共查询到20条相似文献,搜索用时 31 毫秒
1.
Dhamodharan Ramasamy Sahare Kokcha Jean-Christophe Lagier Thi-Thien Nguyen Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,7(2):246-257
Aeromicrobium massiliense strain JC14Tsp. nov. is the type strain of Aeromicrobium massiliense sp. nov., a new species within the genus Aeromicrobium. This strain, whose genome is described here, was isolated from the fecal microbiota of an asymptomatic patient. Aeromicrobium massiliense is an aerobic rod-shaped gram-positive bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,322,119 bp long genome contains 3,296 protein-coding and 51 RNA genes. 相似文献
2.
Ajay Kumar Mishra Gregory Gimenez Jean-Christophe Lagier Catherine Robert Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,6(3):1-16
Alistipes senegalensis strain JC50T is the type strain of A. senegalensis sp. nov., a new species within the Alistipes genus. This strain, whose genome is described here, was isolated from the fecal flora of an asymptomatic patient. A. senegalensis is an anaerobic Gram-negative rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,017,609 bp long genome (1 chromosome, but no plasmid) contains 3,113 protein-coding and 50 RNA genes, including 5 rRNA genes. 相似文献
3.
Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431T (= NBRC 102363T)
Hideki Yamamura Yasuo Ohnishi Jun Ishikawa Natsuko Ichikawa Haruo Ikeda Mitsuo Sekine Takeshi Harada Sueharu Horinouchi Misa Otoguro Tomohiko Tamura Ken-ichiro Suzuki Yasutaka Hoshino Akira Arisawa Youji Nakagawa Nobuyuki Fujita Masayuki Hayakawa 《Standards in genomic sciences》2012,7(2):294-303
Actinoplanes missouriensis Couch 1963 is a well-characterized member of the genus Actinoplanes, which is of morphological interest because its members typically produce sporangia containing motile spores. The sporangiospores are motile by means of flagella and exhibit chemotactic properties. It is of further interest that members of Actinoplanes are prolific sources of novel antibiotics, enzymes, and other bioactive compounds. Here, we describe the features of A. missouriensis 431T, together with the complete genome sequence and annotation. The 8,773,466 bp genome contains 8,125 protein-coding and 79 RNA genes. 相似文献
4.
Stefan Spring Michael Visser Megan Lu Alex Copeland Alla Lapidus Susan Lucas Jan-Fang Cheng Cliff Han Roxanne Tapia Lynne A. Goodwin Sam Pitluck Natalia Ivanova Miriam Land Loren Hauser Frank Larimer Manfred Rohde Markus G?ker John C. Detter Nikos C. Kyrpides Tanja Woyke Peter J. Schaap Caroline M. Plugge Gerard Muyzer Jan Kuever Inês A. C. Pereira Sofiya N. Parshina Rizlan Bernier-Latmani Alfons J.M. Stams Hans-Peter Klenk 《Standards in genomic sciences》2012,7(2):304-319
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.Keywords : anaerobic, motile, sporulating, mesophilic, sulfate-reducer, hydrogen sulfide, incomplete oxidizer, mixotrophic, CSP 2009, Peptococcaceae, Clostridiales 相似文献
5.
Yoko Katano Shun Fujinami Akatsuki Kawakoshi Hidekazu Nakazawa Syoko Oji Takao Iino Akio Oguchi Akiho Ankai Shigehiro Fukui Yasuyuki Terui Sachi Kamata Takeshi Harada Satoshi Tanikawa Ken-ichiro Suzuki Nobuyuki Fujita 《Standards in genomic sciences》2012,6(3):406-414
Oscillibacter valericigenes is a mesophilic, strictly anaerobic bacterium belonging to the clostridial cluster IV. Strain Sjm18-20T (=NBRC 101213T =DSM 18026T) is the type strain of the species and represents the genus Oscillibacter Iino et al. 2007. It was isolated from the alimentary canal of a Japanese corbicula clam (Corbicula japonica) collected on a seacoast in Shimane Prefecture in Japan. Phylogenetically, strain Sjm18-20T is closest to uncultured bacteria in digestive tracts, including the enriched cells thought to represent Oscillospira guilliermondii Chatton and Perard 1913. The isolated phylogenetic position and some distinct characteristics prompted us to determine the complete genome sequence. The 4,410,036 bp chromosome and the 60,586 bp plasmid were predicted to encode a total of 4,723 protein-coding genes. 相似文献
6.
David L. Bernick Kevin Karplus Lauren M. Lui Joanna K. C. Coker Julie N. Murphy Patricia P. Chan Aaron E. Cozen Todd M. Lowe 《Standards in genomic sciences》2012,6(3):336-345
Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot spring in Japan. Here we describe its main chromosome of 2,436,033 bp, with three large-scale inversions and an extra-chromosomal element of 16,887 bp. We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome, including nine H/ACA-like small RNA, 83 predicted C/D box small RNA, and 47 transfer RNA genes. Comparative analyses with the closest known relative, the anaerobe Pyrobaculum arsenaticum from Italy, reveals unexpectedly high synteny and nucleotide identity between these two geographically distant species. Deep sequencing of a mixture of genomic DNA from multiple cells has illuminated some of the genome dynamics potentially shared with other species in this genus. 相似文献
7.
Sahare Kokcha Dhamodharan Ramasamy Jean-Christophe Lagier Catherine Robert Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,7(2):233-245
Brevibacterium senegalense strain JC43T sp. nov. is the type strain of Brevibacterium senegalense sp. nov., a new species within the Brevibacterium genus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. B. senegalense is an aerobic rod-shaped Gram-positive bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,425,960 bp long genome (1 chromosome but no plasmid) contains 3,064 protein-coding and 49 RNA genes. 相似文献
8.
Michael Visser Sofiya N. Parshina Joana I. Alves Diana Z. Sousa Inês A. C. Pereira Gerard Muyzer Jan Kuever Alexander V. Lebedinsky Jasper J. Koehorst Petra Worm Caroline M. Plugge Peter J. Schaap Lynne A. Goodwin Alla Lapidus Nikos C. Kyrpides Janine C. Detter Tanja Woyke Patrick Chain Karen W. Davenport Stefan Spring Manfred Rohde Hans Peter Klenk Alfons J.M. Stams 《Standards in genomic sciences》2014,9(3):655-675
9.
Mohamed Sassi Catherine Robert Didier Raoult Michel Drancourt 《Standards in genomic sciences》2013,8(2):306-317
Mycobacterium simiae is a non-tuberculosis mycobacterium causing pulmonary infections in both immunocompetent and imunocompromized patients. We announce the draft genome sequence of M. simiae DSM 44165T. The 5,782,968-bp long genome with 65.15% GC content (one chromosome, no plasmid) contains 5,727 open reading frames (33% with unknown function and 11 ORFs sizing more than 5000 -bp), three rRNA operons, 52 tRNA, one 66-bp tmRNA matching with tmRNA tags from Mycobacterium avium, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium microti, Mycobacterium marinum, and Mycobacterium africanum and 389 DNA repetitive sequences. Comparing ORFs and size distribution between M. simiae and five other Mycobacterium species M. simiae clustered with M. abscessus and M. smegmatis. A 40-kb prophage was predicted in addition to two prophage-like elements, 7-kb and 18-kb in size, but no mycobacteriophage was seen after the observation of 106
M. simiae cells. Fifteen putative CRISPRs were found. Three genes were predicted to encode resistance to aminoglycosides, betalactams and macrolide-lincosamide-streptogramin B. A total of 163 CAZYmes were annotated. M. simiae contains ESX-1 to ESX-5 genes encoding for a type-VII secretion system. Availability of the genome sequence may help depict the unique properties of this environmental, opportunistic pathogen. 相似文献
10.
《Standards in genomic sciences》2013,8(2):228-238
Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was established as a result of the reclassification of Leptospira parva Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella constitutes the family Leptospiraceae, within the order Spirochaetales. Here we describe the features of this free-living aerobic spirochete together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Turneriella and the 13th member of the family Leptospiraceae for which a complete or draft genome sequence is now available. The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is part of the Genomic
Encyclopedia of
Bacteria and
Archaea project. 相似文献
11.
Jan P. Meier-Kolthoff Megan Lu Marcel Huntemann Susan Lucas Alla Lapidus Alex Copeland Sam Pitluck Lynne A. Goodwin Cliff Han Roxanne Tapia Gabriele P?tter Miriam Land Natalia Ivanova Manfred Rohde Markus G?ker John C. Detter Tanja Woyke Nikos C. Kyrpides Hans-Peter Klenk 《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). 相似文献
12.
《Standards in genomic sciences》2012,7(2):189-199
The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile, non-sporulating and a mesophile bacterium, was isolated from liver, lung and mediastinal lymph node lesions in an antelope from South Africa. This strain is interesting in the sense that it has been found together with non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the lesion formation. In this work, we describe a set of features of C. pseudotuberculosis P54B96, together with the details of the complete genome sequence and annotation. The genome comprises of 2.34 Mbp long, single circular genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a G+C content of 52.19%. The analysis of the genome sequence provides means to better understanding the molecular and genetic basis of virulence of this bacterium, enabling a detailed investigation of its pathogenesis.Keyword: s: biovar ovis, Gram-positive pathogen, caseous lymphadenitis/cheesy gland disease, liver lesion, Antelope, genome sequencing, Ion Torrent 相似文献
13.
Prapaporn Boonma Jennifer K. Spinler Xiang Qin Chutima Jittaprasatsin Donna M. Muzny Harsha Doddapaneni Richard Gibbs Joe Petrosino Somying Tumwasorn James Versalovic 《Standards in genomic sciences》2014,9(3):744-754
Lactobacillus rhamnosus is a facultative, lactic acid bacterium in the phylum Firmicutes. Lactobacillus spp. are generally considered beneficial, and specific strains of L. rhamnosus are validated probiotics. We describe the draft genomes of three L. rhamnosus strains (L31, L34, and L35) isolated from the feces of Thai breastfed infants, which exhibit anti-inflammatory properties in vitro. The three genomes range between 2.8 – 2.9 Mb, and contain approximately 2,700 protein coding genes. 相似文献
14.
Thomas Riedel Stefan Spring Anne Fiebig J?rn Petersen Nikos C. Kyrpides Markus G?ker Hans-Peter Klenk 《Standards in genomic sciences》2014,9(3):1333-1345
Salipiger mucosus Martínez-Cànovas et al. 2004 is the type species of the genus Salipiger, a moderately halophilic and exopolysaccharide-producing representative of the Roseobacter lineage within the alphaproteobacterial family Rhodobacteraceae. Members of this family were shown to be the most abundant bacteria especially in coastal and polar waters, but were also found in microbial mats and sediments. Here we describe the features of the S. mucosus strain DSM 16094T together with its genome sequence and annotation. The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus DSM 16094T was sequenced as part of the activities of the Transregional Collaborative Research Center 51 (TRR51) funded by the German Research Foundation (DFG). 相似文献
15.
16.
Bryndan P. Durham Jana Grote Kerry A. Whittaker Sara J. Bender Haiwei Luo Sharon L. Grim Julia M. Brown John R. Casey Antony Dron Lennin Florez-Leiva Andreas Krupke Catherine M. Luria Aric H. Mine Olivia D. Nigro Santhiska Pather Agathe Talarmin Emma K. Wear Thomas S. Weber Jesse M. Wilson Matthew J. Church Edward F. DeLong David M. Karl Grieg F. Steward John M. Eppley Nikos C. Kyrpides Stephan Schuster Michael S. Rappé 《Standards in genomic sciences》2014,9(3):632-645
Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters. 相似文献
17.
《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. 相似文献
18.
Spyridon Ntougias Alla Lapidus James Han Konstantinos Mavromatis Amrita Pati Amy Chen Hans-Peter Klenk Tanja Woyke Constantinos Fasseas Nikos C. Kyrpides Georgios I. Zervakis 《Standards in genomic sciences》2014,9(3):783-793
Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6T, together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis. 相似文献
19.
Lena Schaffert Andreas Albersmeier Hanna Bednarz Karsten Niehaus J?rn Kalinowski Christian Rückert 《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. 相似文献
20.
Ji-Hyun Yun Yong-Joon Cho Jongsik Chun Dong-Wook Hyun Jin-Woo Bae 《Standards in genomic sciences》2014,9(3):495-504
Leucobacter salsicius M1-8T is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8T, as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments. 相似文献