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Standards in Genomic Sciences

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https://www.readbyqxmd.com/read/28194258/complete-genome-sequence-of-pseudomonas-stutzeri-strain-rch2-isolated-from-a-hexavalent-chromium-cr-vi-contaminated-site
#1
Romy Chakraborty, Hannah Woo, Paramvir Dehal, Robert Walker, Marcin Zemla, Manfred Auer, Lynne A Goodwin, Alexey Kazakov, Pavel Novichkov, Adam P Arkin, Terry C Hazen
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28174620/complete-genome-sequence-of-thermus-brockianus-ge-1-reveals-key-enzymes-of-xylan-xylose-metabolism
#2
Christian Schäfers, Saskia Blank, Sigrid Wiebusch, Skander Elleuche, Garabed Antranikian
Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28174619/complete-genome-sequence-of-jiangella-gansuensis-strain-yim-002-t-dsm-44835-t-the-type-species-of-the-genus-jiangella-and-source-of-new-antibiotic-compounds
#3
Jian-Yu Jiao, Lorena Carro, Lan Liu, Xiao-Yang Gao, Xiao-Tong Zhang, Wael N Hozzein, Alla Lapidus, Marcel Huntemann, T B K Reddy, Neha Varghese, Michalis Hadjithomas, Natalia N Ivanova, Markus Göker, Manoj Pillay, Jonathan A Eisen, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides, Wen-Jun Li
Jiangella gansuensis strain YIM 002(T) is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here we describe the complete genome sequence and annotation of this taxon...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28168014/complete-genome-sequence-of-pseudoalteromonas-phage-vb_psps-h40-1-formerly-h40-1-that-infects-pseudoalteromonas-sp-strain-h40-and-is-used-as-biological-tracer-in-hydrological-transport-studies
#4
René Kallies, Bärbel Kiesel, Matthias Schmidt, Johannes Kacza, Nawras Ghanem, Anja Narr, Jakob Zopfi, Lukas Y Wick, Jörg Hackermüller, Hauke Harms, Antonis Chatzinotas
Pseudoalteromonas phage vB_PspS-H40/1 is a lytic phage that infects Pseudoalteromonas sp. strain H40. Both, the phage and its host were isolated in the 1970s from seawater samples collected from the North Sea near the island of Helgoland, Germany. The phage particle has an icosahedral capsid with a diameter of ~43 to 45 nm and a long non-contractile tail of ~68 nm in length, a typical morphology for members of the Siphoviridae family. The linear dsDNA genome of Pseudoalteromonas phage vB_PspS-H40/1 has a sequence length of 45,306 bp and a GC content of 40...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163828/potential-probiotic-associated-traits-revealed-from-completed-high-quality-genome-sequence-of-lactobacillus-fermentum-3872
#5
Burhan Lehri, Alan M Seddon, Andrey V Karlyshev
The article provides an overview of the genomic features of Lactobacillus fermentum strain 3872. The genomic sequence reported here is one of three L. fermentum genome sequences completed to date. Comparative genomic analysis allowed the identification of genes that may be contributing to enhanced probiotic properties of this strain. In particular, the genes encoding putative mucus binding proteins, collagen-binding proteins, class III bacteriocin, as well as exopolysaccharide and prophage-related genes were identified...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163827/the-complete-genome-sequence-of-the-yogurt-isolate-streptococcus-thermophilus-aca-dc-2
#6
Voula Alexandraki, Maria Kazou, Jochen Blom, Bruno Pot, Effie Tsakalidou, Konstantinos Papadimitriou
Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163826/draft-genome-sequences-of-eight-bacteria-isolated-from-the-indoor-environment-staphylococcus-capitis-strain-h36-s-capitis-strain-h65-s-cohnii-strain-h62-s-hominis-strain-h69-microbacterium-sp-strain-h83-mycobacterium-iranicum-strain-h39-plantibacter-sp-strain
#7
Despoina S Lymperopoulou, David A Coil, Denise Schichnes, Steven E Lindow, Guillaume Jospin, Jonathan A Eisen, Rachel I Adams
We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the "Built Environment Reference Genome" project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163825/genomic-analysis-of-four-strains-of-corynebacterium-pseudotuberculosis-bv-equi-isolated-from-horses-showing-distinct-signs-of-infection
#8
Rafael A Baraúna, Rommel T J Ramos, Adonney A O Veras, Pablo H C G de Sá, Luís C Guimarães, Diego A das Graças, Adriana R Carneiro, Judy M Edman, Sharon J Spier, Vasco Azevedo, Artur Silva
The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content and structure were analyzed. The strains were isolated from horses with distinct signs of infection, including ulcerative lymphangitis, external abscesses on the chest, or internal abscesses on the liver, kidneys, and lungs. The average size of the genomes was 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences (CDSs)...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163824/draft-genome-sequence-of-lactobacillus-plantarum-strains-e2c2-and-e2c5-isolated-from-human-stool-culture
#9
Mangesh V Suryavanshi, Dhiraj Paul, Swapnil P Doijad, Shrikant S Bhute, Tejashri B Hingamire, Rahul P Gune, Yogesh S Shouche
Probiotic Lactobacillus species offer various health benefits, thus have been employed in treatment and prevention of various diseases. Due to the differences in the isolation source and the site of action, most of the lactobacilli tested in-vitro for probiotics properties fail to extend similar effects in-vivo. Consequently, the search of autochthonous, efficacious and probably population specific probiotics is a high priority in the probiotics research. In this regards, whole genome sequencing of as many Lactobacillus as possible will help to deepen our understanding of biology and their health effects...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28163823/draft-genome-sequence-of-type-strain-hbr26-t-and-description-of-rhizobium-aethiopicum-sp-nov
#10
Aregu Amsalu Aserse, Tanja Woyke, Nikos C Kyrpides, William B Whitman, Kristina Lindström
Rhizobium aethiopicum sp. nov. is a newly proposed species within the genus Rhizobium. This species includes six rhizobial strains; which were isolated from root nodules of the legume plant Phaseolus vulgaris growing in soils of Ethiopia. The species fixes nitrogen effectively in symbiosis with the host plant P. vulgaris, and is composed of aerobic, Gram-negative staining, rod-shaped bacteria. The genome of type strain HBR26(T) of R. aethiopicum sp. nov. was one of the rhizobial genomes sequenced as a part of the DOE JGI 2014 Genomic Encyclopedia project designed for soil and plant-associated and newly described type strains...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28138357/genome-sequence-of-a-high-agarase-producing-strain-flammeovirga-sp-sjp92
#11
Qi Dong, Lingwei Ruan, Hong Shi
Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated strain that belongs to the family Flammeovirgaceae of the class Cytophagia. The strain was isolated from the intestine of abalone, which produces many extracellular agarases and exhibits efficient degradation activities on various polysaccharides, especially agarose. Here we present the high-quality draft genome of Flammeovirga sp. SJP92, together with its phenotypic characteristics. The genome sequence is 8, 534, 834 bp, which comprised with one chromosome and no plasmid...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28138356/genome-features-of-moderately-halophilic-polyhydroxyalkanoate-producing-yangia-sp-ccb-mm3
#12
Nyok-Sean Lau, Ka-Kei Sam, Abdullah Al-Ashraf Amirul
Yangia sp. CCB-MM3 was one of several halophilic bacteria isolated from soil sediment in the estuarine Matang Mangrove, Malaysia. So far, no member from the genus Yangia, a member of the Rhodobacteraceae family, has been reported sequenced. In the current study, we present the first complete genome sequence of Yangia sp. strain CCB-MM3. The genome includes two chromosomes and five plasmids with a total length of 5,522,061 bp and an average GC content of 65%. Since a different strain of Yangia sp. (ND199) was reported to produce a polyhydroxyalkanoate copolymer, the ability for this production was tested in vitro and confirmed for strain CCB-MM3...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28138355/draft-genome-sequence-of-arthrobacter-sp-strain-b6-isolated-from-the-high-arsenic-sediments-in-datong-basin-china
#13
Linghua Xu, Wanxia Shi, Xian-Chun Zeng, Ye Yang, Lingli Zhou, Yao Mu, Yichen Liu
Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium, isolated from the arsenic-contaminated aquifer sediment in the Datong basin, China. This strain displays high resistance to arsenic, and can dynamically transform arsenic under aerobic condition. Here, we described the high quality draft genome sequence, annotations and the features of Arthrobacter sp. B6. The G + C content of the genome is 64.67%. This strain has a genome size of 4,663,437 bp; the genome is arranged in 8 scaffolds that contain 25 contigs...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28127420/permanent-draft-genome-of-thiobacillus-thioparus-dsm-505-t-an-obligately-chemolithoautotrophic-member-of-the-betaproteobacteria
#14
Lee P Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Rich Boden
Thiobacillus thioparus DSM 505(T) is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C(T) (=DSM 505(T) = ATCC 8158(T)) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28127419/towards-long-read-metagenomics-complete-assembly-of-three-novel-genomes-from-bacteria-dependent-on-a-diazotrophic-cyanobacterium-in-a-freshwater-lake-co-culture
#15
Connor B Driscoll, Timothy G Otten, Nathan M Brown, Theo W Dreher
Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was assembled to draft-quality. Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as incertae sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28116042/high-quality-draft-genome-sequence-of-janthinobacterium-psychrotolerans-sp-nov-isolated-from-a-frozen-freshwater-pond
#16
Xianzhe Gong, Stig Skrivergaard, Benjamin Smed Korsgaard, Lars Schreiber, Ian P G Marshall, Kai Finster, Andreas Schramm
Strain S3-2(T), isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus Janthinobacterium. Strain S3-2(T) is a facultative anaerobe that lacks the ability to produce violacein but shows antibiotic resistance, psychrotolerance, incomplete denitrification, and fermentation. The draft genome of strain S3-2(T) has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (<35%), and the low whole genome-based average nucleotide identity (ANI) (<86%) with other strains within the genus Janthinobacterium, we propose that strain S3-2(T) is the type strain (= DSM 102223 = LMG 29653) of a new species within this genus...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28116041/high-quality-draft-genome-sequence-of-rhizobium-mesoamericanum-strain-stm6155-a-mimosa-pudica-microsymbiont-from-new-caledonia
#17
Agnieszka Klonowska, Aline López-López, Lionel Moulin, Julie Ardley, Margaret Gollagher, Dora Marinova, Rui Tian, Marcel Huntemann, T B K Reddy, Neha Varghese, Tanja Woyke, Victor Markowitz, Natalia Ivanova, Rekha Seshadri, Mohamed N Baeshen, Nabih A Baeshen, Nikos Kyrpides, Wayne Reeve
Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project...
2017: Standards in Genomic Sciences
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
#18
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
#19
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
#20
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
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