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July 7, 2019

Complete genome sequence of Lelliottia nimipressuralis type strain SGAir0187, isolated from tropical air collected in Singapore.

Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples collected in Singapore. The genome was assembled with an average coverage of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end reads. The genome measures 4.8?Mb and contains 4,424 protein-coding genes, 83 tRNAs, and 25 rRNAs. Copyright © 2018 Heinle et al.

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July 7, 2019

Complete genome sequence of Acinetobacter indicus type strain SGAir0564 isolated from tropical air collected in Singapore.

Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits. Copyright © 2018 Vettath et al.

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July 7, 2019

Genome sequence of Bacillus cereus strain TG1-6, a plant-beneficial rhizobacterium that is highly salt tolerant.

The complete genome sequence of Bacillus cereus strain TG1-6, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress, is reported here. The sequencing process was performed based on a combination of pyrosequencing and single-molecule sequencing. The complete genome is estimated to be approximately 5.42?Mb, containing a total of 5,610 predicted protein-coding DNA sequences (CDSs). Copyright © 2018 Vílchez et al.

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July 7, 2019

Complete genome sequence of Staphylococcus haemolyticus type strain SGAir0252.

Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the skin microbiome and an opportunistic human pathogen. The strain SGAir0252 was isolated from tropical air samples collected in Singapore, and its complete genome comprises one chromosome of 2.63?Mb and one plasmid of 41.6?kb. Copyright © 2018 Premkrishnan et al.

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July 7, 2019

First detection of a blaCTX-M-15-carrying plasmid in Vibrio alginolyticus.

Vibrio alginolyticus is a gram-negative halophilic bacterium, widely distributed in sea-water and seafood all over the world and is the main pathogenic bacteria of marine animals such as fish, shrimp and shellfish. Besides, it is also an important human pathogen causing eye, ear and wound infections, as well as gastroenteritis, septicemia, and necrotizing fasciitis [1]. Resistance to extended-spectrum cephalosporins is rarely ob- served in V. alginolyticus. Here, we report for the first time the identification of a foodborne V. alginolyticus strain Vb0506 carrying plasmid encoding blaCTX-M-15.

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July 7, 2019

Complete genome sequence of Colwellia hornerae PAMC 20917, a cold-active enzyme-producing bacterium isolated from the Arctic Ocean sediment

Psychrophilic bacteria are considered a source of cold-active enzymes that can be used in industrial applications. The Arctic bacterium Colwellia hornerae PAMC 20917 strain has been isolated from the offshore sediment near Ny-Ålesund, Svalbard. The optimal growth temperature of the strain was 10?°C on marine agar. The cell lysate showed alkaline phosphatase activities. Analysis of the enzymatic properties showed that the alkaline phosphatase was cold-active and thermolabile. To explore useful cold-active industrial enzymes further, the entire genome of the PAMC 20917 strain was sequenced. The genome of the strain contained 4,684,314 nucleotides, with 37.87% G+C content. Genome mining analysis revealed that, in the complete genome sequence, three proteins were annotated as alkaline phosphatases. The genome of PAMC 20917 encodes cold shock proteins and an ice-binding protein that inhibits the growth of ice, allowing the bacterium to adapt to cold environments. This genome information may be useful for understanding mechanisms of adaptation to cold stress.

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July 7, 2019

Identification of Pseudomonas mosselii BS011 gene clusters required for suppression of Rice Blast Fungus Magnaporthe oryzae.

Pseudomonas is a Gram-negative, rod-shaped bacteria. Many members of this genus displayed remarkable physiological and metabolic activity against different plant pathogens. However, Pseudomonas mosselii has not yet been characterized in biocontrol against plant disease. Here we isolated a strain of P. mosselii BS011 from the rhizosphere soil of rice plants, and the isolate showed strong inhibitory activity against the rice blast fungus Magnaporthe oryzae. Further we sequenced the complete genome of BS011, which consist of 5.75?Mb with a circular chromosome, 5,170 protein-coding genes, 23 rRNA and 78 tRNA operons. Bioinformatic analysis revealed that seven gene clusters may be involved in the biosynthesis of metabolites. Gene deletion experiments demonstrated that the gene cluster c-xtl is required for inhibitory activity against M. oryzae. Bioassay showed that the crude extract from BS011 fermentation sample significantly inhibited the development of M. oryzae at a concentration of 10?µg/ml. Besides, we illustrated that the crude extract of BS011 impaired the appressorial formation in a dose dependent manner. Collectively our results revealed that P. mosselii BS011 is a promising biocontrol agent and the gene cluster c-xtl is essential for inhibiting the development of M. oryzae. Copyright © 2018. Published by Elsevier B.V.

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July 7, 2019

Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. áviolaceum

Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.

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July 7, 2019

Short genome report of cellulose-producing commensal Escherichia coli 1094.

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E. coli strains. Data deposition: The annotated genome sequence has been deposited at the European Nucleotide Archive under the accession number PRJEB21000.

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July 7, 2019

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.

Thiodictyon syntrophicum sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.

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July 7, 2019

Complete genome sequence of Gordonia sp. YC-JH1, a bacterium efficiently degrading a wide range of phthalic acid esters.

Phthalic acid esters (PAEs) are a family of recalcitrant pollutants mainly used as plasticizer. The strain Gordonia sp.YC-JH1, isolated from petroleum-contaminated soil, is capable of efficiently degrading a wide range of PAEs. In order to pertinently investigate the genetic mechanism of PAEs catabolism by strain YC-JH1, its complete genome sequencing has been performed by SMRT sequencing technology. The genome comprises a circular chromosome and a plasmid with a size of 4,101,557 bp and 91,767 bp respectively. Based on the genome sequence, 3563 protein-coding genes are predicted, of which the genes responsible for PAEs degradation are identified, including the two genes of PAEs hydrolase and the gene clusters for phthalic acid and protocatechuic acid degradation. The genome information provides genomic basis of PAEs degradation to allow the complete metabolism of PAEs. The wide substrate spectrum and its genetic basis of this strain should expand its application potential for environments bioremediation, provide novel gene resources involved in PAEs degradation for biotechnology and gene engineering, and contribute to shed light on the mechanism of PAEs metabolism. Copyright © 2018. Published by Elsevier B.V.

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July 7, 2019

Draft genome sequence of lytic bacteriophage SA7 infecting Staphylococcus aureus isolates

Staphylococcus aureus is a Gram-positive and a round-shaped bacterium of Firmicutes phylum, and is a common cause of skin infections, respiratory infections, and food poisoning. Bacteriophages infecting S. aureus can be an effective treatment for S. aureus infections. Here, the draft genomic sequence is announced for a lytic bacteriophage SA7 infecting S. aureus isolates. The bacteriophage SA7 was isolated from a sewage water sample near a livestock farm in Chungcheongnam-do, South Korea. SA7 has a genome of 34,730 bp and 34.1% G + C content. The genome has 53 protein-coding genes, 23 of which have predicted functions from BLASTp analysis, leaving the others conserved proteins with unknown function.

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