Diversité génomique des espèces bactériennes du genre Flavobacterium

Les bactéries du genre Flavobacterium sont retrouvées dans des types d habitats très divers. Ce genre contient trois espèces ichtyopathogènes: columnare, branchiophilum et psychrophilum qui est responsable de pertes économiques importantes pour l élevage des salmonidés. Un projet de séquençage et de comparaison des génomes de plusieurs flavobactéries pathogènes de poissons ainsi qu isolées de différents environnements a été mis en place pour améliorer les connaissances sur ce genre. Les objectifs étaient l identification des déterminants de virulence et la caractérisation de différents marqueurs moléculaires des traits phénotypiques associés à leur mode de vie. L analyse des génomes de F. psychrophilum a permis de mettre en évidence une diversité des structures chromosomiques au sein de l espèce et d identifier des cibles moléculaires prometteuses pour le développement de tests de diagnostic ainsi que des cibles vaccinales potentielles. Le génome de F. branchiophilum a permis d identifier des mécanismes moléculaires de virulence originaux. Les caractéristiques du génome de F. indicum révèlent un mode de vie environnemental: sa petite taille et ses faibles capacités de dégradation des bio-polymères suggèrent que F. indicum est adapté à une niche écologique restreinte. Ces nouvelles données ont permis de caractériser in silico des marqueurs moléculaires de caractères phénotypiques. En particulier, un groupe de gènes (dnd) rare et responsable d une modification étonnante de la molécule d ADN a été décrit pour la première fois chez les Flavobacteriaceae. Ce projet a permis d enrichir les connaissances sur les bactéries du genre Flavobacterium et a contribué au développement d outils pour la santé animale.Flavobacterium species occur in a wide range of habitats. This genus includes three fish-pathogenic species, namely F. columnare, F. branchiophilum and F. psychrophilum. The latter is responsible for serious economic losses for salmonids farming in France and worlwide. A comparative genomics project including several fish-pathogenic flavobacteria as well as various environmental species has been set up in order to improve the knowledge on this poorly studied genus. Our aims were the identification of virulence determinants associated with pathogenicity and the characterization of various molecular elements reflecting phenotypes associated with their life-style. Analysis of the genomes of several F. psychrophilum isolates revealed the diversity of chromosomal structures within the species and identified in silico promising molecular targets for the development of diagnostic tests as well as potential vaccines targets. Analysis of the F. branchiophilum genome enabled to identify particular molecular virulence mechanisms. The features of the F. indicum genome reflected its environmental lifestyle: its small size and its limited bio-polymers degrading abilities suggested that F. indicum is adapted to a quite narrow ecological niche. These new data have allowed the in silico identification of many molecular elements reflecting phenotypic traits. In particular, a rare gene cluster (dnd) responsible for an unusual DNA structure modification was described for the first time within members of the family Flavobacteriaceae. This project enriched the knowledge on Flavobacterium species and contributed to the development of tools for animal health.EVRY-Bib. électronique (912289901) / SudocSudocFranceF

Alteromonas fortis sp. nov., a non-flagellated bacterium specialized in the degradation of iota-carrageenan, and emended description of the genus Alteromonas

International audienceStrain 1T, isolated in the seventies from the thallus of the carrageenophytic red algae Eucheumaspinosum collected in Hawaii, USA, was retrospectively characterized using phenotypic,phylogenetic and genomic methods. Bacterial cells were Gram-stain-negative, strictly aerobic,non-flagellated, coccoid, ovoid or rod-shaped, and grew at 10-42 °C (optimum 20-25 °C), atpH 5.5-10 (optimum pH 6-9) and with 2-12 % NaCl (optimum 2-4 %). Strain 1T grew on theseaweed polysaccharides i-carrageenan, laminarin and alginic acid as sole carbon sources. Themajor fatty acids (>10 %) were C16:0, C18:1 ω7c and summed feature 3 (C16:1w7c and/or iso-C15:02OH) and significant amounts of C16:0 N alcohol (6.7 %) and 10 methyl C17:0 (8.6 %) were alsopresent. The only respiratory quinone was Q-8, and major polar lipids werephosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. Phylogeneticanalyses based on 16S rRNA gene sequence comparisons showed that the bacterium is affiliatedto the genus Alteromonas (family Alteromonadaceae, class Gammaproteobacteria). Strain 1Texhibits 16S rRNA gene sequence similarity values of 98.8-99.2 % to the type strains ofAlteromonas mediterranea and Alteromonas australica respectively, and of 95.7-98.6 % tothose of the other species of the genus Alteromonas. The DNA G+C content of strain 1T is 43.9mol%. Based on the genome sequence of strain 1T, DNA-DNA hybridization predictions by theaverage nucleotide identity (ANI) and Genome-to-Genome Distance Calculations (GGDC)between strain 1T and other members of the genus Alteromonas showed values of 70-80 %, andbelow 26 %, respectively. The phenotypic, phylogenetic and genomic analyses show that strain 1T is distinct from species of the genus Alteromonas with validly published names and that itrepresents a novel species of the genus Alteromonas, for which the name Alteromonas fortis sp.nov. is proposed. The type strain is 1T (= ATCC 43554T = CIP XXXX)

Bacterial diseases of farmed fish

An overview of bacterial diseases in farmed fish is presented, including bacterial species involved, predisposing factors, routes of infection, modes of transmission, and control. INRA studies on the main bacterial pathogen of salmonid fish worldwide, Flavobacterium psychrophilum, are also presented. Once techniques of culture, identification, and molecular typing of isolates were defined, a reproducible model of experimental infection was developed using the rainbow trout. Molecular studies improved considerably the taxonomy and phylogeny of the whole Flavobacteriaceae family. The full genome of a F. psychrophilum strain has recently been sequenced. Its analysis has already identified many genes involved in the pathogen’s lifestyle, especially in its virulence towards the host.Un aperçu général des infections bactériennes chez les poissons d'élevage est d'abord présenté: espèces bactériennes en cause, facteurs favorisants, types d'infection, modes de transmission, et méthodes de lutte. Les études menées par l'INRA sur le principal pathogène bactérien des salmonidés dans le monde, Flavobacterium psychrophilum, sont ensuite passées en revue. Après les techniques de culture, d'identification et de typage moléculaire des souches, un modèle expérimental reproductible de la maladie sur la truite arc-en-ciel a été mis au point. Les études moléculaires ont considérablement affiné la taxonomie et la phylogénie de l'ensemble de la famille des Flavobacteriaceae. Le génome complet d'une souche de F. psychrophilum vient d'être séquencé. Son analyse a déjà révélé de nombreux gènes impliqués dans le mode de vie de la bactérie, en particulier dans sa virulence pour l'hôte

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches

About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9T (ATCC 43555T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface

Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions.

BACKGROUND: Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledge of the genetic basis of resistance to F. psychrophilum would help to implement this trait in selection schemes and to investigate the immune mechanisms associated with resistance. Various studies have revealed that skin and mucus may contribute to response to infection. However, previous quantitative trait loci (QTL) studies were conducted by using injection as the route of infection. Immersion challenge, which is assumed to mimic natural infection by F. psychrophilum more closely, may reveal different defence mechanisms. RESULTS: Two isogenic lines of rainbow trout with contrasting susceptibilities to F. psychrophilum were crossed to produce doubled haploid F2 progeny. Fish were infected with F. psychrophilum either by intramuscular injection (115 individuals) or by immersion (195 individuals), and genotyped for 9654 markers using RAD-sequencing. Fifteen QTL associated with resistance traits were detected and only three QTL were common between the injection and immersion. Using a model that accounted for epistatic interactions between QTL, two main types of interactions were revealed. A "compensation-like" effect was detected between several pairs of QTL for the two modes of infection. An "enhancing-like" interaction effect was detected between four pairs of QTL. Integration of the QTL results with results of a previous transcriptomic analysis of response to F. psychrophilum infection resulted in a list of potential candidate immune genes that belong to four relevant functional categories (bacterial sensors, effectors of antibacterial immunity, inflammatory factors and interferon-stimulated genes). CONCLUSIONS: These results provide new insights into the genetic determinism of rainbow trout resistance to F. psychrophilum and confirm that some QTL with large effects are involved in this trait. For the first time, the role of epistatic interactions between resistance-associated QTL was evidenced. We found that the infection protocol used had an effect on the modulation of defence mechanisms and also identified relevant immune functional candidate genes

Transcriptional Responses of Resistant and Susceptible Fish Clones to the Bacterial Pathogen Flavobacterium psychrophilum

Flavobacterium psychrophilum is a bacterial species that represents one of the most important pathogens for aquaculture worldwide, especially for salmonids. To gain insights into the genetic basis of the natural resistance to F. psychrophilum, we selected homozygous clones of rainbow trout with contrasted susceptibility to the infection. We compared the transcriptional response to the bacteria in the pronephros of a susceptible and a resistant line by micro-array analysis five days after infection. While the basal transcriptome of healthy fish was significantly different in the resistant and susceptible lines, the transcriptome modifications induced by the bacteria involved essentially the same genes and pathways. The response to F. psychrophilum involved antimicrobial peptides, complement, and a number of enzymes and chemokines. The matrix metalloproteases mmp9 and mmp13 were among the most highly induced genes in both genetic backgrounds. Key genes of both pro- and anti-inflammatory response such as IL1 and IL10, were up-regulated with a greater magnitude in susceptible animals where the bacterial load was also much higher. While higher resistance to F. psychrophilum does not seem to be based on extensive differences in the orientation of the immune response, several genes including complement C3 showed stronger induction in the resistant fish. They may be important for the variation of susceptibility to the infection

Flavobactéries pathogènes des poissons

National audienc

Draft Genome Sequence of the Iridescent Marine Bacterium Cellulophaga lytica CECT 8139

International audienceSome species of the genus Cellulophaga have been reported as having biotechnological interests and noteworthy physiological properties. We report here the draft genome sequence of Cellulophaga lytica CECT 8139, a bacterium that produces an intensely iridescent colony biofilm on agar surfaces

Complete Genome Sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water.

International audienc

Complete genome sequence of Flavobacterium indicum GPSTA100-9T , isolated from warm spring water

International audienc