Clustering of Vibrio parahaemolyticus isolates using MLST and whole-genome phylogenetics and protein motif fingerprinting

Vibrio parahaemolyticus is a ubiquitous and abundant member of native microbial assemblages in coastal waters and shellfish. Though V. parahaemolyticus is predominantly environmental, some strains have infected human hosts and caused outbreaks of seafood-related gastroenteritis. In order to understand differences among clinical and environmental V. parahaemolyticus strains, we used high quality DNA sequencing data to compare the genomes of V. parahaemolyticus isolates (n = 43) from a variety of geographic locations and clinical and environmental sample matrices. We used phylogenetic trees inferred from multilocus sequence typing (MLST) and whole-genome (WG) alignments, as well as a novel classification and genome clustering approach that relies on protein motif fingerprints (MFs), to assess relationships between V. parahaemolyticus strains and identify novel molecular targets associated with virulence. Differences in strain clustering at more than one position were observed between the MLST and WG phylogenetic trees. The WG phylogeny had higher support values and strain resolution since isolates of the same sequence type could be differentiated. The MF analysis revealed groups of protein motifs that were associated with the pathogenic MLST type ST36 and a large group of clinical strains isolated from human stool. A subset of the stool and ST36-associated protein motifs were selected for further analysis and the motif sequences were found in genes with a variety of functions, including transposases, secretion system components and effectors, and hypothetical proteins. DNA sequences associated with these protein motifs are candidate targets for future molecular assays in order to improve surveys of pathogenic V. parahaemolyticus in the environment and seafood

ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies

Viruses, viroids and prions are the smallest infectious biological entities that depend on their host for replication. The number of pathogenic viruses is considerably large and their impact in human global health is well documented. Currently, the International Committee on the Taxonomy of Viruses (ICTV) has classified ∼4379 virus species while the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) database has mapped 617 705 proteins to eight large taxonomic groups. Despite these efforts, an automated approach for mapping the ICTV master list and its officially accepted virus naming to the NCBI-VGR’s taxonomical classification is not available. Due to metagenomic sequencing, it is likely that the discovery and naming of new viral species will increase by at least ten fold. Unfortunately, existing viral databases are not adequately prepared to scale, maintain and annotate automatically ultra-high throughput sequences and place this information into specific taxonomic categories. ORION-VIRCAT is a scalable and interoperable object-relational database designed to serve as a resource for the integration and verification of taxonomical classifications generated by the ICTV and NCBI-VGR. The current release (v1.0) of ORION-VIRCAT is implemented in PostgreSQL and it has been extended to ORACLE, MySQL and SyBase. ORION-VIRCAT automatically mapped and joined 617 705 entries from the NCBI-VGR to the viral naming of the ICTV. This detailed analysis revealed that 399 095 entries from the NCBI-VGR can be mapped to the ICTV classification and that one Order, 10 families, 35 genera and 503 species listed in the ICTV disagree with the the NCBI-VGR classification schema. Nevertheless, we were eable to correct several discrepancies mapping 234 000 additional entries

Strong floristic distinctiveness across Neotropical successional forests.

Forests that regrow naturally on abandoned fields are important for restoring biodiversity and ecosystem services, but can they also preserve the distinct regional tree floras? Using the floristic composition of 1215 early successional forests (<20 years) in 75 human-modified landscapes across the Neotropic realm, we identified 14 distinct floristic groups, with a between-group dissimilarity of 0.97. Floristic groups were associated with location, bioregions, soil pH, temperature seasonality, and water availability. Hence, there is large continental-scale variation in the species composition of early successional forests, which is mainly associated with biogeographic and environmental factors but not with human disturbance indicators. This floristic distinctiveness is partially driven by regionally restricted species belonging to widespread genera. Early secondary forests contribute therefore to restoring and conserving the distinctiveness of bioregions across the Neotropical realm, and forest restoration initiatives should use local species to assure that these distinct floras are maintained

Strong floristic distinctiveness across Neotropical successional forests

Forests that regrow naturally on abandoned fields are important for restoring biodiversity and ecosystem services, but can they also preserve the distinct regional tree floras? Using the floristic composition of 1215 early successional forests (≤20 years) in 75 human-modified landscapes across the Neotropic realm, we identified 14 distinct floristic groups, with a between-group dissimilarity of 0.97. Floristic groups were associated with location, bioregions, soil pH, temperature seasonality, and water availability. Hence, there is large continental-scale variation in the species composition of early successional forests, which is mainly associated with biogeographic and environmental factors but not with human disturbance indicators. This floristic distinctiveness is partially driven by regionally restricted species belonging to widespread genera. Early secondary forests contribute therefore to restoring and conserving the distinctiveness of bioregions across the Neotropical realm, and forest restoration initiatives should use local species to assure that these distinct floras are maintained

大学の教育活動の質をどう把握・評価するか

この論文は国立情報学研究所の学術雑誌公開支援事業により電子化されました

Strong floristic distinctiveness across Neotropical successional forests

Forests that regrow naturally on abandoned fields are important for restoring biodiversity and ecosystem services, but can they also preserve the distinct regional tree floras? Using the floristic composition of 1215 early successional forests (≤20 years) in 75 human-modified landscapes across the Neotropic realm, we identified 14 distinct floristic groups, with a between-group dissimilarity of 0.97. Floristic groups were associated with location, bioregions, soil pH, temperature seasonality, and water availability. Hence, there is large continental-scale variation in the species composition of early successional forests, which is mainly associated with biogeographic and environmental factors but not with human disturbance indicators. This floristic distinctiveness is partially driven by regionally restricted species belonging to widespread genera. Early secondary forests contribute therefore to restoring and conserving the distinctiveness of bioregions across the Neotropical realm, and forest restoration initiatives should use local species to assure that these distinct floras are maintained