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Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T

The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and CCBAU 10071 T were sequenced by DOE–JGI and deposited at the DOE...

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

, David Paez-Espino and Nikos C. Kyrpides provided the data for the figures, and Ioannis Iliopoulos supervised the study. All authors read and approved the final manuscript. Acknowledgments This work was

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

, David Paez-Espino and Nikos C. Kyrpides provided the data for the figures, and Ioannis Iliopoulos supervised the study. All authors read and approved the final manuscript. Acknowledgments This work was

Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T

Here we report the draft genome sequence of Chitinophaga costai A37T2T (=CIP 110584T, =LMG 27458T), which was isolated from the endophytic community of Pinus pinaster tree. The total genome size of C. costaii A37T2T is 5.07 Mbp, containing 4204 coding sequences. Strain A37T2T encoded multiple genes likely involved in cellulolytic, chitinolytic and lipolytic activities. This...

A thermostable Cas9 with increased lifetime in human plasma

Research journals • PubMed • Google Scholar Search for Nikos C. Kyrpides in:Nature Research journals • PubMed • Google Scholar Search for Jennifer A. Doudna in:Nature Research journals • PubMed • Google

Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes

Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0–3.0 μm × 0.5–1 μm, motile and unable to form...

Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565 T = KCTC 5659 T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we...

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks

Objective Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction...

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth’s surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron...

Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov.

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...

Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico

• Google Scholar Search for Bartholomeus P. Lomans in:Nature Research journals • PubMed • Google Scholar Search for Nikos C. Kyrpides in:Nature Research journals • PubMed • Google Scholar Search for Ian M

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of...

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence

, Natalia Ivanova, Tanja Woyke. Investigation: Marcel Huntemann, Alicia Clum. Software: Stefan Langenberg. Supervision: Nikos C. Kyrpides. Writing ± review & editing: Atteyet F. Yassin. 22 / 27 23 / 27 19 ... . Kyrpides 1 0 Institut fuÈr medizinische Mikrobiologie und Immunologie der UniversitaÈt Bonn , Bonn, Germany , 2 Klinik und Poliklinik fuÈr Hals-Nasen-Ohrenheilkunde/Chirurgie , Bonn, Germany , 3

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources

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...

Large-scale contamination of microbial isolate genomes by Illumina PhiX control

With the rapid growth and development of sequencing technologies, genomes have become the new go-to for exploring solutions to some of the world’s biggest challenges such as searching for alternative energy sources and exploration of genomic dark matter. However, progress in sequencing has been accompanied by its share of errors that can occur during template or library...

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

Göker Lorena Carro 0 Maria del Carmen Montero-Calasanz 0 Manfred Rohde Tanja Woyke Nikos C. Kyrpides Hans-Peter Klenk 0 0 School of Biology, Newcastle University , Newcastle upon Tyne NE1 7RY , UK

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a...

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance...

Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica

Göker 4 Tanja Woyke 6 Hans-Peter Klenk 8 Nikos C. Kyrpides 6 Byung Cheol Cho 1 0 Equal contributors 1 Microbial Oceanography Laboratory, School of Earth and Environmental Sciences, and Research Institute

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental...