SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

UNLABELLED: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. AVAILABILITY AND IMPLEMENTATION: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/.

/pdf/prokka-rapid-prokaryotic-genome-annotation-4t1evn8spy.pdf

Prokka: Rapid Prokaryotic Genome Annotation

The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict subcellular localization based on these sorting signals and other sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed step-by-step instructions for the coupled use of the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular.

/pdf/locating-proteins-in-the-cell-using-targetp-signalp-and-39i9pd64rh.pdf

Locating proteins in the cell using TargetP, SignalP and related tools

How much does the microbiota influence the host's phenotype? Ridaura et al. ([1241214][1] ; see the Perspective by [ Walker and Parkhill ][2]) obtained uncultured fecal microbiota from twin pairs discordant for body mass and transplanted them into adult germ-free mice. It was discovered that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids. Moreover, obese-phenotype mice were invaded by members of the Bacteroidales from the lean mice, but, happily, the lean animals resisted invasion by the obese microbiota.

 [1]: http://www.sciencemag.org/content/341/6150/1241214.full
 [2]: /lookup/doi/10.1126/science.1243787

/pdf/gut-microbiota-from-twins-discordant-for-obesity-modulate-5aeltwsuvw.pdf

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Azoarcus sp. strain EbN1 can metabolize many aromatic compounds, including hydrocarbons (Rabus et al., 2005). Although other organisms such as Pseudomonas putida KT2440 can also catabolize aromatics (Jimenez et al., 2002), Azoarcus sp. strain EbN1 can catabolize aromatics under both aerobic and anaerobic conditions. The main chromosome is ~4?3 Mbp long and is GC-rich (see Table 1). There are also two large plasmids, each around 200 kbp in length. Genes encoding more than 150 proteins involved in aromatic degradation were found, in keeping with this organism’s known biochemical lifestyle.

Genome update: 2D clustering of bacterial genomes.

Arsukibacterium ikkense GCM72T and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve as sources of future industrial enzymes.

https://journals.asm.org/doi/pdf/10.1128/genomeA.00585-15

Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments.

Nine new microbial genomes have been published since the last Genome Update was written, seven of which are from bacterial organisms and the other two are Plasmodium genomes. These are summarized in Table 1 and include two a-Proteobacteria, Anaplasma marginale and Zymomonas mobilis, the latter of which is an ethanologenic bacterium; the deep-sea c-proteobacterium Idiomarina loihiensis; the thermophilic Bacillus-related species Geobacillus kaustophilus; a PCE-dechlorinating bacterium, Dehalococcoides ethenogenes, which is the first sequenced genome from the phylum Chloroflexi; Salmonella enterica, which causes typhoid in humans; and Campylobacter jejuni, which is the major cause of human bacterial gastroenteritis. The two Plasmodium genomes, Plasmodium chabaudi and Plasmodium berghei, have also been sequenced for use as model malaria species. A brief discussion of these is given below.

Genome update: base skews in 200+ bacterial chromosomes.

Genomes of the month There are four new microbial genomes listed in this month’s Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1. The method of genome comparison this month is that of genome alignment and, as an example, an alignment of seven Staphylococcus aureus genomes and one Staphylococcus epidermidis genome is presented.

Genome update: alignment of bacterial chromosomes

Rhodonellum psychrophilum GCM71 T , isolated from the cold and alkaline submarine ikaite columns in the Ikka Fjord in Greenland, displays optimal growth at 5 to 10°C and pH 10. Here, we report the draft genome sequence of this strain, which may provide insight into the mechanisms of adaptation to these extreme conditions.

/pdf/draft-genome-sequence-of-the-psychrophilic-and-alkaliphilic-20cbc6fwsy.pdf

Peter Fischer Hallin

Papers

Genome update: 2D clustering of bacterial genomes.

Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments.

Genome update: base skews in 200+ bacterial chromosomes.

Genome update: alignment of bacterial chromosomes

Draft genome sequence of the psychrophilic and alkaliphilic Rhodonellum psychrophilum strain GCM71T