Genome sequence of the unclassified marine Gammaproteobacterium BDW918

The unclassified marine gammaproteobacterium BDW918, which utilizes volatile fatty acids but not most common carbohydrates and amino acids, was isolated from Dokdo seawater in South Korea. Here we present a draft genome of the strain BDW918, which encodes many putative genes related to fatty acid metabolism and aromatic hydrocarbon degradation.     

Genome sequence of Bifidobacterium breve DPC 6330, a strain isolated from the human intestine

The draft genome of Bifidobacterium breve DPC 6330, isolated from an elderly patient, was determined. B. breve DPC 6330 was previously identified to synthesize the beneficial metabolite conjugated linoleic acid from free linoleic acid. The sequence will allow identification and characterization of the genetic determinants of its putative beneficial properties.     

Genome sequence of Stenotrophomonas maltophilia RR-10, isolated as an endophyte from rice root

Stenotrophomonas maltophilia is an endophyte which plays important roles in agricultural production as a plant growth-promoting bacterium. Here, we present the draft genome sequence of strain RR-10, which was isolated from a rice root in a rice field of China.     

Genome sequence of the first human adenovirus type 14 isolated in China

Emergent pathogens may be examined rapidly at high resolution on a molecular level using genomics, allowing an understanding of their evolution. China is a unique environment for studying pathogens, having a large, dense, and generally closed population. Human adenovirus type 14 (HAdV-14) was originally identified as an acute respiratory disease (ARD) pathogen in The Netherlands (1955), with a second isolation in England (1957). Since then, few reports of this virus appeared until an ARD pathogen with a similar genome caused multiple outbreaks in the United States (2006 to 2009). This report presents the first genome of HAdV-B14 isolated in China (2010). As China experienced two recent outbreaks of an emergent ARD pathogen, HAdV-B55, containing much of the HAdV-B14 genome, the availability of this HAdV-B14 sequence will facilitate studies of the epidemiology of these pathogens, as well as provide a foundation for studying adenovirus evolution and the genesis of emergent pathogens. These observations may be invaluable in predicting possible recombination between wild-type viruses and adenoviral gene delivery vectors, including adenovirus vaccines.     

Genome sequence of Leuconostoc inhae KCTC 3774, isolated from Kimchi

Leuconostoc inhae strain KCTC 3774 is a Gram-positive, non-spore-forming, heterofermentative, spherical or lenticular lactic acid bacterium. Here we announce the draft genome sequence of Leuconostoc inhae KCTC 3774, isolated from traditional Korean kimchi, and describe major findings from its annotation.     

Genome sequence of a Salinibacterium sp. isolated from Antarctic soil

The draft genome of Salinibacterium sp. PAMC 21357, isolated from permafrost soil of Antarctica, was determined. Here we present a 3.1-Mb draft genome sequence of Salinibacterium sp. that could provide further insight into the genetic determination of its cold-adaptive properties.     

Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastrointestinal tract

Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract.     

Genome sequence of Microbacterium testaceum StLB037, an N-acylhomoserine lactone-degrading bacterium isolated from potato leaves

Microbacterium testaceum is an endophytic Gram-positive bacterium that resides within plant hosts. M. testaceum StLB037 was isolated from potato leaves and shows N-acylhomoserine lactone-degrading activity. Here, we present the 3.98-Mb complete genome sequence of StLB037, with an average GC content of 70.28%.     

Genome sequence of Acinetobacter calcoaceticus PHEA-2, isolated from industry wastewater

Genome analysis of Acinetobacter calcoaceticus PHEA-2 was undertaken because of the importance of this bacterium for bioremediation of phenol-polluted water and because of the close phylogenetic relationship of this species with the human pathogen Acinetobacter baumannii. To our knowledge, this is the first strain of A. calcoaceticus whose genome has been sequenced.     

Genome sequence of extracellular-protease-producing Alishewanella jeotgali isolated from traditional Korean fermented seafood

Alishewanella jeotgali MS1(T) (= KCTC 22429(T) = JCM 15561(T)) was isolated from a traditional Korean fermented seafood, gajami sikhae (jeotgal), and has been reported as a novel species. A. jeotgali was proven to have extracellular proteolytic activity, which may play an important role in the fermentation environment of food containing fish flesh. Here, we present the genome sequence of Alishewanella jeotgali MS1(T) as the first sequenced strain in the genus Alishewanella and its taxonomic relatives.     

Genome sequence of Lactobacillus johnsonii PF01, isolated from piglet feces

Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was isolated from a fecal sample from a piglet. The strain adhered specifically to the duodenal and jejunal epithelial cells of the piglet and had high bile resistance activity. Here we report the genomic sequence of L. johnsonii PF01.     

Description of an as yet unclassified DNA virus from diseased Cyprinus carpio species

Numerous deaths of koi and common carp (Cyprinus carpio) were observed on many farms throughout Israel, resulting in severe financial losses. The lethal viral disease observed is highly contagious and extremely virulent, but morbidity and mortality are restricted to koi and common carp populations. Diseased fish exhibit fatigue and gasping movements in shallow water. Infected fish had interstitial nephritis and gill necrosis as well as petechial hemorrhages in the liver and other symptoms that were not consistent with viral disease, suggesting a secondary infection. Here we report the isolation of carp nephritis and gill necrosis virus (CNGV), which is the etiologic agent of this disease. The virus propagates and induces severe cytopathic effects by 5 days postinfection in fresh koi or carp fin cell cultures (KFC and CFC, respectively), but not in epithelioma papillosum cyprini cells. The virus harvested from KFC cultures induced the same clinical signs, with a mortality of 75 to 95%, upon inoculation into naive koi and common carp. Using PCR, we provide final proof that the isolated virus is indeed the etiologic agent of food and ornamental carp mortalities in fish husbandry. Electron microscopy revealed viral cores with icosahedral morphology of 100 to 110 nm that resembled herpesviruses. Electron micrographs of purified pelleted CNGV sections, together with viral sensitivities to ether and Triton X-100, suggested that it is an enveloped virus. However, the genome of the isolated virus is a double-stranded DNA (dsDNA) molecule of 270 to 290 kbp, which is larger than known herpesviruses. The viral DNA seems highly divergent and bears only small fragments (16 to 45 bp) that are similar to the genomes of several DNA viruses. Nevertheless, amino acid sequences encoded by CNGV DNA fragments bear similarities primarily to members of the Poxviridae and Herpesviridae and to other large dsDNA viruses. We suggest, therefore, that the etiologic agent of this disease may represent an as yet unclassified virus species that is endemic in C. carpio (carp).     

Genome sequence of Lactobacillus salivarius NIAS840, isolated from chicken intestine

Lactobacillus salivarius is a well-known lactic acid bacterium to which increasing attention has been paid recently for use as probiotics for humans and animals. L. salivarius NIAS840 was first isolated from broiler chicken feces, displaying antimicrobial activities against multidrug-resistant Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Here, we report the genome sequence of L. salivarius NIAS840 (2,046,557 bp) including a small plasmid and two megaplasmids.     

Genome sequence of Lactobacillus amylovorus GRL1118, isolated from pig ileum

Lactobacillus amylovorus is a common member of the beneficial microbiota present in the pig gastrointestinal tract. Here, we report the genome sequence of the surface layer (S-layer) protein-carrying and potentially probiotic strain L. amylovorus GRL1118, which was isolated from porcine ileum and which shows strong adherence to pig intestinal epithelial cells.     

Genome sequence of Escherichia coli AA86, isolated from cow feces

Escherichia coli AA86 (=KACC 15541) is an enteric bacterium that was isolated from a sample of healthy cow feces. Its genome sequence revealed that it is most closely related to the human fecal strain E. coli SE15 and could be classified under E. coli phylogenetic group B2. Here, we report the genome sequence of E. coli AA86, consisting of 3 contigs and 2 plasmids.     

Genome sequence of Lactococcus garvieae 21881, isolated in a case of human septicemia

Lactococcus garvieae is a Gram-positive bacterium considered an important opportunistic emerging human pathogen and also a well-recognized fish pathogen. Here, we present the draft genome sequence of Lactococcus garvieae strain 21881 (2,164,557 bp, with a G+C content of 37.9%), which represents the first report of a genome sequence on Lactococcus garvieae.     

Genome sequence of Helicobacter bizzozeronii strain CIII-1, an isolate from human gastric mucosa

The canine-adapted Helicobacter bizzozeronii is the only nonpylori Helicobacter species isolated from human gastric biopsy tissue. Here we present the genome sequence of strain CIII-1, isolated from a 45-year-old female patient with severe gastric symptoms. This is the first genome sequence of nonpylori gastric Helicobacter isolated from human gastritis.     

Determination of genome size and DNA homology between an unclassified Mycobacterium species isolated from patients with Crohn's disease and other mycobacteria

The genome size of an unclassified Mycobacterium species, isolated from a patient with Crohn's disease, was determined by measurement of DNA renaturation kinetics as 3.1 X 10(9) Da. The percentage of DNA homology of this organism to DNA of related mycobacteria was evaluated by measurement of DNA renaturation with heterologous DNA. These studies supported the classification of this organism as Mycobacterium paratuberculosis but failed to distinguish between M. paratuberculosis and organisms of the Mycobacterium avium-intracellulare groups.     

Characterization of some previously unclassified Pasteurellaceae isolated from hamsters

Bacteria isolated from purulent processes on the jaws of European hamsters ( Cricetus cricetus ) and from intestinal inflammatory processes in Syrian hamsters ( Mesocricetus auratus ), bred as laboratory animals have been shown to be phenotypically similar but not identical with Pasteurella pneumotropica . Deoxyribonucleic acid (DNA)–DNA hybridization studies indicate that with one exception, the strains represent two new species of the family Pasteurellaceae. In the absence of a close genomic relatedness to members of the genera Actinobacillus or Pasteurella or allied organisms, however, the two new taxa are described without any formal designation. The one exception was identified as Actinobacillus capsulatus , a species not previously isolated from hamsters.