Min Wu

Bio: Min Wu is an academic researcher from Zhejiang University. The author has contributed to research in topics: Halomonas & Natrinema. The author has an hindex of 24, co-authored 88 publications receiving 1658 citations.

Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China

Abstract: Three strains of Gram-negative, aerobic, neutrophilic and halophilic bacteria were isolated from samples of a salt lake on the Qinghai-Tibet Plateau and a subterranean saline well in the Si-Chuan Basin of China. These isolates, designated AJ275(T), AJ282(T) and ZG16(T), were investigated using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the isolates could be affiliated to the genus Halomonas. Genomic DNA G+C contents were 65.9 mol% for AJ275(T), 56.7 mol% for AJ282(T) and 57.6 mol% for ZG16(T). The results of DNA-DNA hybridizations, fatty acid analysis and physiological and biochemical tests allowed the isolates to be differentiated genotypically and phenotypically from closely related species. It is proposed that strains AJ275(T) (=CGMCC 1.6493(T)=JCM 14606(T)=LMG 23976(T)), AJ282(T) (=CGMCC 1.6494(T)=JCM 14607(T)=LMG 23978(T)) and ZG16(T) (=CGMCC 1.6495(T)=JCM 14608(T)=LMG 23977(T)) represent the type strains of three novel species in the genus Halomonas: Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., respectively.

Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

Abstract: The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22(T) can completely degrade alginate. This work reveals that strain HZ22(T) has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22(T) are worth further research.

Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae.

Abstract: Two Gram-negative, motile, aerobic bacterial strains, designated B2T and 1_C16_27T, were respectively isolated from a seawater sample collected from the East China Sea and a semi-coke sample from north-eastern Estonia. Their genetic, phenotypic and chemotaxonomic properties were studied. The isolates were short rods with polar flagella and were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids. The major fatty acids were nonadecanoic (C19 : 0 cyclo), octadecanoic (C18 : 0 and C18 : 0 3-OH), octadecenoic (C18 : 1) and hexadecanoic (C16 : 0) acids. The G+C content of the genomic DNA was 58.1–59.3 mol%. 16S rRNA gene sequence analysis revealed that the two isolates represent a distinct lineage within the family Hyphomicrobiaceae. The phylogenetically closest relatives were Cucumibacter (92.7–93.7 % 16S rRNA gene sequence similarity), Devosia (92.9–94.4 %) and Zhangella (91.7–92.1 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strains B2T and 1_C16_27T could be differentiated from each other and from members of the genera Cucumibacter, Devosia and Zhangella. Therefore, it is proposed that strains B2T and 1_C16_27T represent two novel species in a new genus, for which the names Pelagibacterium halotolerans gen. nov., sp. nov. (the type species; type strain B2T = CGMCC 1.7692T = JCM 15775T) and Pelagibacterium luteolum sp. nov. (type strain 1_C16_27T = CGMCC 1.10267T = JCM 16552T = CELMS EEUT 1C1627T) are proposed.

Haloferax larsenii sp. nov., an extremely halophilic archaeon from a solar saltern.

Abstract: Three strains of Gram-negative, aerobic, neutrophilic, extremely halophilic archaea, designated ZJ206(T), ZJ203 and ZJ204, were isolated from a solar saltern in Zhe-Jiang Province, China. Phenotypically and on the basis of 16S rRNA gene sequences, the strains were very similar. Comparative 16S rRNA gene analysis revealed 96.4-97.4 % sequence similarity to members of the genus Haloferax. The major polar lipids were C(20)C(20) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, diglycosyl glycerol diether and sulfated diglycosyl diether. The DNA G+C content of strain ZJ206(T) was 62.2 mol%. The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from closely related species. Therefore the isolates should be classified as members of a novel species, for which the name Haloferax larsenii sp. nov. is proposed. The type strain is ZJ206(T) (=CGMCC 1.5347(T)=JCM 13917(T)).

Current opinions on autophagy in pathogenicity of fungi.

Abstract: The interaction between pathogens and their host plants is a ubiquitous process. Some plant fungal pathogens can form a specific infection structure, such as an appressorium, which is formed by the accumulation of a large amount of glycerin and thereby the creation of an extremely high intracellular turgor pressure, which allows the penetration peg of the appressorium to puncture the leaf cuticle of the host. Previous studies have shown that autophagy energizes the accumulation of pressure by appressoria, which induces its pathogenesis. Similar to other eukaryotic organisms, autophagy processes are highly conserved pathways that play important roles in filamentous fungal pathogenicity. This review aims to demonstrate how the autophagy process affects the pathogenicity of plant pathogens.

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

Abstract: 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.

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

Abstract: 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.