Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)

Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus–Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma’ species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html

Defining Reference Sequences for Nocardia Species by Similarity and Clustering Analyses of 16S rRNA Gene Sequence Data

International audienceBACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM) of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52%) corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra-species variability

Présence en France de

Un Trématode encore inconnu en France, Paramphistomum leydeni Näsmark, 1937, a été recueilli dans les réservoirs gastriques de bovins originaires de Loire-Atlantique et de Camargue.Le parasite est brièvement redécrit et les critères morphologiques permettant de le différencier des autres espèces du groupe Liorchis sont discutés

Les

Les auteurs, à partir d’une quarantaine d’exemplaires de Syngames de Bovidés prélevés dans les collections des Ecoles vétérinaires de Lyon et d’Alfort redécrivent Mammomonogamus laryngeus (Railliet, 1899) et Mammomonogamus nasicola (Von Linstow, 1899). Us indiquent les caractères permettant de différencier les deux espèces, caractères qui reposent sur la structure et la forme de la capsule buccale, la conformation de la bourse caudale du mâle et de la côte dorsale, l’aspect de la queue de la femelle, la taille des parasites et de leurs œufs. Mammomonogamus — vraisemblablement M. nasicola — existe également en République Centrafricaine dans la trachée de Syncerus caffer aequinoxialis

Les Œsophagostomes du porc de la région d’Amboise

L’étude de plusieurs lots d’Œsophagostomes provenant de porcs sacrifiés à la station de recherches vétérinaires Pfizer d’Amboise (Indre-et-Loire) montre qu’il existe indubitablement en France deux espèces principales : Oesophagostomum dentatum et Oesophagostomum quadrispinulatum. Une troisième espèce Oesophagostomum granatensis, a également été mise en évidence : elle est très voisine d’Oesophagostomum dentatum dont elle pourrait être une sous-espèce. Elle en diffère néanmoins par certains caractères biologiques : degré de développement des neufs en cours d’expulsion et évolution chez l’hôte. Les auteurs donnent une clef de détermination des espèces