SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

BACKGROUND: The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. RESULTS: In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. CONCLUSION: Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .

Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment.

Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications.

Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil.

In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.

Comparative genomics and in silico gene evaluation involved in the probiotic potential of Bifidobacterium longum 51A.

The Bifidobacterium longum 51A strain of isolated from feces of a healthy child, has demonstrated probiotic properties by in vivo and in vitro studies, which may be assigned to its production of metabolites such as acetate. Thus, through the study of comparative genomics, the present work sought to identify unique genes that might be related to the production of acetate. To perform the study, the DNA strain was sequenced using Illumina HiSeq technology, followed by assembly and manual curation of coding sequences. Comparative analysis was performed including 19 complete B. longum genomes available in Genbank/NCBI. In the phylogenetic analysis, the CECT 7210 and 157F strains of B. longum subsp. infantis aggregated within the subsp. longum cluster, suggesting that their taxonomic classification should be reviewed. The strain 51A of B. longum has 26 unique genes, six of which are possibly related to carbohydrate metabolism and acetate production. The phosphoketolase pathway from B. longum 51A showed a difference in acetyl-phosphate production. This result seems to corroborate the analysis of their unique genes, whose presence suggests the strain may use different sources of carbohydrates that allow a greater production of acetate and consequently offer benefits to the host health.

Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1.

We present the complete genome sequence of Corynebacterium pseudotuberculosis strain N1. The sequencing was performed with the Ion Torrent Personal Genome Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C content of 52.85%, and a total of 2,045 coding sequences, 12 rRNAs, 49 tRNAs, and 58 pseudogenes.

Complete Genome Sequence of the Attenuated Corynebacterium pseudotuberculosis Strain T1.

We present here the genome sequence of the attenuated Corynebacterium pseudotuberculosis strain T1. The sequencing was performed with an Ion Torrent Personal Genome Machine platform. The genome is a circular chromosome of 2,337,201 bp, with a G+C content of 52.85% and a total of 2,125 coding sequences (CDSs), 12 rRNAs, 49 tRNAs, and 24 pseudogenes.

Determinação de valores de referência séricos para os eletrólitos magnésio, cloretos, cálcio e fósforo em ovinos das raças Dorper e Santa Inês / Determination of magnesium, chloride, calcium and phosphorus serum reference values for Dorper and Santa Inês sheep breeds

A ovinocultura no Brasil é uma atividade em grande expansão e, com o aumento da demanda mundial por carne ovina, aumentou-se o interesse no monitoramento da sanidade do rebanho, utilizando diversas ferramentas como auxiliares no diagnóstico clínico, tais como os intervalos de referência séricos. Os elementos minerais constituem 2 a 5,5% do corpo dos vertebrados, exercendo diversas funções no organismo. O objetivo deste trabalho foi obter intervalos de referência para os eletrólitos magnésio, fósforo, cloreto e cálcio para ovinos das raças Dorper e Santa Inês. Foram coletados soros de 487 animais clinicamente sadios, sendo 146 da raça Dorper e 341 da raça Santa Inês. Os eletrólitos foram mensurados utilizando-se kits comerciais. Os dados foram analisados quanto à raça, sexo e idade, e os intervalos de referência determinados. Os resultados revelaram diferenças significativas nos intervalos de referência obtidos para os eletrólitos cálcio e magnésio na variável raça, e para o eletrólito fósforo na variável faixa etária e, quando confrontados com valores de referência já publicados, comprovou-se a existência de diferença estatística significativa entre os mesmos em todos os analitos estudados.

The sheep industry in Brazil is an important economic activity, and with the increasing global demand for sheep meat there is a great interest in the monitoring of the herd health, and serum reference ranges are basic tools for veterinary clinical pathology assays. Mineral elements correspond to 2-5.5% of the body of vertebrates, holding different functions in their physiology. The objective of this study was to obtain reference intervals of the electrolytes magnesium, phosphorus, chloride and calcium for the Dorper and Saint Ines sheep breeds. Sera samples were collected from 487 clinically healthy sheep, 146 from Dorper and 341 from Santa Ines breed. Electrolytes were measured using commercial kits. Data were analyzed taking the race, sex and age variables in account, and reference ranges were established. The results revealed significant statistical differences in reference ranges obtained for the electrolytes calcium and magnesium concerning the variable race, and for the electrolyte phosphorus in the variable age and, when compared with reference values already published, proved the existence of significant differences.

Infecção por Corynebacterium pseudotuberculosis em equinos: aspectos microbiológicos, clínicos e preventivos / Corynebacterium pseudotuberculosis infection in horses: clinical, microbiological and prevention aspects

Corynebacterium pseudotuberculosis é o agente causador da linfadenite caseosa em caprinos e ovinos, sendo responsável por significativas perdas econômicas na ovinocaprinocultura mundialmente. Esta bactéria Gram-positiva também infecta equinos, causando desde quadros assintomáticos até infecções sistêmicas, podendo levar o animal a óbito. Especificamente no Brasil, não foram relatados casos de infecção em equinos, mas acredita-se que, devido à convivência de pequenos ruminantes infectados com equinos em diversas propriedades rurais, seja natural que ocorra a infecção desses animais. A presente revisão tem como objetivo fornecer informações sobre a bactéria C. pseudotuberculosis, sobre os aspectos epidemiológicos e clínicos da infecção em equídeos, bem como sobre técnicas de manejo para sua prevenção...

Corynebacterium pseudotuberculosis is the etiologic agent of caseous lymphadenitis in sheep and goats, an infectious disease that is responsible for significant economic losses in small ruminants breeding units worldwide. This Gram-positive bacterium can infect horses, causing symptomatic disease to systemic infections, which can lead to animals' death. Specifically in Brazil, there are no scientific records of equine infections, but it is believed that, due to the maintenance of infected small ruminants in close association to horses in many properties, the infection of horses may be a reality. The present work had the objective to present information on the bacteria C. pseudotuberculosis, on the epidemiological and clinical aspects of the infection in horses, as well as information about breeding procedures that can be adopted in order to prevent the infection...