共查询到20条相似文献,搜索用时 31 毫秒
1.
K Mavromatis O Chertkov A Lapidus M Nolan S Lucas H Tice TG Del Rio JF Cheng C Han R Tapia D Bruce LA Goodwin S Pitluck M Huntemann K Liolios I Pagani N Ivanova N Mikhailova A Pati A Chen K Palaniappan M Land EM Brambilla M Rohde S Spring M Göker JC Detter J Bristow JA Eisen V Markowitz P Hugenholtz NC Kyrpides HP Klenk T Woyke 《Standards in genomic sciences》2012,6(2):210-219
Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
2.
Nolan M Tindall BJ Pomrenke H Lapidus A Copeland A Glavina Del Rio T Lucas S Chen F Tice H Cheng JF Saunders E Han C Bruce D Goodwin L Chain P Pitluck S Ovchinikova G Pati A Ivanova N Mavromatis K Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Brettin T Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Detter JC 《Standards in genomic sciences》2009,1(3):283-290
Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
3.
Abt B Teshima H Lucas S Lapidus A Del Rio TG Nolan M Tice H Cheng JF Pitluck S Liolios K Pagani I Ivanova N Mavromatis K Pati A Tapia R Han C Goodwin L Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Rohde M Göker M Tindall BJ Detter JC Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2011,4(1):2-12
Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of the family Cytophagaceae in the phylum Bacteroidetes. Members of the phylum Bacteroidetes are widely distributed in nature, especially in aquatic environments. They are of special interest for their ability to degrade complex biopolymers. L. byssophila occupies a rather isolated position in the tree of life and is characterized by its ability to hydrolyze starch and gelatine, but not agar, cellulose or chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. L. byssophila is already the 16(th) member of the family Cytophagaceae whose genome has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
4.
Chertkov O Brown PJ Kysela DT de Pedro MA Lucas S Copeland A Lapidus A Del Rio TG Tice H Bruce D Goodwin L Pitluck S Detter JC Han C Larimer F Chang YJ Jeffries CD Land M Hauser L Kyrpides NC Ivanova N Ovchinnikova G Tindall BJ Göker M Klenk HP Brun YV 《Standards in genomic sciences》2011,5(3):287-297
The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. baltica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacterium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 protein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008. 相似文献
5.
Kiss H Lang E Lapidus A Copeland A Nolan M Glavina Del Rio T Chen F Lucas S Tice H Cheng JF Han C Goodwin L Pitluck S Liolios K Pati A Ivanova N Mavromatis K Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Detter JC Brettin T Spring S Rohde M Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(3):270-279
Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column undesirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this marine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome sequence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
6.
Sims D Brettin T Detter JC Han C Lapidus A Copeland A Glavina Del Rio T Nolan M Chen F Lucas S Tice H Cheng JF Bruce D Goodwin L Pitluck S Ovchinnikova G Pati A Ivanova N Mavrommatis K Chen A Palaniappan K D'haeseleer P Chain P Bristow J Eisen JA Markowitz V Hugenholtz P Schneider S Göker M Pukall R Kyrpides NC Klenk HP 《Standards in genomic sciences》2009,1(1):12-20
Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. Kytococcus sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
7.
Mariko Naito Yoshitoshi Ogura Takehiko Itoh Mikio Shoji Masaaki Okamoto Tetsuya Hayashi Koji Nakayama 《DNA research》2016,23(1):11-19
Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria. 相似文献
8.
Weissgerber T Zigann R Bruce D Chang YJ Detter JC Han C Hauser L Jeffries CD Land M Munk AC Tapia R Dahl C 《Standards in genomic sciences》2011,5(3):311-330
Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacterium belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus Allochromatium contains currently five species. All members were isolated from freshwater, brackish water or marine habitats and are predominately obligate phototrophs. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the Chromatiaceae within the purple sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp genome with its 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Genome Institute Community Sequencing Program. 相似文献
9.
Sun H Lapidus A Nolan M Lucas S Del Rio TG Tice H Cheng JF Tapia R Han C Goodwin L Pitluck S Pagani I Ivanova N Mavromatis K Mikhailova N Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Djao OD Rohde M Sikorski J Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,3(3):325-336
Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus Nocardiopsis, which in turn is the type genus of the family Nocardiopsaceae. This species is of interest because of its ecological versatility. Members of N. dassonvillei have been isolated from a large variety of natural habitats such as soil and marine sediments, from different plant and animal materials as well as from human patients. Moreover, representatives of the genus Nocardiopsis participate actively in biopolymer degradation. This is the first complete genome sequence in the family Nocardiopsaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a 0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
10.
von Jan M Lapidus A Del Rio TG Copeland A Tice H Cheng JF Lucas S Chen F Nolan M Goodwin L Han C Pitluck S Liolios K Ivanova N Mavromatis K Ovchinnikova G Chertkov O Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Saunders E Brettin T Detter JC Chain P Eichinger K Huber H Spring S Rohde M Göker M Wirth R Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(3):327-346
Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
11.
Anderson I Risso C Holmes D Lucas S Copeland A Lapidus A Cheng JF Bruce D Goodwin L Pitluck S Saunders E Brettin T Detter JC Han C Tapia R Larimer F Land M Hauser L Woyke T Lovley D Kyrpides N Ivanova N 《Standards in genomic sciences》2011,5(1):50-60
Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project. 相似文献
12.
Grote J Bayindirli C Bergauer K Carpintero de Moraes P Chen H D'Ambrosio L Edwards B Fernández-Gómez B Hamisi M Logares R Nguyen D Rii YM Saeck E Schutte C Widner B Church MJ Steward GF Karl DM Delong EF Eppley JM Schuster SC Kyrpides NC Rappé MS 《Standards in genomic sciences》2011,5(3):269-278
Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known as SAR116 within the family Rhodospirillaceae. Here we describe preliminary features of the organism, together with the draft genome sequence and annotation. This is the second genome sequence of a member of the SAR116 clade. The 2,458,945 bp genome contains 2,334 protein-coding and 42 RNA genes. 相似文献
13.
Respiratory Mechanisms in the Flexibacteriaceae: Terminal Oxidase Systems of Saprospira grandis and Vitreoscilla Species 总被引:4,自引:2,他引:2
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Particles from both Saprospira grandis and Vitreoscilla species, obtained by high-pressure extrusion and sonic treatment, respectively, actively catalyze the oxidation of reduced nicotinamide adenine dinucleotide (NADH) and succinate with O(2). These activities are inhibited by cyanide but not by antimycin; Saprospira is also amytal- and rotenone-insensitive. Vitreoscilla preparations were unable to oxidize mammalian ferrocytochrome c and reduced tetramethyl-p-phenylenediamine, whereas the Saprospira preparations did so actively. Low-temperature (77 K) difference spectroscopy of Vitreoscilla cells and particles indicates the presence of three maxima in the cytochrome alpha-region at 554, 558, and 562 nm. All three cytochromes are active in NADH and succinate oxidation, but none is ascorbate reducible. Cytochrome o is the only CO-binding pigment present and is probably the terminal oxidase; it has properties similar to the cytochrome o isolated in solubilized form from this organism. Saprospira cells and membranes exhibit four cytochrome absorption bands whose maxima are at 550, 554, 558, and 603 nm at 77 K. The latter component has not been noted previously. NADH and succinate reduce all four cytochromes, but ascorbate reduces only the 550- and 603-nm pigments. CO spectra indicate the presence of cytochrome a,a(3) which is probably the oxidase. A second CO-binding pigment is present which is not a peroxidase but may be a cytochrome. 相似文献
14.
Pukall R Gehrich-Schröter G Lapidus A Nolan M Glavina Del Rio T Lucas S Chen F Tice H Pitluck S Cheng JF Copeland A Saunders E Brettin T Detter JC Bruce D Goodwin L Pati A Ivanova N Mavromatis K Ovchinnikova G Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Chain P Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Han C 《Standards in genomic sciences》2009,1(3):262-269
Jonesia denitrificans (Prevot 1961) Rocourt et al. 1987 is the type species of the genus Jonesia, and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. J. denitrificans is characterized by a typical coryneform morphology and is able to form irregular nonsporulating rods showing branched and club-like forms. Coccoid cells occur in older cultures. J. denitrificans is classified as a pathogenic organism for animals (vertebrates). The type strain whose genome is described here was originally isolated from cooked ox blood. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus for which a complete genome sequence is described. The 2,749,646 bp long genome with its 2558 protein-coding and 71 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
15.
Abt B Foster B Lapidus A Clum A Sun H Pukall R Lucas S Glavina Del Rio T Nolan M Tice H Cheng JF Pitluck S Liolios K Ivanova N Mavromatis K Ovchinnikova G Pati A Goodwin L Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Rohde M Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,3(1):15-25
Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
16.
Labutti K Pukall R Steenblock K Glavina Del Rio T Tice H Copeland A Cheng JF Lucas S Chen F Nolan M Bruce D Goodwin L Pitluck S Ivanova N Mavromatis K Ovchinnikova G Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Chain P Saunders E Brettin T Detter JC Han C Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Lapidus A 《Standards in genomic sciences》2009,1(2):159-165
Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family 'Peptostreptococcaceae'. A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family 'Peptostreptococcaceae' for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
17.
Schleheck D Weiss M Pitluck S Bruce D Land ML Han S Saunders E Tapia R Detter C Brettin T Han J Woyke T Goodwin L Pennacchio L Nolan M Cook AM Kjelleberg S Thomas T 《Standards in genomic sciences》2011,5(3):298-310
Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae. 相似文献
18.
Copeland A Spring S Göker M Schneider S Lapidus A Del Rio TG Tice H Cheng JF Chen F Nolan M Bruce D Goodwin L Pitluck S Ivanova N Mavrommatis K Ovchinnikova G Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CC Meincke L Sims D Brettin T Detter JC Han C Chain P Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Lucas S 《Standards in genomic sciences》2009,1(1):29-37
Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X(T) is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO(2). Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
19.
Pitluck S Sikorski J Zeytun A Lapidus A Nolan M Lucas S Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Liolios K Pagani I Ivanova N Mavromatis K Pati A Chen A Palaniappan K Hauser L Chang YJ Jeffries CD Detter JC Brambilla E Djao OD Rohde M Spring S Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Land M 《Standards in genomic sciences》2011,4(1):54-62
Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus Calditerrivibrio. The species is of interest because of its important role in the nitrate cycle as nitrate reducer and for its isolated phylogenetic position in the Tree of Life. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the third complete genome sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
20.
Pati A Abt B Teshima H Nolan M Lapidus A Lucas S Hammon N Deshpande S Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Pagani I Mavromatis K Ovchinikova G Chen A Palaniappan K Land M Hauser L Jeffries CD Detter JC Brambilla EM Kannan KP Rohde M Spring S Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Ivanova N 《Standards in genomic sciences》2011,4(2):221-232
Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 is the type species of the genus Cellulophaga, which belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from marine beach mud in Limon, Costa Rica. The species is of biotechnological interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides. After the genome sequence of Cellulophaga algicola this is the second completed genome sequence of a member of the genus Cellulophaga. The 3,765,936 bp long genome with its 3,303 protein-coding and 55 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献