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1.  Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2T, a cyanobacterium isolated from seawater of Chuuk lagoon 
Standards in Genomic Sciences  2013;9(1):197-204.
A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for the first time. The type strain, KORDI 51-2T, was isolated from seawater of Chuuk lagoon located in a tropical area. Although it belonged to a clade exclusively comprised of extremely halotolerant strains by phylogenetic analyses, R. lacunae is known to be incapable of growth at high salt concentration over 10%. Here we report the main features of the genome of R. lacunae strain KORDI 51-2T. The genome of R. lacunae contains a gene cluster for phosphonate utilization encoding three transporters, one regulator and eight C-P lyase subunits.
doi:10.4056/sigs.4398180
PMCID: PMC3910548  PMID: 24501656
Cyanobacteria; phosphonate utilization; photoautotrophy; Rubidibacter lacunae; seawater
2.  Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence 
Staphylococcus aureus subsp. anaerobius is responsible for Morel's disease in animals and a cause of abscess in humans. It is characterized by a microaerophilic growth, contrary to the other strains of S. aureus. The 2,604,446-bp genome (32.7% GC content) of S. anaerobius ST1464 comprises one chromosome and no plasmids. The chromosome contains 2,660 open reading frames (ORFs), 49 tRNAs and three complete rRNAs, forming one complete operon. The size of ORFs ranges between 100 to 4,600 bp except for two ORFs of 6,417 and 7,173 bp encoding segregation ATPase and non-ribosomal peptide synthase, respectively. The chromosome harbors Staphylococcus phage 2638A genome and incomplete Staphylococcus phage genome PT1028, but no detectable CRISPRS. The antibiotic resistance gene for tetracycline was found although Staphylococcus aureus subsp. anaerobius is susceptible to tetracycline in-vitro. Intact oxygen detoxification genes encode superoxide dismutase and cytochrome quinol oxidase whereas the catalase gene is impaired by a stop codon. Based on the genome, in-silico multilocus sequence typing indicates that S. aureus subsp. anaerobius emerged as a clone separated from all other S. aureus strains, illustrating host-adaptation linked to missing functions. Availability of S. aureus subsp. anaerobius genome could prompt the development of post-genomic tools for its rapid discrimination from S. aureus.
doi:10.4056/sigs.3748294
PMCID: PMC3910551  PMID: 24501641
Staphylococcus aureus subsp. anaerobius; genome; SOLiD; Morel’s disease
3.  Non-contiguous finished genome sequence and description of Bartonella florenciae sp. nov. 
Standards in Genomic Sciences  2013;9(1):185-196.
Bartonella florenciae sp. nov. strain R4T is the type strain of B. florenciae sp. nov., a new species within the genus Bartonella. This strain, whose genome is described here, was isolated in France from the spleen of the shrew Crocidura russula. B. florenciae is an aerobic, rod-shaped, Gram-negative bacterium. Here we describe the features of this organism, together with the complete genome sequence and its annotation. The 2,010,844 bp-long genome contains 1,909 protein-coding and 46 RNA genes, including two rRNA operons.
doi:10.4056/sigs.4358060
PMCID: PMC3910550  PMID: 24501655
Bartonella florenciae; genome; France; shrew; Crocidura russula; taxonogenomics
4.  Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. 
Standards in Genomic Sciences  2013;9(1):205-219.
Nosocomiicoccus massiliensis strain NP2T sp. nov. is the type strain of a new species within the genus Nosocomiicoccus. This strain, whose genome is described here, was isolated from the fecal flora of an AIDS-infected patient living in Marseille, France. N. massiliensis is a Gram-positive aerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,645,244 bp long genome (one chromosome but no plasmid) contains 1,738 protein-coding and 45 RNA genes, including 3 rRNA genes.
doi:10.4056/sigs.4378121
PMCID: PMC3910558  PMID: 24501657
Nosocomiicoccus massiliensis; genome; culturomics; taxono-genomics
5.  Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov. 
Standards in Genomic Sciences  2013;9(1):160-174.
Halopiger djelfamassiliensis strain IIH2T sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.
doi:10.4056/sigs.4578289
PMCID: PMC3910545  PMID: 24501653
Halopiger djelfamassiliensis; Draft genome; Archaea; Halophile
6.  Draft genome sequence of Rhodococcus rhodochrous strain ATCC 17895 
Standards in Genomic Sciences  2013;9(1):175-184.
Rhodococcus rhodochrous ATCC 17895 possesses an array of mono- and dioxygenases, as well as hydratases, which makes it an interesting organism for biocatalysis. R. rhodochrous is a Gram-positive aerobic bacterium with a rod-like morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,869,887 bp long genome contains 6,609 protein-coding genes and 53 RNA genes. Based on small subunit rRNA analysis, the strain is more likely to be a strain of Rhodococcus erythropolis rather than Rhodococcus rhodochrous.
doi:10.4056/sigs.4418165
PMCID: PMC3910549  PMID: 24501654
Rhodococcus rhodochrous; Rhodococcus erythropolis; biocatalysis; genome
7.  Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade 
Standards in Genomic Sciences  2013;9(1):128-141.
Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the type species of the genus Leisingera. The genus belongs to the Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed lineage in marine environments. Leisingera and particularly L. methylohalidivorans strain MB2T is of special interest due to its methylotrophy. Here we describe the complete genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. The 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists of three replicons, a single chromosome and two extrachromosomal elements with sizes of 221 kb and 285 kb.
doi:10.4056/sigs.4297965
PMCID: PMC3910543  PMID: 24501651
Methylotrophy; methyl halides; extrachromosomal elements; Alphaproteobacteria; Rhodobacteraceae; Roseobacter clade; aerobe
8.  Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis 
Standards in Genomic Sciences  2013;9(1):142-159.
TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
doi:10.4056/sigs.4287962
PMCID: PMC3910554  PMID: 24501652
Marine microbiology; facultative anaerobe; indigoidine; Rhodobacteraceae; Roseobacter clade
9.  Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. 
Standards in Genomic Sciences  2013;9(1):83-92.
Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67T was initially (1958) identified as a member of ‘Acetobacter aurantius’, a name that was not considered for the approved list. Kondô 67T was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67T is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.4338002
PMCID: PMC3910546  PMID: 24501647
strictly aerobic; motile; rod-shaped; acetogenic; mesophilic; ‘Acetobacter aurantius’; Xanthomonadaceae; GEBA
10.  Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31 
Standards in Genomic Sciences  2013;9(1):42-56.
Lysinibacillus sphaericus strain OT4b.31 is a native Colombian strain having no larvicidal activity against Culex quinquefasciatus and is widely applied in the bioremediation of heavy-metal polluted environments. Strain OT4b.31 was placed between DNA homology groups III and IV. By gap-filling and alignment steps, we propose a 4,096,672 bp chromosomal scaffold. The whole genome (consisting of 4,856,302 bp long, 94 contigs and 4,846 predicted protein-coding sequences) revealed differences in comparison to the L. sphaericus C3-41 genome, such as syntenial relationships, prophages and putative mosquitocidal toxins. Sphaericolysin B354, the coleopteran toxin Sip1A and heavy metal resistance clusters from nik, ars, czc, cop, chr, czr and cad operons were identified. Lysinibacillus sphaericus OT4b.31 has applications not only in bioremediation efforts, but also in the biological control of agricultural pests.
doi:10.4056/sigs.4227894
PMCID: PMC3910547  PMID: 24501644
Lysinibacillus sphaericus OT4b.31; DNA homology; de novo assembly; heavy metal tolerance; Sip1A coleopteran toxin
11.  Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio 
Standards in Genomic Sciences  2013;9(1):57-70.
Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883T, the type strain of T. acidaminovorans, stain Z-9701T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.4237901
PMCID: PMC3910556  PMID: 24501645
obligate anaerobic; motile; curved rods; organotrophic; S0-reduction; cyanobacterial mat; Synergistaceae; Synergistetes; GEBA
12.  Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov. 
Standards in Genomic Sciences  2013;9(1):93-105.
Strain G2T sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes.
doi:10.4056/sigs.4388124
PMCID: PMC3910557  PMID: 24501648
Bacillus massiliogorillae; genome; culturomics; taxonogenomics
13.  Genome sequence of the Litoreibacter arenae type strain (DSM 19593T), a member of the Roseobacter clade isolated from sea sand 
Standards in Genomic Sciences  2013;9(1):117-127.
Litoreibacter arenae Kim et al. 2012 is a member of the genomically well-characterized Rhodobacteraceae clade within the Roseobacter clade. Representatives of this clade are known to be metabolically versatile and involved in marine carbon-producing and biogeochemical processes. They form a physiologically heterogeneous group of Alphaproteobacteria and were mostly found in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or together with invertebrates and vertebrates. Here we describe the features of L. arenae DSM 19593T, including novel aspects of its phenotype, together with the draft genome sequence and annotation. The 3,690,113 bp long genome consists of 17 scaffolds with 3,601 protein-coding and 56 RNA genes. This genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).
doi:10.4056/sigs.4258318
PMCID: PMC3910544  PMID: 24501650
marine; rod-shaped; sea sand; sediment; motile; strictly aerobic; mesophile; chemoorganotrophic; halophilic; virus-like structures; carbon monoxide utilization; sulfur oxidation; Rhodobacteraceae; Alphaproteobacteria; Thalassobacter arenae
14.  Complete genome sequence of Arthrobacter sp. strain FB24 
Standards in Genomic Sciences  2013;9(1):106-116.
Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.
doi:10.4056/sigs.4438185
PMCID: PMC3910542  PMID: 24501649
15.  Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T) 
Standards in Genomic Sciences  2013;9(1):28-41.
Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).
doi:10.4056/sigs.4207886
PMCID: PMC3910552  PMID: 24501643
draft genome; aerobic; chemoheterotrophic; Gram-positive; vegetative and aerial mycelia; spore-forming; non-motile; soil bacterium; Pseudonocardiaceae; CSP 2010
16.  Complete genome sequence of Granulicella mallensis type strain MP5ACTX8T, an acidobacterium from tundra soil 
Standards in Genomic Sciences  2013;9(1):71-82.
Granulicella mallensis MP5ACTX8T is a novel species of the genus Granulicella in subdivision 1of Acidobacteria. G. mallensis is of ecological interest being a member of the dominant soil bacterial community active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates. These include gene modules encoding the carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides including plant based carbon polymers. The genome of Granulicella mallensis MP5ACTX8T consists of a single replicon of 6,237,577 base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes.
doi:10.4056/sigs.4328031
PMCID: PMC3910553  PMID: 24501646
cold adapted; acidophile; tundra soil; Acidobacteria
17.  Non-contiguous finished genome sequence and description of Clostridium dakarense sp. nov. 
Standards in Genomic Sciences  2013;9(1):14-27.
Clostridium dakarense strain FF1T, is the type strain of Clostridium dakarense sp. nov., a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the fecal flora of a 4-month-old Senegalese child suffering from gastroenteritis. C. dakarense sp. nov. strain FF1T is an obligate anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,735,762 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 27.98% and contains 3,843 protein-coding and 73 RNA genes, including 8 rRNA genes.
doi:10.4056/sigs.4097825
PMCID: PMC3910555  PMID: 24501642
Clostridium dakarense; genome; culturomics; taxono-genomics
18.  Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177 
Standards in Genomic Sciences  2013;8(3):539-547.
Francisella tularensis is a facultative intracellular bacterium in the class Gammaproteobacteria. This strain is of interest because it is the etiologic agent of tularemia and a highly virulent category A biothreat agent. Here we describe the draft genome sequence and annotation of Francisella tularensis subsp. holarctica BD11-00177, isolated from the first case of indigenous tularemia detected in The Netherlands since 1953. Whole genome DNA sequence analysis assigned this isolate to the genomic group B.FTNF002–00, which previously has been exclusively reported from Spain, France, Italy, Switzerland and Germany. Automatic annotation of the 1,813,372 bp draft genome revealed 2,103 protein-coding and 46 RNA genes.
doi:10.4056/sigs.4217923
PMCID: PMC3910693  PMID: 24501637
tularaemia; biodefence; zoonotic infection; phylogeography; Netherlands
19.  Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium 
Standards in Genomic Sciences  2013;8(3):548-560.
Anaerococcus pacaensis strain 9403502T, is the type strain of Anaerococcus pacaensis sp. nov., a new species within a new genus Anaerococcus. This strain, whose genome is described here, was isolated from a blood sample. A. pacaensis strain 9403502T is an obligate anaerobic Gram-positive coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2.36 Mbp long genome exhibits a G+C content of 35.05% and contains 2,186 protein-coding and 72 RNA genes, including 3 rRNA genes.
doi:10.4056/sigs.4177252
PMCID: PMC3910703  PMID: 24501638
Anaerococcus pacaensis; genome
20.  Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov. 
Standards in Genomic Sciences  2013;8(3):525-538.
Megasphaera massiliensis strain NP3T sp. nov. is the type strain of Megasphaera massiliensis sp. nov., a new species within the genus Megasphaera. This strain, whose genome is described here, was isolated from the fecal flora of an HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,661,757 bp long genome (1 chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes, including 5 rRNA genes.
doi:10.4056/sigs.4077819
PMCID: PMC3910696  PMID: 24501636
Megasphaera massiliensis; genome; culturomics; taxonogenomics
21.  Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1T (= DSM 45190T) 
Standards in Genomic Sciences  2013;8(3):516-524.
Corynebacterium maris Coryn-1T Ben-Dov et al. 2009 is a member of the genus Corynebacterium which contains Gram-positive, non-spore forming bacteria with a high G+C content. C. maris was isolated from the mucus of the Scleractinian coral Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It displays tolerance to salts (up to 10%) and is related to the soil bacterium Corynebacterium halotolerans. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project, describing the 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584 protein-coding and 67 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.4057796
PMCID: PMC3910691  PMID: 24501635
aerobic; non-motile; Gram-positive; non-spore forming; non-hemolytic; heterotrophic; mesophilic; halotolerant
22.  Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements 
Standards in Genomic Sciences  2013;8(3):389-402.
Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565T together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).
doi:10.4056/sigs.3858183
PMCID: PMC3910692  PMID: 24501625
marine; biofilm; ovoid-shaped; halotolerant; heterotrophic; quorum sensing; plasmid; thiosulfate oxidation; carbon monoxide utilization; Rhodobacteraceae; Alphaproteobacteria
23.  Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov. 
Standards in Genomic Sciences  2013;8(3):465-479.
Bacillus massilioanorexius strain AP8T sp. nov. is the type strain of B. massilioanorexius sp. nov., a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old Caucasian French female suffering from a severe form of anorexia nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive aerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,616,135 bp long genome (one chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes, including 8 rRNA genes.
doi:10.4056/sigs.4087826
PMCID: PMC3910694  PMID: 24501631
Bacillus massilioanorexius; genome; culturomics; taxonogenomics
24.  Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684T), a member of the Roseobacter clade 
Standards in Genomic Sciences  2013;8(3):480-490.
Rubellimicrobium thermophilum Denner et al. 2006 is the type species of the genus Rubellimicrobium, a representative of the Roseobacter clade within the Rhodobacteraceae. Members of this clade were shown to be abundant especially in coastal and polar waters, but were also found in microbial mats and sediments. They are metabolically versatile and form a physiologically heterogeneous group within the Alphaproteobacteria. Strain C-Ivk-R2A-2T was isolated from colored deposits in a pulp dryer; however, its natural habitat is so far unknown. Here we describe the features of this organism, together with the draft genome sequence and annotation and novel aspects of its phenotype. The 3,161,245 bp long genome contains 3,243 protein-coding and 45 RNA genes.
doi:10.4056/sigs.4247911
PMCID: PMC3910695  PMID: 24501632
rod-shaped; reddish-pigmented; thermophile; chemoheterotrophic; prophage-like structures; Rhodobacteraceae; Roseobacter clade; Alphaproteobacteria
25.  Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T 
Standards in Genomic Sciences  2013;8(3):450-464.
Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members are phylogenetically and physiologically diverse. In contrast to the type species of this genus, Phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of P. arcticus. Here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. The 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists of one chromosome and five extrachromosomal elements. Prophage sequences identified via PHAST constitute nearly 5% of the bacterial chromosome and included a potential Mu-like phage as well as a gene-transfer agent (GTA). In addition, the genome of strain DSM 23566T encodes all of the genes necessary for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic distances indicate that the classification of the species might need to be reconsidered.
doi:10.4056/sigs.383362
PMCID: PMC3910698  PMID: 24501630
aerobic; psychrophilic; motile; high-quality draft; prophage-like structures; extrachromosomal elements; assimilatory nitrate reduction; Alphaproteobacteria; Roseobacter clade

Results 1-25 (356)