Kudoid parasites are common in marine fish and their affects range from relatively benign to pathogenic. They are notorious in the seafood industry for spoiling fish meat, either by muscle liquefaction or by producing unsightly macroscopic cysts. Kudoids also infect several other tissues such as brain, heart, gills, connective tissue, intestinal smooth muscle, and epithelia. Since the revised classification of the Kudoidae in 2004, kudoid myxospores have a range of shapes, but with two main characteristics: they have four or more spore valves with the equivalent number of polar capsules. With relatively few morphological traits to base kudoid species descriptions, DNA has proven to be increasingly useful to specifically diagnose infections. However, to properly utilise genetic information, there is a need to understand how genetics relates to the biological characteristics of species. This will ensure the genetic markers used are appropriate for species characterisation. This project aimed to develop an understanding of how biological characteristics including morphology, tissue tropism, host specificity, and geographic distribution correlate with genetic relatedness of kudoid species, and how this information could be employed to facilitate diagnosis and characterisation of species. A taxonomic investigation of kudoid isolates, mostly from the east coast of Queensland, Australia, was conducted using information on host identity, locality, infection status, tissue of infection and histological response to infection. Together with spore morphology and DNA relationships, comparisons were made with existing data from literature. Forty-three small subunit and 68 large subunit ribosomal DNA sequences were generated from kudoid isolates for this project. The two gene regions showed similar relationships amongst the kudoids, however the genetic variability between closely related species was less conserved in the large subunit, and showed superior species resolution that correlated with subtle morphological differences of spores. Broadly speaking, genetic relatedness of kudoids is closest for species infecting the same type of tissue with similar spore morphology. Within these tissue/morphology groups, some relationships were emerging from genetic correlations with pathology, however there are weaknesses in utilising this characteristic since pathology may change with host species or host age. Similar relationships to pathology were seen from geographic locality; however, the limited number of areas that genetic data originates from may have introduced some bias. Lastly, there were very few genetic relationships that correlated with host relatedness. The taxonomic affinities of the new kudoid isolates lead to the characterisation of six novel kudoid species and four additional host-parasite combinations. The investigation into these new species highlighted the broad host ranges and geographic distribution of some kudoid species. Genetic mixing of kudoid species populations from the east coast of Queensland, Australia with Japan was noted. For example, Kudoa amamiensis was discovered from carangid and pomacentrid fish from Queensland, increasing the host range from eight (seven from Japan, one from north Queensland) to 11 host species. Also, geographic distribution was extended to Heron Island on the south Great Barrier Reef (Queensland). The distribution did not extend to rocky temperate reefs further south. Another example is Kudoa yasunagai which was previously recorded from four fish species in Japan and one from the Philippines. Now the distribution has been extended to North Stradbroke Island in Southern Queensland from three additional host species. The connection was made between these host isolates with the assistance of DNA and a novel way of analysing morphological data in species that have variable morphotypes i.e. different numbers of polar capsules in the spores. It was confirmed that the dominant morphotype can vary between different hosts and even host samples of the one species. Genetic data has also proven useful in the determination of host range. An analysis of kudoid host specificity showed just over two thirds of the described kudoid species have been recorded from a single host; the remainder have been recorded from two to 38 host species. By using DNA data, 17 new hosts were recorded for K. thalassomi (total 18 hosts). The new hosts came from six different host families, but these fish shared the same habitat on the Great Barrier Reef. Other high host range kudoid species may be disproportionately broad as similar morphological species may have been misidentified from some hosts. For example, the host range of K. thyrsites (38) is likely to represent a species complex that may be split pending further genetic analyses. From this study, it has been reinforced that a holistic approach to species definition is important. Genetic analysis has become a particularly valuable tool; however, in conjunction with biological data such as spore morphology, pathology, host range, and geographic distribution, our understanding of kudoid parasites becomes more robust and provides important knowledge for diagnostics and aquaculture management. In the future, significant improvements in kudoid understanding will coincide with the solving of kudoid life cycles and transmission patterns.

L’Identification rapide et la classification microbienne précise sont cruciales en microbiologie médicale pour la surveillance de la santé humaine et animale, établir un diagnostic clinique approprié et choisir des mesures thérapeutiques et de contrôle optimales. Cependant, les seuils universels utilisés pour la définition des espèces ne sont pas applicables à de nombreux genres bactériens. C'est notamment le cas des espèces du genre Rickettsia, qui expriment peu de caractéristiques phénotypiques distinctives. Compte tenu de la disponibilité des séquences de près de 100 génomes de Rickettsia, nous avons voulu évaluer une gamme de paramètres taxonomiques basés sur l’analyse des séquences génomiques afin de mettre au point des recommandations pour la classification des isolats au niveau de l’espèce et du genre. En comparant le degré de similarité des séquences de 78 génomes de Rickettsia et 61 génomes de 3 genres étroitement apparentés en utilisant 4 paramètres génomiques, nous avons montré que les outils taxonomiques basés sur les séquences génomiques sont simples à utiliser et rapides, et permettent une classification taxonomique fiable et reproductible des isolats de rickettsies avec des seuils spécifiques. Les résultats obtenus nous ont permis d'élaborer des recommandations pour la classification des isolats de rickettsies au niveau du genre et de l'espèce. À l'aide de la taxono-génomique, nous avons également pu décrire 17 nouvelles espèces bactériennes associées à l'homme. L'utilisation des outils génomiques est donc parfaitement adaptée à la classification taxonomique et peut changer radicalement notre vision de la taxonomie et de l'évolution bactérienne à l'avenir. / Rapid identification and precise microbial classification are crucial in medical microbiology for human and animal health monitoring, appropriate clinical diagnosis and selection of optimal therapeutic and control measures. Indeed, the universal used for the definition of species are not applicable to many bacterial genera. This is particularly true of species of the genus Rickettsia which are strictly intracellular alpha-proteobacteria that express few phenotypic characteristics. Given the availability of genomic sequences of nearly 100 rickettsial genomes, we wanted to evaluate a range of taxonomic parameters based on genomic sequence analysis, to develop guidelines for the classification of Rickettsia isolates at the genus and species levels. By comparing the degree of similarity of the sequences of 78 genomes from Rickettsia species and 61 genomes from 3 closely related genera using several genomic parameters, we have shown that genome-based taxonomic tools are simple to use and fast, and allow for a reliable and reproducible taxonomic classification of isolates within species of the genus Rickettsia, with specific thresholds. The obtained results enabled us to develop guidelines for classifying rickettsial isolates at the genus and species levels. Using taxono-genomics, we have also been able to describe 17 new human-associated bacterial species on the basis of a combination of genomic analysis and phenotypic properties. The use of genomic tools is therefore perfectly adapted to taxonomic classification and can dramatically change our vision of taxonomy and bacterial evolution in the future.

La bio-informatique est essentielle aujourd'hui dans de nombreux domaines comme par exemple la gestion et l'analyse des données, la génomique avec l'assemblage et l'annotation de génomes, la phylogénie, la métagénomique, la recherche de nouvelles espèces bactériennes et la classification taxonomique. Mon premier travail a porté sur l'assemblage et l'analyse d'un génome bactérien à partir de données de métagénomique. Le génome de Akkermansia muciniphila a pu être assemblé par mapping directement à partir de données issues d'échantillons de selle humaine. En 2012, la culturomics a permis de décrire le plus grand génome d'une bactérie isolée chez l'homme ; Microvirga massiliensis (9.3 Mb). Mon deuxième travail a permis d'assembler ce génome. Par la suite, nous avons essayé de comprendre pourquoi cette bactérie a un génome si grand. En effet, on observe qu'elle possède un plasmide, un nombre important d'ORFans et d'ARNr 16S ainsi que des gènes de grande taille. Elle comporte également un nombre important de transposons. Enfin, la troisième et dernière partie de mon travail se base sur les analyses de pan-génome pour la taxonomie bactérienne. La taxonomie est sujette à de nombreux changements selon les données disponibles et les méthodes utilisées, et suit l'évolution des techniques d'identification des bactéries. Nous avons alors redéfinit la notion d'espèce à l'aide du pan-génome pour le genre Klebsiella. En effet, une différence trop importante entraînant une cassure au niveau du ratio core/pan-génome, révèle l'apparition d'une nouvelle espèce. Cette découverte nous amène à utiliser le pan-génome comme outils novateur pour la taxonomie bactérienne. / Since the introduction of DNA sequencing by Sanger and Coulson in 1977, considerable progress has been made. A growing number of data is being generated in several areas and requires more and more advances in computing. Bio-informatics is essential today in many fields such as data management and analysis, genomics with assembly and genome annotation, comparative genomics, phylogeny, metagenomics, research new bacterial species and taxonomic classification. My first work based on assembling and analyzing bacterial genome from metagenomic data. The genome of Akkermansia muciniphila could be assembled by mapping directly from data from human stool sample. In 2012,culturomics allowed to describe the largest genome of a bacterium isolated in human; Microvirga massiliensis (9.3 Mb). My second work allowed to assemble this genome. Subsequently, we tried to understand why this bacterium has such a large genome. Indeed, it is observed that it possesses a plasmid, a large number of ORFans and 16S rRNAs as well as large genes which one is more than 14kb. It also includes a large number of transposasons. Finally, the third and last part of the work concerns pan-genome analyzes for bacterial taxonomy. Taxonomy is a set of many changes based on available data, methods used and evolution of bacterial identification techniques. We have examined the notion of species using the genome at the genus Klebsiella. Indeed, a too large difference leading to a break in the core/pan-genome ratio undoubtedly reveals the appearance of a new species. This discovery leads us to use the pan-genome as an innovative tool for bacterial taxonomy.