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Standards in Genomic Sciences

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https://www.readbyqxmd.com/read/28078051/complete-genome-sequence-of-pseudomonas-brassicacearum-strain-l13-6-12-a-biological-control-agent-from-the-rhizosphere-of-potato
#1
Christin Zachow, Henry Müller, Jana Monk, Gabriele Berg
Pseudomonas brassicacearum strain L13-6-12 is a rhizosphere colonizer of potato, lettuce and sugar beet. Previous studies have shown that this motile, Gram-negative, non-sporulating bacterium is an effective biocontrol agent against different phytopathogens. Here, we announce and describe the complete genome sequence of P. brassicacearum L13-6-12 consisting of a single 6.7 Mb circular chromosome that consists of 5773 protein coding genes and 85 RNA-only encoding genes. Genome analysis revealed genes encoding specialized functions for pathogen suppression, thriving in the rhizosphere and interacting with eukaryotic organisms...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28078050/complete-genome-sequence-of-lutibacter-profundi-lp1-t-isolated-from-an-arctic-deep-sea-hydrothermal-vent-system
#2
Juliane Wissuwa, Sven Le Moine Bauer, Ida Helene Steen, Runar Stokke
Lutibacter profundi LP1(T) within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki's Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1(T) is the first genome to be published within the genus Lutibacter. L. profundi LP1(T) consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28074122/high-quality-draft-genome-of-nakamurella-lactea-type-strain-a-rock-actinobacterium-and-emended-description-of-nakamurella-lactea
#3
Imen Nouioui, Markus Göker, Lorena Carro, Maria Del Carmen Montero-Calasanz, Manfred Rohde, Tanja Woyke, Nikos C Kyrpides, Hans-Peter Klenk
Nakamurella lactea DLS-10(T), isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10(T) and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10(T) presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28074121/complete-genome-sequence-and-whole-genome-phylogeny-of-kosmotoga-pacifica-type-strain-slhlj1-t-from-an-east-pacific-hydrothermal-sediment
#4
Lijing Jiang, Stéphane L'Haridon, Mohamed Jebbar, Hongxiu Xu, Karine Alain, Zongze Shao
Kosmotoga pacifica strain SLHLJ1(T) is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28074120/complete-genome-sequence-of-the-heavy-metal-resistant-bacterium-agromyces-aureus-ar33-t-and-comparison-with-related-actinobacteria
#5
Erika Corretto, Livio Antonielli, Angela Sessitsch, Stéphane Compant, Christoph Höfer, Markus Puschenreiter, Günter Brader
Agromyces aureus AR33(T) is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete genome sequence which is 4,373,124 bp long and has a GC content of 70.1%. Furthermore, we performed a comparative genomic analysis with other related organisms: 6 Agromyces spp...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28074119/complete-genome-sequence-of-the-salmonella-enterica-serovar-enteritidis-bacteriophages-fse1c-and-fse4c-isolated-from-food-matrices
#6
Javier Santander, Jose I Vasquez, Cristopher Segovia, Leonardo Santos, Gabriel Turra, Karen Huber, James Robeson
Salmonella enterica serovar Enteritidis is one of the most common causes of Salmonellosis worldwide. Utilization of bacteriophages as prophylactic agents is a practical solution to prevent Salmonellosis in ready-to-eat products. Shelf stability is one of the desirable properties for prophylactic bacteriophages. Here, we describe the phenotype, genome, and phylogeny of fSE1C and fSE4S Salmonella bacteriophages. fSE1C and fSE4S were previously isolated from pickle sauce and ground beef respectively and selected for their significant shelf stability...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28031775/complete-genome-sequence-of-the-actinomycete-actinoalloteichus-hymeniacidonis-type-strain-hpa-177-t-isolated-from-a-marine-sponge
#7
Lena Schaffert, Andreas Albersmeier, Anika Winkler, Jörn Kalinowski, Sergey B Zotchev, Christian Rückert
Actinoalloteichus hymeniacidonis HPA 177(T) is a Gram-positive, strictly aerobic, black pigment producing and spore-forming actinomycete, which forms branching vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis. Actinomycete bacteria are prolific producers of secondary metabolites, some of which have been developed into anti-microbial, anti-tumor and immunosuppressive drugs currently used in human therapy. Considering this and the growing interest in natural products as sources of new drugs, actinomycete bacteria from the hitherto poorly explored marine environments may represent promising sources for drug discovery...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27999625/genome-sequence-and-overview-of-oligoflexus-tunisiensis-shr3-t-in-the-eighth-class-oligoflexia-of-the-phylum-proteobacteria
#8
Ryosuke Nakai, Takatomo Fujisawa, Yasukazu Nakamura, Tomoya Baba, Miyuki Nishijima, Fatma Karray, Sami Sayadi, Hiroko Isoda, Takeshi Naganuma, Hironori Niki
Oligoflexus tunisiensis Shr3(T) is the first strain described in the newest (eighth) class Oligoflexia of the phylum Proteobacteria. This strain was isolated from the 0.2-μm filtrate of a suspension of sand gravels collected in the Sahara Desert in the Republic of Tunisia. The genome of O. tunisiensis Shr3(T) is 7,569,109 bp long and consists of one scaffold with a 54.3% G + C content. A total of 6,463 genes were predicted, comprising 6,406 protein-coding and 57 RNA genes. Genome sequence analysis suggested that strain Shr3(T) had multiple terminal oxidases for aerobic respiration and various transporters, including the resistance-nodulation-cell division-type efflux pumps...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27999624/complete-genome-sequence-of-new-bacteriophage-phie142-which-causes-simultaneously-lysis-of-multidrug-resistant-escherichia-coli-o157-h7-and-salmonella-enterica
#9
Luis Amarillas, Cristobal Chaidez, Arturo González-Robles, Josefina León-Félix
The emergence of antibiotic-resistant foodborne bacteria is a global health problem that requires immediate attention. Bacteriophages are a promising biotechnological alternative approach against bacterial pathogens. However, a detailed analysis of phage genomes is essential to assess the safety of the phages prior to their use as biocontrol agents. Therefore, here we report the complete genome sequence of bacteriophage phiE142, which is able to lyse Salmonella and multidrug-resistant Escherichia coli O157:H7 strains...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27980706/metagenome-phylogenetic-profiling-of-microbial-community-evolution-in-a-tetrachloroethene-contaminated-aquifer-responding-to-enhanced-reductive-dechlorination-protocols
#10
Rebecca A Reiss, Peter Guerra, Oleg Makhnin
Chlorinated solvent contamination of potable water supplies is a serious problem worldwide. Biostimulation protocols can successfully remediate chlorinated solvent contamination through enhanced reductive dechlorination pathways, however the process is poorly understood and sometimes stalls creating a more serious problem. Whole metagenome techniques have the potential to reveal details of microbial community changes induced by biostimulation. Here we compare the metagenome of a tetrachloroethene contaminated Environmental Protection Agency Superfund Site before and after the application of biostimulation protocols...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27942352/complete-genome-anatomy-of-the-emerging-potato-pathogen-dickeya-solani-type-strain-ipo-2222-t
#11
Slimane Khayi, Pauline Blin, Teik Min Chong, Kok-Gan Chan, Denis Faure
Several species of the genus Dickeya provoke soft rot and blackleg diseases on a wide range of plants and crops. Dickeya solani has been identified as the causative agent of diseases outbreaks on potato culture in Europe for the last decade. Here, we report the complete genome of the D. solani IPO 2222(T). Using PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp was assembled. The G + C content reaches 56% and the genomic sequence contains 4,059 predicted proteins. The ANI values calculated for D...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27833718/two-draft-genome-sequences-of-pseudomonas-jessenii-strains-isolated-from-a-copper-contaminated-site-in-denmark
#12
Yanan Qin, Dan Wang, Kristian K Brandt, Christopher Rensing
Pseudomonas jessenii C2 and Pseudomonas jessenii H16 were isolated from low-Cu and high-Cu industrially contaminated soil, respectively. P. jessenii H16 displayed significant resistance to copper when compared to P. jessenii C2. Here we describe genome sequences and interesting features of these two strains. The genome of P. jessenii C2 comprised 6,420,113 bp, with 5814 protein-coding genes and 67 RNA genes. P. jessenii H16 comprised 6,807,788 bp, with 5995 protein-coding genes and 70 RNA genes. Of special interest was a specific adaptation to this harsh copper-contaminated environment as P...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27800124/draft-genome-sequence-of-streptomyces-sp-tp-a0867-an-alchivemycin-producer
#13
Hisayuki Komaki, Natsuko Ichikawa, Akio Oguchi, Moriyuki Hamada, Enjuro Harunari, Shinya Kodani, Nobuyuki Fujita, Yasuhiro Igarashi
Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated alchivemycins A and B. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation, and analysis of the genome sequence. The 9.9 Mb genome of Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were assigned with COG categories. We successfully identified a hybrid polyketide synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27795808/draft-genome-sequence-of-micromonospora-sp-dsw705-and-distribution-of-biosynthetic-gene-clusters-for-depsipeptides-bearing-4-amino-2-4-pentadienoate-in-actinomycetes
#14
Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, Enjuro Harunari, Arisa Ishikawa, Yasuhiro Igarashi
Here, we report the draft genome sequence of Micromonospora sp. DSW705 (=NBRC 110037), a producer of antitumor cyclic depsipeptides rakicidins A and B, together with the features of this strain and generation, annotation, and analysis of the genome sequence. The 6.8 Mb genome of Micromonospora sp. DSW705 encodes 6,219 putative ORFs, of which 4,846 are assigned with COG categories. The genome harbors at least three type I polyketide synthase (PKS) gene clusters, one nonribosomal peptide synthetase (NRPS) gene clusters, and three hybrid PKS/NRPS gene clusters...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27785333/draft-genome-sequence-of-streptomyces-sp-mww064-for-elucidating-the-rakicidin-biosynthetic-pathway
#15
Hisayuki Komaki, Arisa Ishikawa, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, Enjuro Harunari, Takuya Nihira, Watanalai Panbangred, Yasuhiro Igarashi
Streptomyces sp. MWW064 (=NBRC 110611) produces an antitumor cyclic depsipeptide rakicidin D. Here, we report the draft genome sequence of this strain together with features of the organism and generation, annotation and analysis of the genome sequence. The 7.9 Mb genome of Streptomyces sp. MWW064 encoded 7,135 putative ORFs, of which 6,044 were assigned with COG categories. The genome harbored at least three type I polyketide synthase (PKS) gene clusters, seven nonribosomal peptide synthetase (NRPS) gene clusters, and four hybrid PKS/NRPS gene clusters, from which a hybrid PKS/NRPS gene cluster responsible for rakicidin synthesis was successfully identified...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777652/draft-genome-of-prochlorothrix-hollandica-ccap-1490-1-t-calu1027-the-chlorophyll-a-b-containing-filamentous-cyanobacterium
#16
Natalia Velichko, Mikhail Rayko, Ekaterina Chernyaeva, Alla Lapidus, Alexander Pinevich
Prochlorothrix hollandica is filamentous non-heterocystous cyanobacterium which possesses the chlorophyll a/b light-harvesting complexes. Despite the growing interest in unusual green-pigmented cyanobacteria (prochlorophytes) to date only a few sequenced genome from prochlorophytes genera have been reported. This study sequenced the genome of Prochlorothrix hollandica CCAP 1490/1(T) (CALU1027). The produced draft genome assembly (5.5 Mb) contains 3737 protein-coding genes and 114 RNA genes.
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777651/draft-genome-sequence-of-the-marine-rhodobacteraceae-strain-o3-65-cultivated-from-oil-polluted-seawater-of-the-deepwater-horizon-oil-spill
#17
Helge-Ansgar Giebel, Franziska Klotz, Sonja Voget, Anja Poehlein, Katrin Grosser, Andreas Teske, Thorsten Brinkhoff
The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777650/complete-genome-sequence-of-methanoculleus-bourgensis-strain-mab1-the-syntrophic-partner-of-mesophilic-acetate-oxidising-bacteria-saob
#18
Shahid Manzoor, Anna Schnürer, Erik Bongcam-Rudloff, Bettina Müller
Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been assigned tentative functions...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777649/genome-sequences-and-annotation-of-two-urinary-isolates-of-e-coli
#19
Travis K Price, Arya Mehrtash, Laurynas Kalesinskas, Kema Malki, Evann E Hilt, Catherine Putonti, Alan J Wolfe
The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis...
2016: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/27777648/mixs-hcr-a-mixs-extension-defining-a-minimal-information-standard-for-sequence-data-from-environments-pertaining-to-hydrocarbon-resources
#20
Nicolas Tsesmetzis, Pelin Yilmaz, Peter C Marks, Nikos C Kyrpides, Ian M Head, Bart P Lomans
Here we introduce a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources. The proposed MIxS-HCR package incorporates the core features of the MIxS standard for marker gene (MIMARKS) and metagenomic (MIMS) sequences along with a hydrocarbon resources customized environmental package. Adoption of the MIxS-HCR standard will enable the comparison and better contextualization of investigations related to hydrocarbon rich environments. The insights from such standardized way of reporting could be highly beneficial for the successful development and optimization of hydrocarbon recovery processes and management of microbiological issues in petroleum production systems...
2016: Standards in Genomic Sciences
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