA (Adonis) identified a statistically significant difference (FDR=0.024) between the peri-implantitis patient diseased sites and non-peri-implantitis patient control sites. Compared to non-peri-implantitis patient control sites, diseased but not control sites in patients with peri-implantitis showed significantly higher levels of Peptostreptococcus stomatitis and Mogibacterium spp. However, both diseased and control sites in patients with peri-implantitis had higher abundance of Olsenella uli, Atopobium spp. and Actinomyces spp. compared to non-peri-implantitis patient control sites. No differences at FDR ≤ 0.25 were found between diseased and control sites in patients with peri-implantitis, but Porphyromonas endodontalis tended to be elevated in diseased sites while Veillonella parvula tended to increase in control sites. These findings suggest a distinct dysbiotic microbiome is associated with peri-implantitis sites in Moroccan patients. / Oral Biology

Antimicrobial resistance poses a significant challenge to human health and is also a pressing One Health concern. The routine use of antibiotics as growth promoters in agricultural animals has contributed to the emergence of antibiotic resistance, which can subsequently affect human populations. Discontinuing this practice has led to a surge in infections and therapeutic antibiotic use in these animals. This increased susceptibility to infections may be linked, at least partially, to the loss of colonization resistance resulting from alterations in the microbiome. This study focuses on poultry, as the consumption of chicken meat can introduce antibiotic-resistant microbes into the human population. The overarching hypothesis for this research project is that a rationally designed consortium of microbes sourced from healthy chickens will increase colonization resistance and decrease susceptibility to infections as an alternative to growth-promoting antibiotics. The first goal was to analyze the broiler chicken’s gut microbiome and to establish a comprehensive culture collection of microorganisms from healthy chickens. Culture-enriched and culture-independent 16S sequencing was applied to assess the cultivability of the samples and to analyze their microbial profiles. Isolates were identified using MALDI-TOF and 16S rRNA gene sequencing. Frozen samples (from antibiotic-free farms) had a greater microbial diversity than fresh samples (from a university research facility). However, a greater proportion of the microbiome was recovered by culture from the fresh compared to the frozen samples. A strain collection of 1121 isolates representing 121 species was constructed. In Aim 2, I carried out a functional screen to identify isolates from the culture collection that inhibited the growth of the predominant poultry pathogens, E. coli and C. perfringens. Several isolates were identified that inhibited one or the other pathogens and a small number of isolates killed both pathogens. These microbes form the basis of therapeutic consortia to increase colonization resistance in chickens. / Thesis / Master of Science (MSc) / In the poultry industry, antibiotics have been used to promote chicken’s growth. This has contributed to the spread of antibiotic resistance to animal/human pathogens. When the use of growth-promoting antibiotics is stopped, the chickens become more susceptible to infections. These chickens have possibly lost protective bacteria that help fight pathogens. I thought that bacteria from healthy chicken’s intestine could help fight pathogens. To do this, I isolated a large collection of chicken gut’s good bacteria from healthy birds after individually separating them from the mixture using growing methods and sequencing. I separated bacteria from frozen and fresh mixtures, found that more bacteria grow from fresh mixtures. I then tested individual bacteria from this collection to see if they stop pathogenic bacteria like E. coli and C. perfringens from growing. I found that many bacteria could do this which may be used to develop a therapeutic community of good bugs to colonize chickens to make them more disease resistant.

Disertacijos darbo tikslas – aptikti ir identifikuoti Lietuvoje paplitusias fitoplazmas vabzdžiuose, surinktuose nuo įvairių augalų su fitoplazminiais simptomais ir nustatyti fitoplazmų vabzdžius pernešėjus bei atskleisti identifikuotų ir kitų fitoplazmų filogenetinius giminingumus. Lietuvoje jau žinomos keletas labiausiai paplitusių fitoplazmų grupių bei pogrupių, taip pat aptikta nemažai jų augalų-šeimininkų. Duomenų apie galimus šių bakterijų pernešėjus Lietuvoje beveik nėra. Pernešėjų identifikavimas ir tyrimas padės kurti veiksmingesnes strategijas bei sistemas kovai su fitoplazminėmis infekcijomis. Fitoplazmų ir jų pernešėjų identifikavimas suteiks svarbių duomenų tiriant šių patogenų ekologiją, paplitimą, kilmę, epidemiologiją, plitimo kelius. Informacija bus naudinga Lietuvos ir kaimyninių šalių augalų apsaugai. Taip pat galės padėti nustatant galimų invazinių vabzdžių rūšių bei fitoplazmų kamienų atsiradimą Lietuvoje dėl klimato kaitos. Šio darbo metu pirmą kartą Lietuvoje molekuliniais metodais buvo išaiškinti fitoplazmų vabzdžiai pernešėjai. Daugelis aptiktų fitoplazmų pogrupių nustatytos identifikotuose vabzdžiuose pirmą kartą, kaip Lietuvoje taip ir pasaulyje. Penkiose augalų rūšyse fitoplazmos aptiktos pirmą kartą Lietuvoje. Darbo metu nustatytas vienas visiškai naujas Lietuvai ir pasauliui ir vienas naujas Lietuvai fitoplazmų pogrupiai bei jų augalai šeimininkai, kas prisideda prie Lietuvoje bei pasaulyje aptinkamų fitoplazmų paplitimo ir bioįvairovės tyrimo... [toliau žr. visą tekstą] / The aim of the research was to identify the phytoplasmas detected in insects that were found on various phytoplasma-infected plants, and to reveal phytoplasma insect-vectors as well as phytogenetical relationships of identified phytoplasmas. From previous research, we already know a few mostly widespread phytoplasma groups, subgroups, and many of their host plants in Lithuania. The data on potential vectors of these bacteria are very scarce in Lithuania. The identification and research of insect vectors will help to create more effective strategies and systems to fight with phytoplasmal infections. Identification of phytoplasmas and their vectors will provide important data for research of ecology, distribution, origin, epidemiology, and ways of spreading of these pathogens. Such information is beneficial for plant protection institutions and plant growers in Lithuania and neighbouring countries. It will help to ascertain possible invasive insect species and phytoplasma strains in Lithuania. During this research for the first time in Lithuania, we determined possible phytoplasma insect vectors using molecular biology methods. Most of the detected phytoplasma subgroups were found in the identified insect species for the first time in Lithuania and worldwide. Our data on new potential insect vector species extend the spectrum of phytoplasma vectors in our region. Phytoplasmas were detected for the first time in five plant species in Lithuania. We identified in this work one... [to full text]

The aim of the research was to identify the phytoplasmas detected in insects that were found on various phytoplasma-infected plants, and to reveal phytoplasma insect-vectors as well as phytogenetical relationships of identified phytoplasmas. From previous research, we already know a few mostly widespread phytoplasma groups, subgroups, and many of their host plants in Lithuania. The data on potential vectors of these bacteria are very scarce in Lithuania. The identification and research of insect vectors will help to create more effective strategies and systems to fight with phytoplasmal infections. Identification of phytoplasmas and their vectors will provide important data for research of ecology, distribution, origin, epidemiology, and ways of spreading of these pathogens. Such information is beneficial for plant protection institutions and plant growers in Lithuania and neighbouring countries. It will help to ascertain possible invasive insect species and phytoplasma strains in Lithuania. During this research for the first time in Lithuania, we determined possible phytoplasma insect vectors using molecular biology methods. Most of the detected phytoplasma subgroups were found in the identified insect species for the first time in Lithuania and worldwide. Our data on new potential insect vector species extend the spectrum of phytoplasma vectors in our region. Phytoplasmas were detected for the first time in five plant species in Lithuania. We identified in this work one... [to full text] / Disertacijos darbo tikslas – aptikti ir identifikuoti Lietuvoje paplitusias fitoplazmas vabzdžiuose, surinktuose nuo įvairių augalų su fitoplazminiais simptomais ir nustatyti fitoplazmų vabzdžius pernešėjus bei atskleisti identifikuotų ir kitų fitoplazmų filogenetinius giminingumus. Lietuvoje jau žinomos keletas labiausiai paplitusių fitoplazmų grupių bei pogrupių, taip pat aptikta nemažai jų augalų-šeimininkų. Duomenų apie galimus šių bakterijų pernešėjus Lietuvoje beveik nėra. Pernešėjų identifikavimas ir tyrimas padės kurti veiksmingesnes strategijas bei sistemas kovai su fitoplazminėmis infekcijomis. Fitoplazmų ir jų pernešėjų identifikavimas suteiks svarbių duomenų tiriant šių patogenų ekologiją, paplitimą, kilmę, epidemiologiją, plitimo kelius. Informacija bus naudinga Lietuvos ir kaimyninių šalių augalų apsaugai. Taip pat galės padėti nustatant galimų invazinių vabzdžių rūšių bei fitoplazmų kamienų atsiradimą Lietuvoje dėl klimato kaitos. Šio darbo metu pirmą kartą Lietuvoje molekuliniais metodais buvo išaiškinti fitoplazmų vabzdžiai pernešėjai. Daugelis aptiktų fitoplazmų pogrupių nustatytos identifikotuose vabzdžiuose pirmą kartą, kaip Lietuvoje taip ir pasaulyje. Penkiose augalų rūšyse fitoplazmos aptiktos pirmą kartą Lietuvoje. Darbo metu nustatytas vienas visiškai naujas Lietuvai ir pasauliui ir vienas naujas Lietuvai fitoplazmų pogrupiai bei jų augalai šeimininkai, kas prisideda prie Lietuvoje bei pasaulyje aptinkamų fitoplazmų paplitimo ir bioįvairovės tyrimo... [toliau žr. visą tekstą]

Récemment, les microbiotes pulmonaires bactériens d’un nombre très limité de patients atteints de mucoviscidose et de pneumopathies acquises sous ventilation mécanique (PAVM) ont été étudiés en utilisant l'amplification du gène 16S rDNA bactérien suivie par la construction de librairies de clones et différentes approches de séquençage. Ces études ont montré que la population microbienne de patients atteints de maladies respiratoires était plus diversifiée que prévue. Dans l'étude actuelle, nous utilisons une approche comparable pour identifier exhaustivement les agents pathogènes (bactéries, virus, et champignons) composant le microbiote pulmonaire associé aux pneumopathies développées en unités de réanimation. L'étude a inclus des patients admis en réanimation et présentant des formes de pneumopathies acquises sous ventilation mécanique (n = 106), de pneumopathies communautaires (n = 32), de pneumopathies nosocomiales sans ventilation mécanique (n = 22) et de pneumopathies d’aspiration (n = 25). Une cohorte de 25 patients admis en réanimation et ne présentant pas de symptômes de pneumopathie a été étudiée comme contrôle. Cette première partie du travail amènera ainsi à réaliser un catalogue exhaustif des agents de pneumopathies nosocomiales ; à connaître la prévalence des agents identifiés et d’identifier les co-infections fréquemment observées, et surtout à vérifier si ces agents peuvent être identifiés ou pas dans les prélèvements respiratoires profonds de patients non symptomatiques. Pour réaliser cette partie du travail, des séries de prélèvements, incluant des prélèvements de lavage broncho-alvéolaire (LBA), des prélèvements de sang et d'urine ont été étudiés. Ces prélèvements ont été testés par des moyens d’identification moléculaire moderne basés sur l’amplification de gènes conservés (gènes16S rDNA des bactéries et gène 18S rDNA des champignons) suivie par clonage et séquençage à grande échelle. D’autres pathogènes atypiques sont ciblés par des tests de PCR avec utilisation d’amorces spécifiques. Nous avons également inclus la culture, la co-culture d’amibes, la détection sérologique d'anticorps dirigés contre des agents sélectionnés et des tests d'antigène urinaire, afin de comparer ces tests de routine aux approches moléculaires. Comme résultats, les tests moléculaires nous ont permis d’identifier un vaste répertoire de 160 espèces bactériennes dont 73 n'ont jamais été précédemment rapportées à l’étiologie des pneumopathies. En outre, nous avons trouvé 37 phylotypes bactériens potentiellement nouveaux. Nous avons également identifié 24 espèces de champignons dont 6 n'ont pas été précédemment rapportées à l’étiologie des pneumopathies, 7 virus et étonnamment 6 espèces de plantes. De plus, certains agents pathogènes considérés comme typiques aux pneumopathies nosocomiales tels que Pseudomonas aeruginosa et des Streptococci ont été détectés chez les contrôles comme chez les patients. Cet étonnant résultat souligne l'existence d'un noyau de microbiote pulmonaire.Dans un deuxième travail, faisant suite aux travaux effectués dans notre laboratoire et qui ont pu mettre en évidence que 19% des pneumopathies nosocomiales étaient déterminées par des microorganismes associés aux amibes (MAAs) de l’eau préalablement ignorés ou négligés, nous avons utilisé un test d'immunofluorescence multiplexe pour tester la prévalence des anticorps contre les MAAs dans le sang de patients admis en réanimation et atteints de pneumopathies et la comparer à la prévalence au moment de l'admission. Comme résultat, nous démontrons que certains MAAs peuvent être plus fréquemment détectés après des épisodes de pneumopathies nosocomiales que lors de l’admission. En outre, la réponse immunitaire aux MAAs semble augmenter lorsque le séjour en réanimation est prolongé. Enfin, nous avons mis au point une stratégie de metagénomique pour tester les prélévements pour lesquels aucune étiologie n’a été retrouvée. [...] / Recently, bacterial microbiota from a limited number of patients with cystic fibrosis and ventilator-associated pneumonia (VAP) was studied using 16S rDNA gene amplification followed by clone libraries construction and sequencing. These studies have showed that the microbial population of patients with respiratory infections was more diverse than expected. In the current study, we use a similar approach to identify exhaustively the pathogens (bacteria, viruses, and fungi) comprising the microbiota associated with episodes of pneumonia developed in the intensive care units (ICU). Our study included patients admitted to ICUswith with episodes of ventilator-associated pneumonia (n = 106), community-acquired pneumonia (n = 32), nosocomial pneumonia without mechanical ventilation (n = 22) and aspiration pneumonia (n = 25). A cohort of 25 patients admitted to ICUs without symptoms of pneumonia were studied as controls. This first part of the work enables to prepare an exhaustive repertoire of nosocomial pneumonia pathogenes; to know the prevalence of the pathogens identified and to identify co-infections frequently observed, and especially to ascertain whether these agents can be identified or not in the respiratory samples of patients without symptoms of pneumonia. To perform this part of work, series of samples, including bronchoalveolar lavage (BAL) samples, blood samples and urine samples were collected. These samples were tested by means of modern molecular tools based on the amplification of conserved genes (bacterial 16S rDNA and fungal 18S rDNA genes), followed by highthroutput cloning and sequencing. The atypical pathogens are targeted by PCR tests using specific primers and probes. We also included culture, amoeba co-culture, serological detection of antibodies against selected agents and urinary antigen testing, to compare these routine tests to molecular approaches. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 were never previously reported in pneumonia samples. Moreover, we found 37 putative new bacterial phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia, 7 viruses and surprisingly 6 plant species. Some pathogens considered being typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species may be detected as commonly in controls as in pneumonia patients which strikingly highlight the existence of a core of pulmonary microbiota.In a second work, following previous works performed in our laboratory which were able to show that 19% of nosocomial pneumonia were determined by micro-organisms associated to amoebae (AAMs) previously ignored or neglected, we used a recent test based on multiplex serology to test for the prevalence of antibodies against the AAMs in the blood of patients admitted to ICU and developed episodes of pneumonia and compare it to the prevalence at the time of admission (controls). As a result, we demonstrate that some AAMs may be more frequently detected after episodes of nosocomial pneumonia than at the admission. In addition, the immune response to AAMS appears to increase when the ICU stay is prolonged.Finally, in order to explore samples for which no microbial aetiology was found, we have developed a subtractive hybridization metagenomic strategy and tested it on different clinical samples. The sensitivity of this strategy was also evaluated. We have demonstrated that our method, based on the detection of DNA and RNA of microorganisms in a single test, allows sensitive detection of different types of microorganisms.

Les communautés du coralligène dominées par des gorgonaires ont été sévèrement affectées par des évènements de mortalités massives liés au réchauffement de la Méditerranée. Pour évaluer la contribution des bactéries associées à l’holobionte Paramuricea clavata à son fonctionnement et sa santé, il est apparu primordial de caractériser le compartiment microbien naturel de ce gorgonaire tempéré.Dans ce contexte, l’objectif général de cette thèse était de décrire les interactions existant entre la gorgone rouge P. clavata et ses bactéries associées en Méditerranée nord-occidentale. Les analyses entreprises par des techniques culture-indépendantes basées sur l’analyse des ADN ribosomiques 16S bactériens ont inclus (i) la caractérisation de la variation spatio-temporelle des communautés bactériennes, (ii) la localisation des bactéries dans les tissus de l’hôte, (iii) l’évaluation de la stabilité des associations gorgones-bactéries en conditions de stress et (iv) la détermination de la spécificité d’hôte des bactéries dominantes entre différentes espèces de gorgonaires sympatriques (Eunicella singularis, Eunicella cavolini et Corallium rubrum). Les résultats obtenus ont établi que P. clavata et son microbiote forment un holobionte au sein duquel hôte et bactéries vivent en étroite association, stable dans le temps et l’espace ou en conditions de stress. Les communautés bactériennes associées sont principalement endosymbiotiques et dominées par un ribotype bactérien appartenant à un genre nouveau de la famille des Hahellaceae qui semble présenter une forte spécificité d’hôte. Ces résultats suggèrent un rôle particulier de ce genre bactérien chez les holobiontes gorgonaires. / Coralligenous communities dominated by gorgonian species have been severely affected by diseases and mass mortality events linked to the current warming trends reported for the Mediterranean Sea. The characterization of the natural microbial compartment of this temperate gorgonian species becomes a crucial step in the evaluation of the bacterial contribution to health and functioning of the Paramuricea clavata holobiont.Under these circumstances, the global aim of this PhD work was to describe the interactions existing between the red gorgonian P. clavata and its associated bacteria in the Northwestern Mediterranean basin. The culture-independent analyses based on the bacterial 16S ribosomal DNA included (i) the characterization of spatiotemporal variation of the bacterial communities, (ii) the localization of the bacteria within host tissues, (iii) the evaluation of the stability of gorgonian-bacterial associations under stress conditions and (iv) the determination of the host-specificity of dominant bacteria in different sympatric gorgonian species (Eunicella singularis, Eunicella cavolini and Corallium rubrum).The results of this study highlighted that P. clavata and its microbiota form a holobiont in which host and bacteria live in close association. This association is spatiotemporally stable and maintained under stress conditions. Associated bacterial communities are mostly endosymbiotic and dominated by a bacterial ribotype belonging to a new genus within the Hahellaceae family that seems to be host-specific. These results suggest a particular role of this bacterial genus in the gorgonian holobionts.