The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Evolution of Protein Molecules

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

http://academic.oup.com/milmed/article-pdf/146/1/60/24125826/milmed-146-1-60.pdf

Biochemical Tests for Identification of Medical Bacteria

Venn diagrams with three curves are used extensively in various medical and scientific disciplines to visualize relationships between data sets and facilitate data analysis. The area of the regions formed by the overlapping curves is often directly proportional to the cardinality of the depicted set relation or any other related quantitative data. Drawing these diagrams manually is difficult and current automatic drawing methods do not always produce appropriate diagrams. Most methods depict the data sets as circles, as they perceptually pop out as complete distinct objects due to their smoothness and regularity. However, circles cannot draw accurate diagrams for most 3-set data and so the generated diagrams often have misleading region areas. Other methods use polygons to draw accurate diagrams. However, polygons are non-smooth and non-symmetric, so the curves are not easily distinguishable and the diagrams are difficult to comprehend. Ellipses are more flexible than circles and are similarly smooth, but none of the current automatic drawing methods use ellipses. We present eulerAPE as the first method and software that uses ellipses for automatically drawing accurate area-proportional Venn diagrams for 3-set data. We describe the drawing method adopted by eulerAPE and we discuss our evaluation of the effectiveness of eulerAPE and ellipses for drawing random 3-set data. We compare eulerAPE and various other methods that are currently available and we discuss differences between their generated diagrams in terms of accuracy and ease of understanding for real world data.

/pdf/eulerape-drawing-area-proportional-3-venn-diagrams-using-3rj538yivx.pdf

eulerAPE: drawing area-proportional 3-Venn diagrams using ellipses.

A novel strictly anaerobic, halophilic and fermentative strain, designated E2RT, was isolated from sediments of Xiaokule salt lake in Xinjiang Province, China. Cells were straight to slightly curved, Gram-stain-positive rods that were motile by means of flagella and formed endospores. Strain E2RT was moderately halophilic and grew optimally in the presence of 7.5 % NaCl, at pH 8.0 and at 32 °C. Substrates used include yeast extract, Casamino acids, tryptone, fructose, sucrose, xylose, ribose, lactate and tartrate. Thiosulfate could be used as an accessory electron acceptor and stimulated growth. The main fermentation products from fructose were formate and acetate. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 F and iso-C13 : 0. 16S rRNA gene sequence analyses revealed that strain E2RT was related most closely to members of the genus Alkaliphilus (95.5–91.1 % similarity). The G+C content of strain E2RT was 28.5 mol%. Strain E2RT could be differentiated from its closest relatives based on its halophilic nature and its lower DNA G+C content. It could also be differentiated based on its substrate utilization pattern and relatively high levels of iso-C15 : 0. On the basis of these data, strain E2RT is considered to represent a novel species of the genus Alkaliphilus, for which the name Alkaliphilus halophilus sp. nov. is proposed. The type strain is E2RT (=CGMCC 1.5124T =JCM 16124T). An emended description of the genus Alkaliphilus is also provided.

Alkaliphilus halophilus sp. nov., a strictly anaerobic and halophilic bacterium isolated from a saline lake, and emended description of the genus Alkaliphilus

A novel strain, named S4(T), was obtained from industrial wastewater in Xiaoshan, Zhejiang Province, China Cells were Gram-negative, neutrophilic and non-spore-forming and moved by means of a polar flagellum Normal cells were 08-09 × 13-19 µm and the cells elongated to 10-25 µm when cultivated at high temperatures Strain S4(T) grew at 15-50 °C (optimum at 48 °C), pH 55-85 (optimum 70-75) and 0-2% (optimum 05%) (w/v) NaCl Ubiquinone-8 was the predominant respiratory quinone C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and C17:0 cyclo were the major cellular fatty acids The major 3-OH fatty acid was C10:0 3-OH The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminoglycolipid The genomic DNA G+C content was 688 mol% Based on 16S rRNA gene sequences alignment, the most closely related strains were members of the genera Comamonas (946-956% similarities), Giesbergeria (949-956%), Acidovorax (948-954%), Brachymonas (941-952%) and Macromonas (951%) Phylogenetic analysis showed the closest relatives of strain S4(T) were members of the genus Macromonas Based on phenotypic and phylogenetic characteristics, we suggest that strain S4(T) represents a novel species of a new genus of the family Comamonadaceae, for which the name Extensimonas vulgaris gen nov, sp nov is proposed The type strain of Extensimonas vulgaris is S4(T) (=CGMCC 110977(T)=JCM 17803(T))

Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae.

A Gram-stain-negative, short-rod-shaped bacterium, designated 22DY03T, was isolated from a sediment sample collected from the East Pacific Rise. The isolate required NaCl and grew best with 3–7 % (w/v) sea salts at temperature of between 30 and 35 °C at pH 7.0. It formed non-pigmented colonies and produced exopolysaccharide, but did not produce bacteriochlorophyll a. Strain 22DY03T was positive for hydrolysis of aesculin and Tween 20 and negative for hydrolysis of casein, DNA, gelatin, starch and Tween 40, 60 and 80. The major respiratory quinone was ubiquinone-10. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, two unidentified phospholipids and four unidentified polar lipids. The major fatty acids were C19 : 0 cyclo ω8c, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The genomic DNA G+C content was 64.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain 22DY03T should be assigned to the genus 
Roseivivax
. The 16S rRNA gene sequence similarities between the isolate and the type strains of species of the genus 
Roseivivax
were in the range of 94.1–95.8 %. On the basis of phenotypic and genotypic data, it is concluded that strain 22DY03T represents a novel species of the genus 
Roseivivax
, for which the name Roseivivax pacificus sp. nov. (type strain 22DY03T = CGMCC 1.12410T = JCM 18866T) is proposed.

Roseivivax pacificus sp. nov., isolated from deep-sea sediment.

Culturable halophilic archaeal diversity of Ayakekumu salt lake located in Xinjiang, China

A taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus 
Gilvimarinus
. ‘Gilvimarinus agarilyticus’ KCTC 23325 and 
Gilvimarinus chinensis
QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus 
Gilvimarinus
, for which the name Gilvimarinus
polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus 
Gilvimarinus
is also presented.

Min Wu

Papers

Alkaliphilus halophilus sp. nov., a strictly anaerobic and halophilic bacterium isolated from a saline lake, and emended description of the genus Alkaliphilus

Extensimonas vulgaris gen. nov., sp. nov., a member of the family Comamonadaceae.

Roseivivax pacificus sp. nov., isolated from deep-sea sediment.

Culturable halophilic archaeal diversity of Ayakekumu salt lake located in Xinjiang, China

Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus.