IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes.

The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.

Draft genome sequence of CL-YJ9 (DSM 18822), isolated from the rhizosphere of the coastal tidal-flat plant .

The genus belongs to the family within the class and was reported in 1997. Currently the genus contains 16 species. CL-YJ9 was isolated from sediment associated with the roots of a plant growing in a tidal flat of Youngjong Island, Korea.

High-quality draft genome sequence of Mlalz-1, a microsymbiont of (L.) miller collected in Lanzarote, Canary Islands, Spain.

10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of (L.

Draft genome sequence of strain AHT1, a gram-positive sulfidogenic polyextremophile.

strain AHT1 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 . Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.

Permanent Draft Genome Sequence of Strain Z-533, a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia.

Z-533, a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO, and hydrogen. Unlike Z-1312, it cannot use cellulose and is inhibited by hydrogen. The reported draft genome sequence of Z-533 will help to understand the molecular basis for these differences.

High-quality permanent draft genome sequence of the type strain USDA 76, isolated from (L.) Merr.

USDA 76 (INSCD = ARAG00000000), the type strain for , is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, USDA 76 was selected as part of the DOE Joint Genome Institute 2010 sequencing project.

Genomic Analysis of , the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum .

The genome of , the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H during fermentation, and one is apparently bidirectional.

Complete genome sequence of strain YIM 002 (DSM 44835), the type species of the genus and source of new antibiotic compounds.

strain YIM 002 is the type strain of the type species of the genus , 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 project, and here we describe the complete genome sequence and annotation of this taxon.

High-quality draft genome sequence of strain STM6155, a microsymbiont from New Caledonia.

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 L.. STM6155 was isolated in 2009 from a nodule of the trap host grown in nickel-rich soil collected near Mont Dore, New Caledonia.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools.

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.

Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria.

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1(T).

Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1(T) is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon.

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India.

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F.

Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.

Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus.

High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods.

Phaseolibacter flectens strain ATCC 12775(T) (Halpern et al., Int J Syst Evol Microbiol 63:268-273, 2013) is a Gram-negative, rod shaped, motile, aerobic, chemoorganotroph bacterium. Ph.

Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland.

This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S.

High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil.

Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.

Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos.

Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an Australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of Mediterranean species of lupins (Lupinus angustifolius, L.

High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.

Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic.

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia.

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp.

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6.

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts.

High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T).

Burkholderia dilworthii strain WSM3556(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556(T) thus represents a potential inoculant quality strain for L.

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym.

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994.