A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis / 生物医学与环境科学（英文）

OBJECTIVE@#A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis.@*METHODS@#In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.@*RESULTS@#We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.@*CONCLUSION@#This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis.

Studies on the enzymatic specificity of diguanylate cyclases domains and the production of new second messengers / Estudos na especificidade enzimática de diguanilato ciclases e na produção de novos segundos mensageiros

In the first chapter, studies on substrate recognition and enzymatic activity of GGDEF domains are presented. Many proteins containing GGDEF domains are diguanylate cyclases (DGCs, EC 2.7.7.65), enzymes that catalyze the conversion of 2 GTP molecules into the second messenger c-di-GMP in prokaryotes. This molecule is primarily implicated in the transition between motile and sessile lifestyles, as well several other phenotypes. Redundancy and diversity of GGDEF domain sequences in many bacterial genomes raises the possibility that other enzymatic functions may yet be discovered. To test this hypothesis, i) the effect of point mutations on the structure and enzymatic activity of GGDEF domains is analyzed, ii) the enzymatic specificity of wild-type GGDEF domains from different proteins is also tested, and iii) when non-canonical products are detected, enzymatic models are studied to understand its preferential production. The principal results obtained from these studies are as follows. Seven mutants of the DGC PleD (a GGDEF containing-protein from Caulobacter crescentus) were constructed and the crystallographic structure of two of them was solved, showing that they are unlikely to bind the guanine moiety in its active site. Additionally, five mutants of XAC0610, another DGC from Xanthomonas citr, were constructed and their substrate specificities were evaluated. None of those mutants were able to use ATP as a substrate. Finally, seven different GGDEF domain-containing DGCs from different sources were expressed and purified and their enzymatic specificities were tested with several nucleotide triphosphates. One enzyme, GSU1658 from Geobacter sulfurreducens was particularly promiscuous and shown to produce c-di-GMP, c-di-AMP, c-di-IMP, c-di-2´dGMP, cGAMP, c-GIMP, and c-AIMP. Interestingly, XAC0610 was able to recognize 2´dGTP as substrate. Analysis of enzyme kinetics of XAC0610 in presence of 2´dGTP and/or GTP showed the preferential formation of the hybrid linear product pppGp2´dG. The second chapter present studies on cyanide metabolism in Bacillus with focus on the cyanide dihydratase of Bacillus safensis. Cyanide is widely used in industries due to its high affinity for metals. This same ability confers potent toxicity to this compound. Thus, industries must reduce the cyanide concentration from wastewater before its final disposal. Physical, chemical, and biological methods have been developed to achieve this goal, but knowledge about metabolic pathways and the biology of enzymes involved in cyanide degradation is still scarce. Here, the isolation of a Bacillus safensis strain from mine tailings in Peru is described. Classification of this strain was done through a comparative analysis of 132 core genomes of strains from the Bacillus pumilus group. Sequence analysis determined that a cyanide dihydratase (CynD, EC 3.5.5.1)) encoded in the genome of the isolated strain was likely the enzyme responsible for cyanide degradation. Confirmation of the cyanide degrading activity of CynD from this strain was achieved by cloning, expression and purification of the enzyme and its enzymatic characterization. CynD from this strain was active up to pH 9 and oligomerization patterns analyzed by SEC-MALS and electron microscopy showed that the enzyme forms large helical structures at pH 8 and smaller structures at higher pHs. Finally, we show that CynD expression is strongly induced in the presence of cyanide. The last two years of graduate studies were carried out in the context of the COVID-19 pandemic. Thanks to the large amount of publicly available genomic data, we were able to carry out studies on the worldwide dynamics of the spread of SARS-CoV-2 mutants forms. In the first year of the pandemic, genomic classification of 171,461 genomes showed the presence of five major haplotypes based on nine mutations. The worldwide distribution and the temporal evolution of frequency of these haplotypes was carefully analyzed. All the haplotypes were identified in the six regions analyzed (South America, North America, Europe, Asia, Africa, and Oceania); however, the frequency of each of them was different in each of these regions. As of September 30, 2020, haplotype 3 (or operational taxonomic unit 3, OTU_3) was the most prevalent in four regions (South America, Asia, Africa, and Oceania). OTU_5 was the most prevalent in North America and OTU_2 in Europe. Temporal dynamics of the haplotypes showed that OTU_1 became nearly extinct after 8 months of pandemic (November 2020). Other OTUs are still present in different frequencies all around the world, while currently generating new variants. Based on their temporal dynamics, a classification scheme of 115 SARS-CoV-2 mutations identified from 1,058,020 SARS-COV-2 genomes was also performed. Three types of temporal dynamics of mutations were identified: i) High-Frequency mutations are characterized by a rapid increase in frequency upon its appearance, ii) medium and iii) low-frequency mutations maintain mid or low-frequencies for several months and can be region-specific. Finally, we performed a correlation analysis of the effective reproduction number (Rt) of SARS-CoV-2 harboring the high-frequency mutation N501Y with the level of control measures adopted in specific jurisdictions. We show that Rt is negatively correlated with the level of control measures in eight of the nine countries analyzed. This negative correlation was similar when we analyzed the Rt of SARS-CoV-2 not-harboring N501Y. Thus, the control measures likely diminish the Rt of both SARSCoV-2 wild-type and N501Y

O presente trabalho está dividido em três capítulos sobre linhas de pesquisa diferentes desenvolvidas pelo autor durante o período de doutorado No primeiro capítulo, são apresentados estudos relacionados ao reconhecimento estrutural de substratos e análise enzimática de domínios GGDEF com atividade diguanilato ciclase (EC 2.7.7.65). As proteínas contendo domínios GGDEF estão relacionados à produção enzimática do segundo mensageiro c-di-GMP, a partir de duas moléculas de GTP, em procariotos. Esta molécula está principalmente envolvida na transição entre os estilos de vida móveis e sésseis, bem como vários outros fenótipos. Redundância e diversidade de sequências de domínio GGDEF aumentam a possibilidade de que outras funções enzimáticas ainda possam ser descobertas. Para testar esta hipótese, i) o efeito de mutações pontuais na estrutura e atividade enzimática dos domínios GGDEF é analisado, ii) a especificidade enzimática de domínios GGDEF de enzimas diferentes também é testada e iii) quando produtos não canônicos são detectados, modelos enzimáticos são estudados para entender sua produção preferencial. Como resultados mais importantes, sete mutantes do PleD (uma proteína contendo GGDEF) foram construídos e a estrutura cristalográfica de dois delas foi resolvida, mostrando que é improvável que eles liguem à porção guanina em seu sítio ativo. Além disso, cinco mutantes da proteína XAC0610 de Xanthomonas citri foram construídos e sua capacidade de usar ATP ou GTP como substrato foi avaliada. Nenhum desses mutantes foi capaz de usar ATP como substrato. Finalmente, sete outras proteínas contendo GGDEF foram purificadas e sua especificidade enzimática foi avaliada com vários trifosfatos de nucleotídeos. Uma enzima promíscua chamada GSU1658 mostrou produzir c-di-GMP, c-di-AMP, c-di-IMP, c-di-2´dGMP, c-GAMP, cGIMP e c-AIMP. Curiosamente, o XAC0610 foi capaz de reconhecer 2´dGTP como substrato. A análise da cinética enzimática de XAC0610 na presença de 2´dGTP e GTP mostrou a formação preferencial do produto linear híbrido pppGp2´dG. O segundo capítulo aborda estudos sobre o metabolismo do cianeto em Bacillus com foco na cianeto dihidratase de Bacillus safensis. O cianeto é amplamente utilizado nas indústrias devido à sua alta afinidade com os metais. Esta mesma capacidade confere toxicidade potente a este composto. Assim, as indústrias têm que reduzir a concentração de cianeto das águas residuais antes de sua disposição final. Métodos físicos, químicos e biológicos têm sido desenvolvidos para atingir esse objetivo, mas o conhecimento sobre as vias metabólicas e a biologia das enzimas envolvidas na degradação do cianeto ainda é escasso. Aqui, é descrito o isolamento de uma cepa de Bacillus safensis de rejeitos de minas no Peru. A classificação desta cepa foi feita através de uma análise comparativa de 132 core genomes de cepas do grupo de Bacillus pumilus. Em seguida, determinamos que uma cianeto dihidratase (CynD, EC 3.5.5.1) codificada no genoma da cepa isolada era provavelmente a enzima responsável pela degradação do cianeto. A confirmação da atividade degradante de cianeto de CynD desta cepa foi feita por clonagem, expressão e purificação da enzima e realização de caracterização enzimática. O CynD desta cepa é ativo até pH 9 e os padrões de oligomerização analisados por SEC-MALS mostraram que a enzima forma longas estruturas helicoidais em pH 8 e estruturas menores enquanto o pH aumenta. Finalmente, foi demonstrado que a expressão de CynD é fortemente induzida na presença de cianeto. Os últimos dois anos do doutorado foram realizados no contexto da pandemia COVID- 19. Vários laboratórios se dedicaram a gerar conhecimento para ajudar no combate à pandemia. Nesta situação e graças à grande quantidade de dados genômicos disponíveis publicamente, estudos sobre a dinâmica das mutações do SARS-CoV-2 foram realizados. No primeiro ano da pandemia, a classificação genômica de 171.461 genomas mostrou a presença de cinco haplótipos principais com base em nove mutações. A distribuição mundial e a mudança de frequência desses haplótipos foram analisadas cuidadosamente. Todos os haplótipos foram identificados nas seis regiões analisadas (América do Sul, América do Norte, Europa, Ásia, África e Oceania); no entanto, a frequência de cada um deles foi diferente em cada uma dessas regiões. Em 30 de setembro de 2020, o haplótipo 3 (ou unidade taxonômica operacional 3, OTU_3) era o mais prevalente em quatro regiões (América do Sul, Ásia, África e Oceania). OTU_5 foi o mais prevalente na América do Norte e OTU_2 na Europa. A dinâmica temporal dos haplótipos mostrou que OTU_1 parece perto da extinção após 8 meses de pandemia (novembro de 2020). Outros OTUs ainda estão presentes em diferentes frequências em todo o mundo, mesmo atualmente gerando novas variantes. Com base em sua dinâmica temporal, um esquema de classificação de 115 mutações SARS-CoV-2 identificadas a partir de 1.058.020 genomas SARS-COV-2 também foi feito. Três tipos de dinâmica temporal de mutações foram identificados: i) Mutações de alta frequência, ii) mutações de média frequência e iii) mutações de baixa frequência. Finalmente, foi analisada a correlação do número de reprodução efetiva (Rt) do SARS-CoV-2 que contém a mutação de alta frequência N501Y com o nível de medidas de controle, mostrando que seu Rt está negativamente correlacionado com o nível de medidas de controle em oito dos nove países analisados. Esta correlação negativa foi semelhante quando foi analisado o Rt de SARS-CoV-2 sem a mutação N501Y. Assim, as medidas de controle provavelmente diminuirão o Rt de SARS-CoV-2 tipo selvagem e N501Y

Immunogenicity of Whole / 生物医学与环境科学（英文）

Objectives@#To evaluate the immunogenicity of @*Methods@#Protein extracts from @*Results@#Immunization with @*Conclusion@#This is the advanced study to investigate the immunogenicity of

A real-time quantitative PCR based on molecular beacon for detecting Brucella infection / PCR quantitativo em tempo real, baseado em guia molecular para detecção de infeção por Brucella

O objetivo deste comunicado é desenvolver um método quantitativo PCR em tempo real, baseado em guia molecular (MB) (MB-qPCR) para detecção de infecção por espécies de Brucella, e avaliar seu potencial de utilização clínica. Os primers e as sondas MB foram desenhados para amplificação específica e determinação de sequência conservada do código do gene para os primeiros 58-aa da proteína de membrana externa OMP-2a, que é compartilhada em cinco espécies de Brucella epidêmicas. A avaliação metodológica foi realizada por análise de sensibilidade, especificidade, coeficiente de variação intra e inter, e a linearidade do qPCR. O potencial diagnóstico foi avaliado comparando-se o método qPCR desenvolvido com ensaios de exames bacteriológicos convencionais, incluindo os testes de soroaglutinação convencionais (SATs) e os testes do Rosa Bengala (RBPTs). O método exibiu alta sensibilidade (tão baixo quanto 50 cópias) e grande faixa de linearidade (102-108 cópias). Nenhuma reação cruzada foi encontrada com bactéria clínica comum. A sensibilidade diagnóstica foi superior ao exame bacteriológico, e a especificidade diagnóstica foi superior ao SAT ou ao RBPT. Um método MB-qPCR altamente sensível e específico para DNA de Brucella foi estabelecido com sucesso, provando ser uma ferramenta útil no diagnóstico molecular de brucelose.(AU)

Evaluation of genome similarities using a wavelet-domain approach

Abstract INTRODUCTION: Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent. METHODS: The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent. RESULTS: The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains. CONCLUSION: The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.

Caracterização de mecanismos de regulação transcricional dos genes do sistema de secreção do tipo VI em Klebsiella pneumoniae / Characterization of mechanisms of transcriptional regulation of genes in the type VI secretion system in Klebsiella pneumoniae

Klebsiella pneumoniae é um patógeno oportunista que causa principalmente infecções respiratórias e do trato urinário. A ocorrência frequente de isolados virulentos resistentes a múltiplas drogas levou a inclusão dessa espécie na lista da OMS das principais prioridades para pesquisa e desenvolvimento de alternativas terapêuticas. O conhecimento abrangente dos mecanismos moleculares subjacentes à virulência da K. pneumoniae pode levar à proposta de medicamentos mais eficientes e específicos. O Sistema de Secreção Tipo VI (T6SS) contribui para a competição bacteriana, invasão celular e colonização in vivo. Apesar dos estudos que mostram o envolvimento do T6SS na patogênese da K. pneumoniae, pouco se conhece sobre a regulação de sua expressão. O entendimento dos mecanismos regulatórios pode fornecer pistas sobre a função desse sistema e contribuir para o desenvolvimento de novas abordagens terapêuticas para o tratamento de infecções por K. pneumoniae. Esse trabalho teve como objetivo identificar mecanismos de regulação transcricional dos genes do T6SS de K. pneumoniae

Para isso, analisamos os genomas de três cepas (Kp52.145, HS11286 e NTUH-K2044) de forma a predizer e padronizar a anotação dos genes de T6SS através de buscas de similaridade. Foram encontrados 38 genes do T6SS em Kp52.145, 29 em HS11286 e 30 em NTUH-K2044. Nas adjacências dos genes do T6SS foram encontrados genes envolvidos em sistemas de captação de ferro, sugerindo que o T6SS de K. pneumoniae também pode desempenhar um papel na importação de íons. Foram identificadas 17 regiões promotoras dependentes de σ70 em Kp52.145, 12 em HS11286 e 12 em NTUH-K2044. Identificamos ainda 17, 12 e 15 sequências promotoras a partir dos sítios putativos de σ54. Também identificamos 165 sítios de ligação para reguladores transcricionais em Kp52.145, 125 em HS11286 e 134 em NTUH-K2044. Nossos resultados in silico sugerem que o T6SS de K. pneumoniae seja regulado em resposta a sinais ambientais e devem direcionar experimentos in vitro que testem a resposta de K. pneumoniae a variações de temperatura (H-NS), de nutrientes (GcvA e Fis), estresse oxidativo (OxyR) e osmolaridade (RscAB e OmpR). (AU)

Application of whole genome sequencing technology and bioinformatics analysis in antimicrobial resistance researches / 生物工程学报

The emergence and spread of antimicrobial resistance has become a serious global issue. Bacterial characteristics, such as antimicrobial resistance genes, virulence-associated genes, plasmid types, and phylogenetic relationship among different strains, are the keys to unravel the occurrence and dissemination of antimicrobial resistance. However, the accuracy and efficiency of the traditional techniques, such as polymerase chain reaction and pulsed field gel electrophoresis is insufficient to underlying the mystery of antimicrobial resistance. Recently, the whole genome sequencing and high-throughput bioinformatics analysis have been successfully used in antimicrobial resistance studies, helping scientists to obtain the nature of antimicrobial resistance bacteria quickly, and more precisely to paint the evolutionary relationship among different strains. Therefore, in this study, we aim to systematically introduce the recent development of whole genome sequencing analysis, including different methods and corresponding characteristics of library preparation, platform sequencing, data analysis, and the latest application of the technology in the antimicrobial resistance research. We hope that this review can provide more comprehensive knowledge about whole genome sequencing and bioinformatic analysis for antimicrobial resistance research.

GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation / 基因组蛋白质组与生物信息学报·英文版

Identifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations (CNVs) for given genes. Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria, named as Genetic Polymorphisms Assignments (GPA). Simulation results showed that GPA has reduced the false discovery rate (FDR) and mean absolute error (MAE) in CNV and single nucleotide variant (SNV) identification. This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models, and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations. The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains. Also, the framework together with the genome annotation and population comparison tools has been integrated into an application, which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples. The GPA package is available at https://github.com/IID-DTH/GPA-package.

Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates / 基因组蛋白质组与生物信息学报·英文版

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.

Whole Genome Sequence Determination and Analysis of Strain CGMCC 12426 / 中国医学科学院学报

Objective To describe the microbiological characteristics of ()CGMCC 12426 and determine and analyze its complete genome sequences.Methods strain CGMCC 12426 genomic DNA sequencing was performed on a single molecule real-time sequencing(SMRT)platform and the annotation was completed in the NCBI Prokaryotic Genomic Annotation Pipeline(pGAP).Results The complete genomic sequences of the released CGMCC 12426 consisted of a 4 138 265-bp circular chromosome and a 74 165-bp plasmid,which resulted in the prediction of 4581 genes including 4222 coding sequences,87 tRNAs,and 30 rRNAs(which included 5S rRNA,16S rRNA,and 23S rRNA).Conclusion The genome sequencing provided a basis for further investigations on the genetic background of and on the metabolic and regulatory mechanisms.

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil

ABSTRACT The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an "eco-friendly agricultural practice". Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA-DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils.

Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium

Abstract Paraburkholderia tropica (syn Burkholderia tropica) are nitrogen-fixing bacteria commonly found in sugarcane. The Paraburkholderia tropica strain Ppe8 is part of the sugarcane inoculant consortium that has a beneficial effect on yield. Here, we report a draft genome sequence of this strain elucidating the mechanisms involved in its interaction mainly with Poaceae. A genome size of approximately 8.75 Mb containing 7844 protein coding genes distributed in 526 subsystems was de novo assembled with ABySS and annotated by RAST. Genes related to the nitrogen fixation process, the secretion systems (I, II, III, IV, and VI), and related to a variety of metabolic traits, such as metabolism of carbohydrates, amino acids, vitamins, and proteins, were detected, suggesting a broad metabolic capacity and possible adaptation to plant association.

Genome sequence of Streptomyces gilvigriseus MUSC 26T isolated from mangrove forest

Abstract Streptomycetes remain as one of the important sources for bioactive products. Isolated from the mangrove forest, Streptomyces gilvigriseus MUSC 26T was previously characterised as a novel streptomycete. The high quality draft genome of MUSC 26T contained 5,213,277 bp with G + C content of 73.0%. Through genome mining, several gene clusters associated with secondary metabolites production were revealed in the genome of MUSC 26T. These findings call for further investigations into the potential exploitation of the strain for production of pharmaceutically important compounds.

Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis

Background: Draft and complete genome sequences from bacteria are key tools to understand genetic determinants involved in pathogenesis in several disease models. Piscirickettsia salmonis is a Gram-negative bacterium responsible for the Salmon Rickettsial Syndrome (SRS), a bacterial disease that threatens the sustainability of the Chilean salmon industry. In previous reports, complete and draft genome sequences have been generated and annotated. However, the lack of transcriptome data underestimates the genetic potential, does not provide information about transcriptional units and contributes to disseminate annotation errors. Results: Here we present the draft genome and transcriptome sequences of four P. salmonis strains. We have identified the transcriptional architecture of previously characterized virulence factors and trait-specific genes associated to cation uptake, metal efflux, antibiotic resistance, secretion systems and other virulence factors. Conclusions: This data has provided a refined genome annotation and also new insights on the transcriptional structures and coding potential of this fish pathogen.

Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as "Salar del Huasco", located in the Altiplano in the North of Chile

ABSTRACT In this report, we present a draft genome of 2,886,173 bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.

Genome sequence of Streptomyces mangrovisoli MUSC 149T isolated from intertidal sediments

ABSTRACT As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149T was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149T comprises 9,165,825 bp with G + C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites. The presence of these biosynthetic gene clusters in MUSC 149T suggests the potential exploitation of the strain for production of medically important compounds.

Draft genome sequence of Chryseobacterium limigenitum SUR2T (LMG 28734T) isolated from dehydrated sludge

ABSTRACT The type strain SUR2 of the novel species Chryseobacterium limigenitum was isolated from a dehydrated sludge of the municipal sewage treatment plant in Dogoše near Maribor in Slovenia. The draft genome, with 60 contigs, 4,697,725 bp, 34.4% of G+C content, was obtained using the Illumina HiSeq 2500-1 platform. Joint Genome Institute Microbial Genome Annotation Pipeline (MGAP v.4) has identified 4322 protein-coding sequences including resistance genes against arsenic and other heavy metals. In addition, a subclass B3 metallo-β-lactamase, which confers resistance to penicillins, cephalosporins and carbapenems, was also present in the genome. The genome sequence provides important information regarding bioremediation potential and pathogenic properties of this newly identified species.

Draft genome sequence of Vitellibacter aquimaris D-24T isolated from seawater

ABSTRACT Vitellibacter aquimaris D-24T (=KCTC 42708T = DSM 101732T), a halophilic marine bacterium, was isolated from seawater collected from Desaru beach, Malaysia. Here, we present the draft genome sequence of D-24T with a genome size of approximately 3.1 Mbp and G + C content of 39.93%. The genome of D-24T contains genes involved in reducing a potent greenhouse gas (N2O) in the environment and the degradation of proteinaceous compounds. Genome availability will provide insights into potential biotechnological and environmental applications of this bacterium.

Genome sequencing of two Bacillus anthracis strains: a virulent strain and a vaccinal strain

ABSTRACT Bacillus anthracis strain SPV842_15 was isolated from bovine fetus, while B. anthracis strain Brazilian vaccinal was recovered from a commercial vaccine. We report here the genome sequences of both strains. The SPV842_15 genome is composed of a single circular chromosome with a length of 5,228,664 base pairs, and comprises 5911 coding sequences. In turn, the Brazilian vaccinal genome remains in 201 contigs with 5733 coding sequences. Both genomes have an overall C + G content of 35.4%, and 11 genes encoding the ribosomal RNAs (rRNAs) 5S, 16S and 23S. Only the plasmid pX01 sequence, which carries genes for toxins synthesis, was detected and completely assembled for both strains. These plasmids have a length of 181,684 base pairs and a C + G content of 32.5%. These genomic data generate insights about vaccinal B. anthracis virulence.

Complete genome sequence of human pathogen Kosakonia cowanii type strain 888-76T

ABSTRACT Kosakonia cowanii type strain 888-76T is a human pathogen which was originally isolated from blood as NIH group 42. In this study, we report the complete genome sequence of K. cowanii 888-76T. 888-76T has 1 chromosome and 2 plasmids with a total genome size of 4,857,567 bp and C+G 56.15%. This genome sequence will not only help us to understand the virulence features of K. cowanii 888-76T but also provide us the useful information for the study of evolution of Kosakonia genus.