Quality scores for 32,000 genomes
More than 80% of the microbial genomes in GenBank are of ‘draft’ quality (12,553 draft vs. 2,679 finished, as of October, 2013). We have examined all the microbial DNA sequences available for complete, draft, ...
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More than 80% of the microbial genomes in GenBank are of ‘draft’ quality (12,553 draft vs. 2,679 finished, as of October, 2013). We have examined all the microbial DNA sequences available for complete, draft, ...
In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaero...
As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement...
We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using tho...
Ornithobacterium rhinotracheale strain ORT-UMN 88 is a Gram-negative, pleomorphic, rod-shaped bacterium and an etiologic agent of pneumonia and airsacculitis in poultry. It is a member of the family Flavobacteri...
Methanobacterium formicicum BRM9 was isolated from the rumen of a New Zealand Friesan cow grazing a ryegrass/clover pasture, and its genome has been sequenced to provide information on the phylogenetic diversity...
This report details the outcome of the 1st Skin Microbiota Workshop, Boulder, CO, held on October 15th-16th 2012. The workshop was arranged to bring Department of Defense personnel together with experts in mic...
The UK Science and Innovation Network UK-USA workshop ‘Beating the Superbugs: Hospital Microbiome Studies for tackling Antimicrobial Resistance’ was held on October 14th 2013 at the UK Department of Health, Lo...
When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for under...
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication ...
The family Rickettsiaceae currently includes two genera: Orientia that contains one species, Orientia tsutsugamushi, and Rickettsia that contains 28 species.
Clostridium saudii strain JCCT sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collecte...
Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a Lotus divaricatus root nodule. Compared to most other M. loti strains, it has a broad host range and is one of very ...
Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing microsymbionts of species of the African crotalarioid genus Listia. Strain WSM2598 is an aerobic, motile, Gram-negative, non-sp...
Ensifer medicae Di28 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago spp. Di28 was isolated in 1998 from a nodule recovere...
Mesorhizobium loti strain R88B was isolated in 1993 in the Rocklands range in Otago, New Zealand from a Lotus corniculatus root nodule. R88B is an aerobic, Gram-negative, non-spore-forming rod. This report revea...
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of t...
Prevotella timonensis strain 4401737T is a member of the genus Prevotella, which contains anaerobic Gram-negative bacteria. It was isolated from a human breast abscess. In this work, we describe a set of features...
Kurthia senegalensis strain JC8ET sp. nov. is the type strain of K. senegalensis sp. nov., a new species within the genus Kurthia. This strain, whose genome is described here, was isolated from the fecal flora of...
The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of th...
Microbial genome sequence submissions to the International Nucleotide Sequence Database Collaboration (INSDC) have been annotated with organism names that include the strain identifier. Each of these strain-le...
The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize ...
Members of genus Skermanella were described as Gram-negative, motile, aerobic, rod-shaped, obligate-heterotrophic bacteria and unable to fix nitrogen. In this study, the genome sequence of Skermanella stibiiresis...
Anaerococcus provenciensis strain 9402080T sp. nov. is the type strain of A. provenciensis sp. nov., a new species within the genus Anaerococcus. This strain was isolated from a cervical abscess sample. A. proven...
Microvirga lupini LUT6T is an aerobic, non-motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Lupinus texensis. LUT6T was isolated in 2006 from a nodu...
Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isol...
Corynebacterium timonense strain 5401744T is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. It was isolated from the blood of a patient with endocarditis. In ...
Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. The invertebrate iridoviruses 22 (IIV22) and 25 (IIV25) were originally isolated from a sing...
We report the genome sequence of a healthcare-associated MRSA type ST239 clone isolated from a patient with septicemia in Malaysia. This clone typifies the characteristics of ST239 lineage, including resistanc...
Dyadobacter tibetensis Y620-1 is the type strain of the species Dyadobacter tibetensis, isolated from ice at a depth of 59 m from a high altitude glacier in China (5670 m above sea level). It is psychrotolerant w...
Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occu...
Bacillus amyloliquefaciens HB-26, a Gram-positive bacterium was isolated from soil in China. SDS-PAGE analysis showed this strain secreted six major protein bands of 65, 60, 55, 34, 25 and 20 kDa. A bioassay of t...
Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain o...
Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to deter...
Anoxybacillus flavithermus subsp. yunnanensis is the only strictly thermophilic bacterium that is able to tolerate a broad range of toxic solvents at its optimal temperature of 55–60°C. The type strain E13T was i...
The Enterobacter cloacae complex is genetically very diverse. The increasing number of complete genomic sequences of E. cloacae is helping to determine the exact relationship among members of the complex. E. cloa...
Fenollaria massiliensis strain 9401234T, is the type strain of Fenollaria massiliensis gen. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated f...
Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to reduce nitrate and selenite and for its resistance to arsenic under anaerobic conditions. Here we describe some key fe...
Bacillus thuringiensis represents one of the six species of “Bacillus cereus group” in the genus Bacillus within the family Bacillaceae. Strain Sbt003 was isolated from soil and identified as B. thuringiensis. It...
Gluconobacter thailandicus strain NBRC 3257, isolated from downy cherry (Prunus tomentosa), is a strict aerobic rod-shaped Gram-negative bacterium. Here, we report the features of this organism, together with the...
Ensifer meliloti strain RRI128 is an aerobic, motile, Gram-negative, non-spore-forming rod. RRI128 was isolated from a nodule recovered from the roots of barrel medic (Medicago truncatula) grown in the greenhouse...
The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting...
Agrobacterium radiobacter is the only known non-phytopathogenic species in Agrobacterium genus. In this study, the whole-genome sequence of A. radiobacter type strain DSM 30147T was described and compared to the ...
Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has served as a model organism, with an extensive literature extending over 40 years. The strain has three distinct nitrogen...
Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia...
Rhizobium leguminosarum bv. trifolii is a soil-inhabiting bacterium that has the capacity to be an effective N2-fixing microsymbiont of Trifolium (clover) species. R. leguminosarum bv. trifolii strain WSM1689 is ...
Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated fr...
Leucobacter salsicius M1-8T is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented f...
Mesorhizobium ciceri bv. biserrulae strain WSM1271T was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, G...
Granulicella tundricola strain MP5ACTX9T is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperature...