共查询到20条相似文献,搜索用时 31 毫秒
1.
Iain Anderson Huzuki Teshima Matt Nolan Alla Lapidus Hope Tice Tijana Glavina Del Rio Jan-Fang Cheng Cliff Han Roxanne Tapia Lynne A. Goodwin Sam Pitluck Konstantinos Liolios Konstantinos Mavromatis Ioanna Pagani Natalia Ivanova Natalia Mikhailova Amrita Pati Amy Chen Krishna Palaniappan Miriam Land Manfred Rohde Elke Lang John C. Detter Markus G?ker Tanja Woyke James Bristow Jonathan A. Eisen Victor Markowitz Philip Hugenholtz Nikos C. Kyrpides Hans-Peter Klenk 《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. 相似文献
2.
Ikram Imene Hassani Catherine Robert Caroline Michelle Didier Raoult Hocine Hacène Christelle Desnues 《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. 相似文献
3.
Heike M. Freese Hajnalka Dalingault J?rn Petersen Silke Pradella Karen Davenport Hazuki Teshima Amy Chen Amrita Pati Natalia Ivanova Lynne A. Goodwin Patrick Chain John C. Detter Manfred Rohde Sabine Gronow Nikos C. Kyrpides Tanja Woyke Thorsten Brinkhoff Markus G?ker J?rg Overmann Hans-Peter Klenk 《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. 相似文献
4.
Dong-Wook Hyun Tae Woong Whon Yong-Joon Cho Jongsik Chun Min-Soo Kim Mi-Ja Jung Na-Ri Shin Joon-Yong Kim Pil Soo Kim Ji-Hyun Yun Jina Lee Sei Joon Oh Jin-Woo Bae 《Standards in genomic sciences》2013,8(2):255-263
Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain CrmT and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments. 相似文献
5.
Anne Fiebig Thomas Riedel Sabine Gronow J?rn Petersen Hans-Peter Klenk Markus G?ker 《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. 相似文献
6.
Su Yean Ong Chandra Bhan Pratap Xuehua Wan Shaobin Hou Ahmad Yamin Abdul Rahman Jennifer A. Saito Gopal Nath Maqsudul Alam 《Standards in genomic sciences》2013,7(3):483-496
Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative, facultatively anaerobic bacterium. It belongs to the family Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of residing in the human gallbladder by forming a biofilm and hence causing the person to become a typhoid carrier. Here we present the complete genome of Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was isolated from a chronic carrier in Varanasi, India. The complete genome comprises a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella enterica serovar Typhi strain CT18, although their genome structure is slightly different. 相似文献
7.
Oleg Mediannikov Khalid El Karkouri Catherine Robert Pierre-Edouard Fournier Didier Raoult 《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. 相似文献
8.
Ajay Kumar Mishra Jean-Christophe Lagier Anne Pfleiderer Thi Thien Nguyen Aurelia Caputo Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2013,9(2):395-409
Holdemania massiliensis strain AP2T sp. nov. is the type strain of H. massiliensis sp. nov., a new species within the genus Holdemania. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA genes. 相似文献
9.
Chunming Dong Xin Chen Yanrong Xie Qiliang Lai Zongze Shao 《Standards in genomic sciences》2014,9(3):893-901
Strain R6-15 belongs to the genus Thalassolituus, in the family Oceanospirillaceae of Gammaproteobacteria. Representatives of this genus are known to be the obligate hydrocarbonoclastic marine bacteria. Thalassolituus oleivorans R6-15 is of special interest due to its dominance in the crude oil-degrading consortia enriched from the surface seawater of the Arctic Ocean. Here we describe the complete genome sequence and annotation of this strain, together with its phenotypic characteristics. The genome with size of 3,764,053 bp comprises one chromosome without any plasmids, and contains 3,372 protein-coding and 61 RNA genes, including 12 rRNA genes. 相似文献
10.
Sophie Edouard Senthil Sankar Nicole Prisca Makaya Dangui Jean-Christophe Lagier Caroline Michelle Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2014,9(3):866-882
Nesterenkonia massiliensis sp. nov., strain NP1T, is the type strain of Nesterenkonia massiliensis sp. nov., a new species within the genus Nesterenkonia. This strain, whose genome is described here, was isolated from the feces of a 32-year-old French woman suffering from AIDS and living in Marseille. Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains 2,663 protein-coding and 51 RNA genes, including 1 rRNA operon. 相似文献
11.
《Standards in genomic sciences》2013,7(3):469-482
Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006. 相似文献
12.
Jan Kuever Michael Visser Claudia Loeffler Matthias Boll Petra Worm Diana Z. Sousa Caroline M. Plugge Peter J. Schaap Gerard Muyzer Ines A.C. Pereira Sofiya N. Parshina Lynne A. Goodwin Nikos C. Kyrpides Janine Detter Tanja Woyke Patrick Chain Karen W. Davenport Manfred Rohde Stefan Spring Hans-Peter Klenk Alfons J.M. Stams 《Standards in genomic sciences》2014,9(3):821-839
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes. 相似文献
13.
Nora Buddruhs Olga Chertkov J?rn Petersen Anne Fiebig Amy Chen Amrita Pati Natalia Ivanova Alla Lapidus Lynne A. Goodwin Patrick Chain John C. Detter Sabine Gronow Nikos C. Kyrpides Tanja Woyke Markus G?ker Thorsten Brinkhoff Hans-Peter Klenk 《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. 相似文献
14.
Esma Bendjama Lotfi Loucif Seydina M. Diene Caroline Michelle Djamila Gacemi-Kirane Jean-Marc Rolain 《Standards in genomic sciences》2014,9(3):1046-1061
Strain EB01T sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes. 相似文献
15.
Ulrike Kappler Karen Davenport Scott Beatson Susan Lucas Alla Lapidus Alex Copeland Kerrie W. Berry Tijana Glavina Del Rio Nancy Hammon Eileen Dalin Hope Tice Sam Pitluck Paul Richardson David Bruce Lynne A. Goodwin Cliff Han Roxanne Tapia John C. Detter Yun-juan Chang Cynthia D. Jeffries Miriam Land Loren Hauser Nikos C. Kyrpides Markus G?ker Natalia Ivanova Hans-Peter Klenk Tanja Woyke 《Standards in genomic sciences》2012,7(1):44-58
Starkeya novella (Starkey 1934) Kelly et al. 2000 is a member of the family Xanthobacteraceae in the order ‘Rhizobiales’, which is thus far poorly characterized at the genome level. Cultures from this species are most interesting due to their facultatively chemolithoautotrophic lifestyle, which allows them to both consume carbon dioxide and to produce it. This feature makes S. novella an interesting model organism for studying the genomic basis of regulatory networks required for the switch between consumption and production of carbon dioxide, a key component of the global carbon cycle. In addition, S. novella is of interest for its ability to grow on various inorganic sulfur compounds and several C1-compounds such as methanol. Besides Azorhizobium caulinodans, S. novella is only the second species in the family Xanthobacteraceae with a completely sequenced genome of a type strain. The current taxonomic classification of this group is in significant conflict with the 16S rRNA data. The genomic data indicate that the physiological capabilities of the organism might have been underestimated. The 4,765,023 bp long chromosome with its 4,511 protein-coding and 52 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008. 相似文献
16.
Roshan Padmanabhan Jean-Christophe Lagier Nicole Prisca Makaya Dangui Caroline Michelle Carine Couderc Didier Raoult Pierre-Edouard Fournier 《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. 相似文献
17.
Dhamodharan Ramasamy Jean-Christophe Lagier Morgane Rossi-Tamisier Anne Pfleiderer Caroline Michelle Carine Couderc Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2014,9(3):1181-1197
Bacteroides timonensis strain AP1T (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes. 相似文献
18.
Oliver Frank Silke Pradella Manfred Rohde Carmen Scheuner Hans-Peter Klenk Markus G?ker J?rn Petersen 《Standards in genomic sciences》2014,9(3):914-932
Phaeobacter gallaeciensis CIP 105210T (= DSM 26640T = BS107T) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107T was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210T (= DSM 26640T) is the sole genome-sequenced representative of P. gallaeciensis. 相似文献
19.
Suman R. Rawat Minna K. M?nnist? Valentin Starovoytov Lynne Goodwin Matt Nolan Loren J. Hauser Miriam Land Karen Walston Davenport Tanja Woyke Max M. H?ggblom 《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. 相似文献
20.
《Standards in genomic sciences》2013,8(2):165-176
Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain of the species, Z-7692T, was isolated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second ''true'' member of the genus Spirochaeta with a genome-sequenced type strain to be published. The 3,285,855 bp long genome of strain Z-7692T with its 2,817 protein-coding and 57 RNA genes is a part of the G enomic
E ncyclopedia of
B acteria and
A rchaea project. 相似文献