Draft genome sequence of <i>Chelonobacter oris</i> strain 1662^T, associated with respiratory disease in Hermann’s tortoises

Chelonobacter oris 1662(T) is a type strain of the recently described species of the Pasteurellaceae family. The strain was isolated from the choanae of a captive tortoise with signs of respiratory tract infection. The genome reported here is approximately 2.6 Mb in size and has a G+C content of 47.1%

PIG—the pathogen interaction gateway

Protein–protein interactions (PPIs) play a vital role in initiating infection in a number of pathogens. Identifying which interactions allow a pathogen to infect its host can help us to understand methods of pathogenesis and provide potential targets for therapeutics. Public resources for studying host–pathogen systems, in particular PPIs, are scarce. To facilitate the study of host–pathogen PPIs, we have collected and integrated host–pathogen PPI (HP–PPI) data from a number of public resources to create the Pathogen Interaction Gateway (PIG). PIG provides a text based search and a BLAST interface for searching the HP–PPI data. Each entry in PIG includes information such as the functional annotations and the domains present in the interacting proteins. PIG provides links to external databases to allow for easy navigation among the various websites. Additionally, PIG includes a tool for visualizing a single HP–PPI network or two HP–PPI networks. PIG can be accessed at http://pig.vbi.vt.edu

ARDB—Antibiotic Resistance Genes Database

The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic resistance genes also have the potential to be used for bio-terror purposes through genetically modified organisms. In order to facilitate the identification and characterization of these genes, we have created a manually curated database—the Antibiotic Resistance Genes Database (ARDB)—unifying most of the publicly available information on antibiotic resistance. Each gene and resistance type is annotated with rich information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. Our database also supports sequence similarity searches and implements an initial version of a tool for characterizing common mutations that confer antibiotic resistance. The information we provide can be used as compendium of antibiotic resistance factors as well as to identify the resistance genes of newly sequenced genes, genomes, or metagenomes. Currently, ARDB contains resistance information for 13 293 genes, 377 types, 257 antibiotics, 632 genomes, 933 species and 124 genera. ARDB is available at http://ardb.cbcb.umd.edu/

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

DBETH: A Database of Bacterial Exotoxins for Human

Pathogenic bacteria produce protein toxins to survive in the hostile environments defined by the host's defense systems and immune response. Recent progresses in high-throughput genome sequencing and structure determination techniques have contributed to a better understanding of mechanisms of action of the bacterial toxins at the cellular and molecular levels leading to pathogenicity. It is fair to assume that with time more and more unknown toxins will emerge not only by the discovery of newer species but also due to the genetic rearrangement of existing bacterial genomes. Hence, it is crucial to organize a systematic compilation and subsequent analyses of the inherent features of known bacterial toxins. We developed a Database for Bacterial ExoToxins (DBETH, http://www.hpppi.iicb.res.in/btox/), which contains sequence, structure, interaction network and analytical results for 229 toxins categorized within 24 mechanistic and activity types from 26 bacterial genuses. The main objective of this database is to provide a comprehensive knowledgebase for human pathogenic bacterial toxins where various important sequence, structure and physico-chemical property based analyses are provided. Further, we have developed a prediction server attached to this database which aims to identify bacterial toxin like sequences either by establishing homology with known toxin sequences/domains or by classifying bacterial toxin specific features using a support vector based machine learning techniques

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

The EC2KEGG output for the RV1423 analysis sorted in ascending order by the FDR value. (XLSX 58 kb

Transcriptome analysis of amyloodinium ocellatum tomonts revealed basic information on the major potential virulence factors

The ectoparasite protozoan Amyloodinium ocellatum (AO) is the etiological agent of amyloodiniosis in European seabass (Dicentrarchus labrax) (ESB). There is a lack of information about basic molecular data on AO biology and its interaction with the host. Therefore, de novo transcriptome sequencing of AO tomonts was performed. AO trophonts were detached from infested ESB gills, and quickly becoming early tomonts were purified by Percoll\uae density gradient. Tomont total RNA was processed and quality was assessed immediately. cDNA libraries were constructed using TruSeq\uae Stranded mRNA kit and sequenced using Illumina sequencer. CLC assembly was used to generate the Transcriptome assembly of AO tomonts. Out of 48,188 contigs, 56.12% belong to dinophyceae wherein Symbiodinium microadriaticum had 94.61% similarity among dinophyceae. Functional annotations of contigs indicated that 12,677 had associated GO term, 9005 with KEGG term. The contigs belonging to dinophyceae resulted in the detection of several peptidases. A BLAST search for known virulent factors from the virulence database resulted in hits to Rab proteins, AP120, Ribosomal phosphoprotein, Heat-shock protein70, Casein kinases, Plasmepsin IV, and Brucipain. Hsp70 and casein kinase II alpha were characterized in-silico. Altogether, these results provide a reference database in understanding AO molecular biology, aiding to the development of novel diagnostics and future vaccines

Identification of the Edwardsiella Ictaluri Genes Causing Impaired Growth in Complex Medium

Edwardsiella ictaluri is the causative agent of enteric septicemia of catfish (ESC). Although some virulence mechanisms in E. ictaluri have been identified, further research is needed to discover new virulence genes, which could be used to develop safe and efficacious live vaccines. Here, we report production of growth deficient E. ictaluri mutants on complex agar media and identification of genes causing this growth deficiency. The overall goal of this project is to generate growth deficient E. ictaluri mutants and identify genes causing this growth deficiency on complex media. Mutants exhibiting slow growth in complex media may be potential candidates for vaccine development. In this study, 56 unique E. ictaluri genes have been identified. 32 of them showed host protein binding properties while 30 of them were found to be involved in bacterial virulence in other pathogenic bacteria

Whole-genome analysis of Mannheimia haemolytica serotype A2 to identify potential vaccine candidates against acute pneumonia in alpacas

El objetivo del presente trabajo fue identificar antígenos inmunoprotectivos en la secuencia genómica de Mannheimia haemolytica serotipo A2 Ovino, aislado de ovino y disponible en las bases de datos, que puedan ser utilizados como potenciales candidatos vacunales contra la neumonía en alpacas. Para ello, se empleó la secuencia completa del genoma de este microorganismo disponible en las bases de datos y mediante el uso de herramientas bioinformáticas se procedió a la búsqueda e identificación de genes candidatos, la anotación funcional, la predicción de la localización subcelular y la identificación de motivos de secuencias, incluyendo dominios transmembrana, peptidos señal de secreción y lipoproteínas. Los factores de virulencia fueron identificados en la base de datos de factores de virulencia (VFDB) y en la base de datos microbiana de virulencia (MvirDB). Los criterios de selección incluyeron proteínas conservadas, secretadas y asociadas a superficie con hélices transmembrana d»1. Se realizó la búsqueda de homología de genes con la base de datos de antígenos protectivos (Protegen), permitiendo la identificación de 23 antígenos potencialmente inmunoprotectivos, conservados entre los serotipos virulentos de M. haemolytica y otros patógenos de la familia Pasteurellaceae. Los genes identificados están relacionados con la patogénesis, virulencia y evasión del sistema immune del hospedero y podrían ser grandes candidatos a ser evaluados como potenciales vacunas contra la pasteurelosis neumónica.The aim of this study was to identify immunoprotective antigens in the genomic sequence of Mannheimia haemolytica serotype A2 isolated from sheep and available in databases that can be used as potential vaccine candidates against pneumonia in alpacas. To do this, the complete genome sequence of this organism available in databases was used and by using bioinformatics tools was proceeded to search for and identification of candidate genes, functional annotation, predicting the subcellular localization and identification of sequence motifs including transmembrane domains, secretion signal peptides and lipoproteins. Virulence factors were identified in the database of virulence factors (VFDB) and the microbial database of virulence factors (MvirDB). Selection criteria included conserved proteins, secreted and associated surface with transmembrane helices &lt;1. Homology search of genes was performed with the database of protective antigens (Protegen), allowing the identification of 23 potentially immunoprotective antigens conserved between virulent M. haemolytica serotypes and other pathogens of the family Pasteurellaceae. The genes identified are related to the pathogenesis, virulence and immune system evasion of the host and they could be great candidates to be evaluated as potential vaccines against pneumonic pasteurellosis