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More than 75 "species-level" phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet-uncultivated taxa or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly conserved 16S rRNA, pyrH, recA, and flaA genes. We utilized this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n = 71) of diverse geographical origins. This comprises phylogroup 1 (n = 23) and phylogroup 2 (n = 48) treponeme strains, including all relevant American Type Culture Collection reference strains. The taxonomy of all strains was confirmed or inferred via the analysis of ca. 1,450-bp 16S rRNA gene sequences using a combination of bioinformatic and phylogenetic approaches. Taxonomic and phylogenetic relationships between the respective treponeme strains were further investigated by analyzing individual and concatenated flaA (1,074-nucleotide [nt]), recA (1,377-nt), and pyrH (696-nt) gene sequence data sets. Our data confirmed the species differentiation between Treponema denticola (n = 41) and Treponema putidum (n = 7) strains. Notably, our results clearly supported the differentiation of the 23 phylogroup 1 treponeme strains into five distinct "species-level" phylotypes. These respectively corresponded to "Treponema vincentii" (n = 11), Treponema medium (n = 1), "Treponema sinensis" (Treponema sp. IA; n = 4), Treponema sp. IB (n = 3), and Treponema sp. IC (n = 4). In conclusion, our MLSA-based approach can be used to effectively discriminate oral treponeme taxa, confirm taxonomic assignment, and enable the delineation of species boundaries with high confidence. [ABSTRACT FROM AUTHOR]

Background:  Many countries worldwide have reported increasing numbers of emm89 group A Streptococcus (GAS) infections during last decade. Pathogen genetic factors linked to this increase need assessment.Methods:  We investigated epidemiological characteristics of emm89 GAS bacteremic infections, including 7-day and 30-day case-fatality rates, in Finland during 2004-2014 and linked them to whole-genome sequencing data obtained from corresponding strains. The Fisher exact test and exact logistic regression were used to compare differences between bacteremic infections due to emm89 GAS belonging to different genetic clades and subclades.Results:  Out of 1928 cases of GAS bacteremic infection, 278 were caused by emm89 GAS. We identified 2 genetically distinct clades, arbitrarily designated clade 2 and clade 3. Both clades were present during 2004-2008, but clade 3 increased rapidly from 2009 onward. Six subclades (designated subclades A-F) were identified within clade 3, based on phylogenetic core genome analysis. The case-fatality rate differed significantly between subclades (P < .05), with subclade D having the highest 30-day estimated case-fatality rate (19% vs 3%-14%).Conclusions:  A new emm89 clone, clade 3, emerged in 2009 and spread rapidly in Finland. Patients infected with certain subclades of clade 3 were significantly more likely to die. A specific polymerase chain reaction assay was developed to follow the spread of subclade D in 2015. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Human activities have greatly increased the input of nitrate to natural and managed ecosystems, but the fate of excess soil nitrate is still unclear. Many studies assume that dissimilatory reduction of nitrate to nitrite is an anaerobic process, but this first step of denitrification can occur in some bacteria at oxygen concentrations that are high enough to repress downstream reduction of nitrite to gaseous products. Here, we examine whether dissimilatory reduction of nitrate under aerobic conditions is an additional, underappreciated fate of nitrate in soil. Aerobic nitrate reduction occurred in soils when provided with both nitrate and a carbon source, with the greatest nitrite accumulation in the wetland sites. The addition of a nitrification inhibitor did not significantly reduce aerobic nitrate reduction activity, nor did an assimilation repressor. Average nitrite production in soils with added carbon, nitrate, and nitrification inhibitor ranged from 7.5 to 50% of added N-nitrate in a five-hour incubation. Bacteria capable of aerobic nitrate reduction were readily isolated from these soils, comprising approximately 35% of the isolates retrieved. Sequencing16S rDNA of these isolates revealed both gram-negative and gram-positive bacteria, with the majority being gram-negative proteobacteria. In six of the isolates, onset of nitrate reduction occurred at 45–86% of atmospheric oxygen concentrations. Reduction of nitrate under aerobic and semi-aerobic conditions did not result in significant enhancements in carbon dioxide production or total electron flow rate to electron acceptors. The genomes of these six isolates were sequenced and targeted RT-qPCR revealed a wide diversity of regulatory controls on the nitrate reductase(s). The results suggest that aerobic nitrate reduction can occur in diverse bacteria, have multiple types of physiological controls, and can occur independently of the gas-forming reactions of denitrification. Thus, it is an unappreciated fate of nitrate in soil. [ABSTRACT FROM AUTHOR]

[Objectives] In order to isolate lignocellulosic bacteria and find important enzyme and pathway of lignocellulose degradation from its genome, the present study was designed to isolate high-performance lignocellulosic bacteria from the soil. [Methods] Cellulose was used as the sole carbon source to isolate strains with high cellulose enzyme activities from rotten leaves. The cellulose-degrading activities were measured, and the complete genome were sequenced on the MiSeq platform. Taxonomy of strain J1 was investigated through the comparisons of its genomic sequencing with five available genomes from other bacteria. Whole genome of strain J1 was annotated by blasting on COG databases, CAZy databases and so on.[Results] Over 27 cellulose-degrading bacteria were isolated and strain J1 was finally selected. The peak value of endocellullase, filter paper enzyme activity and β-glucosidase were 0.39,0.18 and 0.11 IU·mL-1,respectively. Strain J1 was primarily identified as Pseudoxanthomonas sp. The predicted lignocellulose-degrading genes on the genome of strain J1 include β-glucosidase gene and endo-β-1,4-glucanase gene and so on. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed strain J1 could convert cellulose to ethanol. [Conclusions] Strain J1 has high lignocellulose-degrading activity and may utilize cellulose to produce ethanol. Strain J1 is a candidate for ethanol fermentative production and its genomic information provided insights into lignocellulose-degrading pathways in the environment. [ABSTRACT FROM AUTHOR]

Background. Listeriosis is a serious foodborne infection. Outbreaks of listeriosis occur rarely, but have often proved difficult to solve. In June 2014, we detected and investigated a listeriosis outbreak in Denmark using patient interviews and whole-genome sequencing (WGS). Methods. We performed WGS on Listeria monocytogenes isolates from patients and available isolates from ready-to-eat foods and compared them using single-nucleotide polymorphism (SNP) analysis. Case patients had L. monocytogenes with ≤3 SNPs (the outbreak strain) isolated in September 2013-December 2014. Through interviews, we established case patients' food and clinical histories. Food production facilities were inspected and sampled, and we performed trace-back/trace-forward of food delivery chains. Results. In total, 41 cases were identified; 17 deaths occurred (41%). An isolate from a delicatessen meat (spiced meat roll) from company A was identical to the outbreak strain. Half of the patients were infected while hospitalized/institutionalized; institutions were supplied food by company A. The outbreak strain was repeatedly isolated from further samples taken within this company and within companies in its distribution chain. Products from company Awere traced and recalled from >6000 food establishments, after which the outbreak ended. Conclusions. Ready-to-eat spiced meat roll from a single production facility caused this outbreak. The product, served sliced and cold, is popular among the elderly; serving it at hospitals probably contributed to the high case-fatality rate. WGS used for patient isolates and isolates from food control inspections, coupled with routine epidemiological follow-up, was instrumental in swiftly locating the source of infections, preventing further illnesses and deaths. [ABSTRACT FROM AUTHOR]

Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols, halides, and protons. They belong to α/β-hydrolases, and their principal catalytic mechanism is S2 nucleophilic substitution followed by the addition of water. Since HLDs generally have broad and different substrate specificities, they have various biotechnological applications. HLDs have previously been believed to be present only in bacterial strains that utilize xenobiotic halogenated compounds, and three archetypal HLDs, i.e., DhlA, DhaA, and LinB, have been intensively investigated by biochemical, structural, and computational analyses. Furthermore, by using the resulting data and target-selected random mutagenesis approaches, these HLDs have been successfully engineered to improve their substrate specificities and activities. In addition, important insights into protein evolution have been obtained by studying these HLDs. At the same time, the genome and metagenome information has revealed that HLD homologues are widely distributed in many bacterial strains, including ones that have not been reported to degrade halogenated compounds. Some of these cryptic HLD homologues have been experimentally confirmed to be 'true' HLDs with unique substrate specificities and enantioselectivities. Although their biological functions and physiological roles remain mysterious, these potential HLDs are considered promising materials for the development of new biocatalysts. [ABSTRACT FROM AUTHOR]

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care. [ABSTRACT FROM AUTHOR]