1,348 results on '"Land, Miriam"'
Search Results
2. Metagenome-assembled genome extraction and analysis from microbiomes using KBase
- Author
-
Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Robert W., Henry, Chris S., and Arkin, Adam P.
- Published
- 2023
- Full Text
- View/download PDF
3. KBase: The United States Department of Energy Systems Biology Knowledgebase
- Author
-
Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel MD, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong
- Subjects
Computational Biology ,Database Management Systems ,Humans ,Knowledge Bases ,Systems Biology ,United States - Published
- 2018
4. Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7
- Author
-
Utturkar, Sagar M, Bayer, Edward A, Borovok, Ilya, Lamed, Raphael, Hurt, Richard A, Land, Miriam L, Klingeman, Dawn M, Elias, Dwayne, Zhou, Jizhong, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, TBK, Ngan, Chew Yee, Daum, Chris, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Woyke, Tanja, and Brown, Steven D
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Infection - Abstract
We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
- Published
- 2016
5. Complete genome sequence of Methanospirillum hungatei type strain JF1.
- Author
-
Gunsalus, Robert P, Cook, Lauren E, Crable, Bryan, Rohlin, Lars, McDonald, Erin, Mouttaki, Housna, Sieber, Jessica R, Poweleit, Nicole, Zhou, Hong, Lapidus, Alla L, Daligault, Hajnalka Erzsebet, Land, Miriam, Gilna, Paul, Ivanova, Natalia, Kyrpides, Nikos, Culley, David E, and McInerney, Michael J
- Subjects
Anaerobic ,Formate ,Hydrogen ,Methangenic archaea ,Methanomicrobiales ,Motile ,Syntrophic partnerships ,Genetics ,Human Genome ,Biochemistry and Cell Biology - Abstract
Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type species of the genus Methanospirillum, which belongs to the family Methanospirillaceae within the order Methanomicrobiales. Its genome was selected for sequencing due to its ability to utilize hydrogen and carbon dioxide and/or formate as a sole source of energy. Ecologically, M. hungatei functions as the hydrogen- and/or formate-using partner with many species of syntrophic bacteria. Its morphology is distinct from other methanogens with the ability to form long chains of cells (up to 100 μm in length), which are enclosed within a sheath-like structure, and terminal cells with polar flagella. The genome of M. hungatei strain JF1 is the first completely sequenced genome of the family Methanospirillaceae, and it has a circular genome of 3,544,738 bp containing 3,239 protein coding and 68 RNA genes. The large genome of M. hungatei JF1 suggests the presence of unrecognized biochemical/physiological properties that likely extend to the other Methanospirillaceae and include the ability to form the unusual sheath-like structure and to successfully interact with syntrophic bacteria.
- Published
- 2016
6. Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477T)
- Author
-
Kappler, Ulrike, Davenport, Karen, Beatson, Scott, Lapidus, Alla, Pan, Chongle, Han, Cliff, Montero-Calasanz, Maria del Carmen, Land, Miriam, Hauser, Loren, Rohde, Manfred, Göker, Markus, Ivanova, Natalia, Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Aerobic ,Obligate chemolithoautotroph ,Sulfur oxidizer ,Gram-negative ,Mono Lake ,Piscirickettsiaceae ,CSP 2008 - Abstract
Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1(T) is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1(T) is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
- Published
- 2016
7. The DOE Systems Biology Knowledgebase (KBase)
- Author
-
Arkin, Adam P, Stevens, Rick L, Cottingham, Robert W, Maslov, Sergei, Henry, Christopher S, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Harris, Nomi L, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Gunter, Dan, Murphy-Olson, Dan, Chan, Stephen, Kamimura, Roy T, Brettin, Thomas S, Meyer, Folker, Chivian, Dylan, Weston, David J, Glass, Elizabeth M, Davison, Brian H, Kumari, Sunita, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Drake, Meghan M, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Mills, Marissa, Novichkov, Pavel, Oh, Taeyun, Olsen, Gary J, Olson, Bob, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel MD, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, and Yoo, Shinjae
- Subjects
Bioengineering ,Genetics ,Human Genome ,Networking and Information Technology R&D (NITRD) ,Generic health relevance - Abstract
The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system.
- Published
- 2016
8. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34
- Author
-
Anderson, Iain J, DasSarma, Priya, Lucas, Susan, Copeland, Alex, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Dalin, Eileen, Bruce, David C, Goodwin, Lynne, Pitluck, Sam, Sims, David, Brettin, Thomas S, Detter, John C, Han, Cliff S, Larimer, Frank, Hauser, Loren, Land, Miriam, Ivanova, Natalia, Richardson, Paul, Cavicchioli, Ricardo, DasSarma, Shiladitya, Woese, Carl R, and Kyrpides, Nikos C
- Subjects
Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Archaea ,Halophile ,Halorubrum ,Extremophile ,Cold adaptation ,Tree of life - Abstract
Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
- Published
- 2016
9. Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes
- Author
-
Kotak, Malini, Isanapong, Jantiya, Goodwin, Lynne, Bruce, David, Chen, Amy, Han, Cliff S, Huntemann, Marcel, Ivanova, Natalia, Land, Miriam L, Nolan, Matt, Pati, Amrita, Woyke, Tanja, and Rodrigues, Jorge LM
- Subjects
Genetics ,Human Genome - Abstract
The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. We report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.
- Published
- 2015
10. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater
- Author
-
Ramsay, Bradley D, Hwang, Chiachi, Woo, Hannah L, Carroll, Sue L, Lucas, Susan, Han, James, Lapidus, Alla L, Cheng, Jan-Fang, Goodwin, Lynne A, Pitluck, Samuel, Peters, Lin, Chertkov, Olga, Held, Brittany, Detter, John C, Han, Cliff S, Tapia, Roxanne, Land, Miriam L, Hauser, Loren J, Kyrpides, Nikos C, Ivanova, Natalia N, Mikhailova, Natalia, Pagani, Ioanna, Woyke, Tanja, Arkin, Adam P, Dehal, Paramvir, Chivian, Dylan, Criddle, Craig S, Wu, Weimin, Chakraborty, Romy, Hazen, Terry C, and Fields, Matthew W
- Subjects
Microbiology ,Biological Sciences ,Genetics - Abstract
Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.
- Published
- 2015
11. Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle
- Author
-
Walworth, Nathan, Pfreundt, Ulrike, Nelson, William C, Mincer, Tracy, Heidelberg, John F, Fu, Feixue, Waterbury, John B, del Rio, Tijana Glavina, Goodwin, Lynne, Kyrpides, Nikos C, Land, Miriam L, Woyke, Tanja, Hutchins, David A, Hess, Wolfgang R, and Webb, Eric A
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Ecology ,Genetics ,Microbiology ,Human Genome ,1.1 Normal biological development and functioning ,Generic health relevance ,Bacterial Proteins ,Carbon ,Computational Biology ,Cyanobacteria ,DNA ,Bacterial ,DNA ,Intergenic ,Ecosystem ,Gene Expression Regulation ,Bacterial ,Genes ,Bacterial ,Genome ,Genomics ,Molecular Sequence Data ,Nitrogen ,Nitrogen Fixation ,Nucleic Acid Conformation ,Oceans and Seas ,Prochlorococcus ,RNA ,Signal Transduction ,Synechococcus ,Transposases ,marine microbiology ,oligotrophic ,evolution genomics ,nitrogen fixation - Abstract
Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual "inflation" of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.
- Published
- 2015
12. Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4
- Author
-
Shetty, Ameesha R, de Gannes, Vidya, Obi, Chioma C, Lucas, Susan, Lapidus, Alla, Cheng, Jan-Fang, Goodwin, Lynne A, Pitluck, Samuel, Peters, Linda, Mikhailova, Natalia, Teshima, Hazuki, Han, Cliff, Tapia, Roxanne, Land, Miriam, Hauser, Loren J, Kyrpides, Nikos, Ivanova, Natalia, Pagani, Ioanna, Chain, Patrick SG, Denef, Vincent J, Woyke, Tanya, and Hickey, William J
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Delftio acidovorans Cs1-4 ,Genome ,phn island ,Phenanthrene ,polycyclic aromatic hydrocarbons ,Nanopods ,Delftia acidovorans Cs1-4 - Abstract
Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.
- Published
- 2015
13. Complete genome sequence of Anabaena variabilis ATCC 29413
- Author
-
Thiel, Teresa, Pratte, Brenda S, Zhong, Jinshun, Goodwin, Lynne, Copeland, Alex, Lucas, Susan, Han, Cliff, Pitluck, Sam, Land, Miriam L, Kyrpides, Nikos C, and Woyke, Tanja
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Biochemistry and Cell Biology - Abstract
Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has served as a model organism, with an extensive literature extending over 40 years. The strain has three distinct nitrogenases that function under different environmental conditions and is capable of photoautotrophic growth in the light and true heterotrophic growth in the dark using fructose as both carbon and energy source. While this strain was first isolated in 1964 in Mississippi and named Anabaena flos-aquae MSU A-37, it clusters phylogenetically with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile, growing well at approximately 40(°) C. Here we provide some additional characteristics of the strain, and an analysis of the complete genome sequence.
- Published
- 2014
14. Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil
- Author
-
Rawat, Suman R, Männistö, Minna K, Starovoytov, Valentin, Goodwin, Lynne, Nolan, Matt, Hauser, Loren, Land, Miriam, Davenport, Karen Walston, Woyke, Tanja, and Häggblom, Max M
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,cold adapted ,acidophile ,tundra soil ,Acidobacteria ,Biochemistry and Cell Biology - Abstract
Granulicella tundricola strain MP5ACTX9(T) is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism 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, including gene modules encoding for the carbohydrate-active enzyme (CAZy) families for the breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of G. tundricola strain MP5ACTX9(T) consists of 4,309,151 bp of a circular chromosome and five mega plasmids with a total genome content of 5,503,984 bp. The genome comprises 4,705 protein-coding genes and 52 RNA genes.
- Published
- 2014
15. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T)
- Author
-
Nandasena, Kemanthi, Yates, Ron, Tiwari, Ravi, O’Hara, Graham, Howieson, John, Ninawi, Mohamed, Chertkov, Olga, Detter, Chris, Tapia, Roxanne, Han, Shunseng, Woyke, Tanja, Pitluck, Sam, Nolan, Matt, Land, Miriam, Liolios, Konstantinos, Pati, Amrita, Copeland, Alex, Kyrpides, Nikos, Ivanova, Natalia, Goodwin, Lynne, Meenakshi, Uma, and Reeve, Wayne
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,root-nodule bacteria ,nitrogen fixation ,evolution ,lateral gene transfer ,integrative and conjugative elements ,symbiosis ,Alphaproteobacteria ,Biochemistry and Cell Biology - Abstract
Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus - a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
- Published
- 2014
16. Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species
- Author
-
Moulin, Lionel, Klonowska, Agnieszka, Caroline, Bournaud, Booth, Kristina, Vriezen, Jan AC, Melkonian, Rémy, James, Euan K, Young, J Peter W, Bena, Gilles, Hauser, Loren, Land, Miriam, Kyrpides, Nikos, Bruce, David, Chain, Patrick, Copeland, Alex, Pitluck, Sam, Woyke, Tanja, Lizotte-Waniewski, Michelle, Bristow, Jim, and Riley, Margaret
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Burkholderia ,symbiosis ,Mimosa ,rhizobia ,nitrogen fixation ,Biochemistry and Cell Biology - Abstract
Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815(T), was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).
- Published
- 2014
17. Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring
- Author
-
Göker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D, Rohde, Manfred, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Lapidus, Alla
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,anaerobic ,motile ,thermophilic ,chemoorganotrophic ,solfataric spring ,outer sheath-like structure ,Thermotogaceae ,GEBA - Abstract
Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2014
18. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia
- Author
-
Göker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C, Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,anaerobic ,motile ,mesophilic ,methanogen ,swamp ,improved-high-quality draft ,Methanomicrobiaceae ,GEBA - Abstract
Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pre-genome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and annotation of the type strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia of B acteria and Archaea project.
- Published
- 2014
19. Complete genome sequence of Micromonospora L.5, a potential plant-growth regulating actinomycete, originally isolated from Casuarina equisetifolia root nodules
- Author
-
Hirsch, Ann M., Alvarado, Johana, Bruce, David, Chertkov, Olga, Hoff, Peter L. De, Detter, Chris, Fujishige, Nancy A., Goodwin, Lynne, Han, James, Han, Shunsheng, Ivanova, Natalia, Land, Miriam L., Lum, Michelle R., Martinez, Claudia, Milani-Nejad, Nima, Nolan, Matt, Pati, Amrita, Pitluck, Sam, Woyke, Tanja, and Valdes, Maria
- Subjects
Micromonospora L5 ,actinomycete ,Casuarina Equisetifolia root nodules ,Illumina GAii - Published
- 2014
20. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae
- Author
-
Scheuner, Carmen, Tindall, Brian J, Lu, Megan, Nolan, Matt, Lapidus, Alla, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D, Hauser, Loren, Land, Miriam, Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John C, Woyke, Tanja, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Göker, Markus, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Non-peptidoglycan bacteria ,Stalked bacteria ,Halotolerant ,Gram-negative ,Taxonomic descriptions ,Planctomycetales ,Planctomycetes ,GEBA - Abstract
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
- Published
- 2014
21. Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina equisetifolia Root Nodules
- Author
-
Hirsch, Ann M, Alvarado, Johana, Bruce, David, Chertkov, Olga, De Hoff, Peter L, Detter, John C, Fujishige, Nancy A, Goodwin, Lynne A, Han, James, Han, Shunsheng, Ivanova, Natalia, Land, Miriam L, Lum, Michelle R, Milani-Nejad, Nima, Nolan, Matt, Pati, Amrita, Pitluck, Sam, Tran, Stephen S, Woyke, Tanja, and Valdés, Maria
- Subjects
Microbiology ,Biological Sciences ,Genetics - Abstract
Micromonospora species live in diverse environments and exhibit a broad range of functions, including antibiotic production, biocontrol, and degradation of complex polysaccharides. To learn more about these versatile actinomycetes, we sequenced the genome of strain L5, originally isolated from root nodules of an actinorhizal plant growing in Mexico.
- Published
- 2013
22. Genome sequence of Frateuria aurantia type strain (Kondô 67(T)), a xanthomonade isolated from Lilium auratium Lindl.
- Author
-
Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
GEBA ,Xanthomonadaceae ,acetogenic ,mesophilic ,motile ,rod-shaped ,strictly aerobic ,‘Acetobacter aurantius’ ,'Acetobacter aurantius' ,Biotechnology ,Genetics ,Human Genome ,Biochemistry and Cell Biology - Abstract
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 67(T) was initially (1958) identified as a member of 'Acetobacter aurantius', a name that was not considered for the approved list. Kondô 67(T) 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 67(T) 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 G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
23. Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075T
- Author
-
Reeve, Wayne, Nandasena, Kemanthi, Yates, Ron, Tiwari, Ravi, O’Hara, Graham, Ninawi, Mohamed, Chertkov, Olga, Goodwin, Lynne, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Shunseng, Woyke, Tanja, Pitluck, Sam, Nolan, Matt, Land, Miriam, Copeland, Alex, Liolios, Konstantinos, Pati, Amrita, Mavromatis, Konstantinos, Markowitz, Victor, Kyrpides, Nikos, Ivanova, Natalia, Meenakshi, Uma, and Howieson, John
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,root-nodule bacteria ,nitrogen fixation ,evolution ,lateral gene transfer ,integrative and conjugative elements ,symbiosis ,Alphaproteobacteria ,Biochemistry and Cell Biology - Abstract
Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075(T) contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
- Published
- 2013
24. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema.
- Author
-
Abt, Birte, Göker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D, Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Detter, John C, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Woyke, Tanja, and Klenk, Hans-Peter
- Subjects
GEBA ,Gram-negative ,Spirochaeta ,Spirochaetaceae ,Treponema ,chemoorganotrophic ,motile ,obligately anaerobic ,periplasmic flagella ,spiral-shaped ,thermophilic ,Biochemistry and Cell Biology ,Genetics - Abstract
Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain, H1(T), was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of interest because it enhances the degradation of cellulose when grown in co-culture with Clostridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassification of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional genomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1(T) with its 2,869 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
25. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).
- Author
-
Mavromatis, Konstantinos, Stackebrandt, Erko, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Rohde, Manfred, Gronow, Sabine, Göker, Markus, Detter, John C, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
- Subjects
GEBA ,Gram-negative ,Rikenellaceae ,chemoorganotrophic ,mesophile ,non-motile ,non-sporulating ,rod-shaped ,strictly anaerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with a validly published name: family Rikenellaceae, order Bacteroidetes, class Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic organism has been isolated mostly from human tissues. Here we describe the features of the type strain of this species, together with the complete genome sequence, and annotation. A. finegoldii is the first member of the genus Alistipes for which the complete genome sequence of its type strain is now available. The 3,734,239 bp long single replicon genome with its 3,302 protein-coding and 68 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
26. Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug).
- Author
-
Stackebrandt, Erko, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Chang, Yun-Juan, Land, Miriam, Hauser, Loren, Rohde, Manfred, Pukall, Rüdiger, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
Actinobacteria ,Coriobacteriaceae ,GEBA ,Gram-positive ,chemoorganotroph ,endosymbiont ,insect intestinal tract ,mesophile ,non-motile ,non-sporulating ,obligatory anaerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Coriobacterium glomerans Haas and König 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2(T) is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for which complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
27. Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)).
- Author
-
Mavromatis, Konstantinos, Stackebrandt, Erko, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja, Detter, John C, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C
- Subjects
GEBA ,Gram-negative ,Synergistaceae ,Synergistetes ,anaerobic ,chemoorganotrophic ,crotonate-reducer ,flagellum ,motile ,non-spore forming ,rod-shaped ,Human Genome ,Genetics ,Biotechnology ,2.2 Factors relating to physical environment ,Biochemistry and Cell Biology - Abstract
Anaerobaculum mobile Menes and Muxí 2002 is one of three described species of the genus Anaerobaculum, family Synergistaceae, phylum Synergistetes. This anaerobic and motile bacterium ferments a range of carbohydrates and mono- and dicarboxylic acids with acetate, hydrogen and CO2 as end products. A. mobile NGA(T) is the first member of the genus Anaerobaculum and the sixth member of the phylum Synergistetes with a completely sequenced genome. Here we describe the features of this bacterium, together with the complete genome sequence, and annotation. The 2,160,700 bp long single replicon genome with its 2,053 protein-coding and 56 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
28. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (HT), and emendation of the species Turneriella parva
- Author
-
Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Gronow, Sabine, Göker, Markus, Detter, John C, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Woyke, Tanja, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Generic health relevance ,Gram-negative ,motile ,axial filaments ,helical ,flexible ,non-sporulating ,aerobic ,mesophile ,Leptospiraceae ,GEBA - Abstract
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 13(th) 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 G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
29. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T)
- Author
-
Huntemann, Marcel, Stackebrandt, Erko, Held, Brittany, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Gronow, Sabine, Göker, Markus, Detter, John C, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Woyke, Tanja, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Lapidus, Alla
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Generic health relevance ,Gram-negative ,flexible ,motile ,cytoplasmatic tubules ,non-sporulating ,axial flagella ,aerobic ,chemoorganotrophic ,Leptospiraceae ,GEBA - Abstract
Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
30. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692T) from the alkaline Lake Magadi in the East African Rift
- Author
-
Liolos, Konstantinos, Abt, Birte, Scheuner, Carmen, Teshima, Hazuki, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J, Detter, John C, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Infectious Diseases ,anaerobic ,aerotolerant ,mesophilic ,halophilic ,spiral-shaped ,motile ,periplasmic flagella ,Gram-negative ,chemoorganotrophic ,Spirochaetaceae ,GEBA - Abstract
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-7692(T), 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-7692(T) 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.
- Published
- 2013
31. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).
- Author
-
Anderson, Iain, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Ivanova, Natalia
- Subjects
Chitinophagaceae ,GEBA ,Gram-negative ,aerobic ,chemoorganotrophic ,glycosyl hydrolases ,mesophilic ,non-motile ,soil ,Biochemistry and Cell Biology ,Genetics - Abstract
Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8(T) is of interest for its ability to produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T) is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.
- Published
- 2012
32. Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).
- Author
-
Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J, Detter, John C, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
- Subjects
Flavobacteriaceae ,GEBA ,aerobic ,chemoheterotrophic ,microbial mat ,moderately halotolerant ,motile ,proteorhodopsin ,psychrophilic ,rod-shaped ,yellow-pigmented ,chemohete-rotrophic ,Biochemistry and Cell Biology ,Genetics - Abstract
Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G. limnea R-8282(T) is the first sequenced genome (permanent draft) from a type strain of the genus Gillisia. Here we describe the features of this organism, together with the permanent-draft genome sequence and annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569 protein-coding and 51 RNA genes is a part of the GenomicEncyclopedia of Bacteria and Archaea project.
- Published
- 2012
33. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).
- Author
-
Copeland, Alex, Zhang, Xiaojing, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Jeffries, Cynthia D, Detter, John C, Brambilla, Evelyne-Marie, Rohde, Manfred, Djao, Olivier D Ngatchou, Göker, Markus, Sikorski, Johannes, Tindall, Brian J, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Mavromatis, Konstantinos
- Subjects
Cytophagaceae ,Cytophagia ,GEBA ,Gram-negative ,chemoorganotrophic ,non-motile ,psychrotolerant ,strictly aerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the Cytophagaceae, a family that was only recently classified to the order Cytophagales in the class Cytophagia. The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2012
34. Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)).
- Author
-
Anderson, Iain, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D, Chang, Yun-Juan, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
GEBA ,Gram-negative ,Thermodesulfobacteria ,Thermodesulfobacteriaceae ,black smoker ,chemolithoautotrophic ,motile ,strictly anaerobic ,sulfate-reducing ,thermophilic ,Biochemistry and Cell Biology ,Genetics - Abstract
Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2012
35. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney.
- Author
-
Copeland, Alex, Gu, Wei, Yasawong, Montri, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Tindall, Brian J, Sikorski, Johannes, Göker, Markus, Detter, John C, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
- Subjects
GEBA ,Gram-negative ,Thermaceae ,hydrothermal vent ,neutrophilic heterotroph ,non-motile ,strictly aerobic ,thermophilic ,Biochemistry and Cell Biology ,Genetics - Abstract
Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1(T) was the first isolate within the phylum "Thermus-Deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1(T) is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2012
36. Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)).
- Author
-
Han, Cliff, Kotsyurbenko, Oleg, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Detter, John C
- Subjects
GEBA ,Gram-negative ,Helicobacteracea ,chemolithoautotrophic ,facultatively anaerobic ,mesophilic ,microaerobic ,motile ,sulfur-oxidizing ,Biochemistry and Cell Biology ,Genetics - Abstract
Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus Sulfuricurvum, which belongs to the family Helicobacteraceae in the class Epsilonproteobacteria. The species is of interest because it is frequently found in crude oil and oil sands where it utilizes various reduced sulfur compounds such as elemental sulfur, sulfide and thiosulfate as electron donors. Members of the species do not utilize sugars, organic acids or hydrocarbons as carbon and energy sources. This genome sequence represents the type strain of the only species in the genus Sulfuricurvum. The genome, which consists of a circular chromosome of 2,574,824 bp length and four plasmids of 118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp length, respectively, harboring a total of 2,879 protein-coding and 61 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2012
37. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent.
- Author
-
Göker, Markus, Daligault, Hajnalka, Mwirichia, Romano, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Han, Cliff, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Wirth, Reinhard, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
Desulfurobacteriaceae ,GEBA ,Gram-negative ,anaerobic ,marine ,neutrophilic ,obligately chemolithoautotrophic ,sulfur-reducing ,thermophilic ,Biochemistry and Cell Biology ,Genetics - Abstract
Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the genus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents the first thermophilic bacterium that can act as a primary producer in the temperature range of 45-75 °C (optimum 70°C) and is incapable of growing under microaerophilic conditions. Strain BSA(T) preferentially synthesizes high-melting-point fatty acids (C(18) and C(20)) which is hypothesized to be a strategy to ensure the functionality of the membrane at high growth temperatures. This is the second completed genome sequence of a member of the family Desulfurobacteriaceae and the first sequence from the genus Desulfurobacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
38. Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).
- Author
-
Lapidus, Alla, Nolan, Matt, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
- Subjects
GEBA ,Gram-negative ,Thiotrichaceae ,filaments ,gliding motility ,mesophile ,sheath ,strictly aerobic ,sulfur granules ,Biochemistry and Cell Biology ,Genetics - Abstract
Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
39. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010.
- Author
-
Klenk, Hans-Peter, Lapidus, Alla, Chertkov, Olga, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Daum, Chris, Chen, Amy, Palaniappan, Krishna, Chang, Yun-Juan, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D, Detter, John C, Rohde, Manfred, Abt, Birte, Pukall, Rüdiger, Göker, Markus, Bristow, James, Markowitz, Victor, Hugenholtz, Philip, and Eisen, Jonathan A
- Subjects
Bacillaceae ,GEBA ,aerobe ,facultative chemolithoautotroph ,free-living ,hydrogen-oxidizing ,solfatara ,spore-forming ,thermoacidophile ,Biochemistry and Cell Biology ,Genetics - Abstract
Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2 as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
40. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).
- Author
-
Chang, Yun-Juan, Land, Miriam, Hauser, Loren, Chertkov, Olga, Del Rio, Tijana Glavina, Nolan, Matt, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Mavromatis, Konstantinos, Liolios, Konstantinos, Brettin, Thomas, Fiebig, Anne, Rohde, Manfred, Abt, Birte, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Lapidus, Alla
- Subjects
Chloroflexi ,GEBA ,Gram-positive ,Ktedonobacteraceae ,aerobic ,broken-stick distribution ,entropy ,filamentous ,heterotrophic ,moderately acidophilic ,non-motile ,sporulating ,transposon ,Biochemistry and Cell Biology ,Genetics - Abstract
Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
41. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).
- Author
-
Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C
- Subjects
Cryomorphaceae ,GEBA ,Gram-negative ,chemoorganotrophic ,flexirubin-synthesizing ,mesophilic ,motile by gliding ,strictly aerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na(+) ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
42. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).
- Author
-
Pati, Amrita, Gronow, Sabine, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Detter, John C, Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Ivanova, Natalia
- Subjects
GEBA ,Gram-negative ,Prevotellaceae ,chemoorganotrophic ,mesophilic ,non-motile ,obligately anaerobic ,opportunistic pathogen ,Biochemistry and Cell Biology ,Genetics - Abstract
Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
43. Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).
- Author
-
Lapidus, Alla, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Spring, Stefan, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
- Subjects
Deferribacteraceae ,GEBA ,Gram-negative ,brine ,heterotrophic ,marine ,moderately thermophilic ,non-motile ,strictly anaerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the family Deferribacteraceae. The species is of interest because of its isolated phylogenetic location in a genomically under-characterized region of the tree of life, and because of its origin from a multiply extreme environment; the Atlantis Deep brines of the Red Sea, where it had to struggle with high temperatures, high salinity, and a high concentrations of heavy metals. This is the fourth completed genome sequence to be published of a type strain of the family Deferribacteraceae. The 2,526,590 bp long genome with its 2,346 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
44. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).
- Author
-
Liolios, Konstantinos, Sikorski, Johannes, Lu, Meagan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kotsyurbenko, Oleg, Rohde, Manfred, Tindall, Brian J, Abt, Birte, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C
- Subjects
GEBA ,Gram-negative ,Sphingobacteriaceae ,chemoorganotrophic ,gliding motility ,heparinolytic ,mesophilic ,strictly aerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
45. Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).
- Author
-
Göker, Markus, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
GEBA ,Syntrophaceae ,anaerobic ,mesophile ,non-motile ,organoheterotroph ,sludge bed reactor ,sulfate-reducing ,Biochemistry and Cell Biology ,Genetics - Abstract
Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca, which belongs to the family Syntrophaceae in the class Deltaproteobacteria. The species was first observed in a study on the competition of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D. acetoxidans is considered to be the most abundant acetate-degrading sulfate reducer in sludge. It is of interest due to its isolated phylogenetic location in the 16S rRNA-based tree of life. This is the second completed genome sequence of a member of the family Syntrophaceae to be published and only the third genome sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
46. Complete genome sequence of Mahella australiensis type strain (50-1 BON).
- Author
-
Sikorski, Johannes, Teshima, Hazuki, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Ngatchou-Djao, Olivier D, Rohde, Manfred, Pukall, Rüdiger, Spring, Stefan, Abt, Birte, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Markowitz, Victor, Hugenholtz, Philip, Eisen, Jonathan A, Kyrpides, Nikos C, Klenk, Hans-Peter, and Lapidus, Alla
- Subjects
GEBA ,Gram-positive ,Thermoanaerobacteraceae ,chemoorganotrophic ,moderately thermophilic ,motile ,spore-forming ,strictly anaerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
47. Complete genome sequence of Treponema succinifaciens type strain (6091).
- Author
-
Han, Cliff, Gronow, Sabine, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Zeytun, Ahmed, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Detter, John C
- Subjects
GEBA ,Gram-negative ,Spirochaetaceae ,anaerobic ,chemoorganotrophic ,mesophilic ,motile ,Biochemistry and Cell Biology ,Genetics - Abstract
Treponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this strictly anaerobic, apathogenic member of the genus Treponema oxidizes carbohydrates and couples the Embden-Meyerhof pathway via activity of a pyruvate-formate lyase to the production of acetyl-coenzyme A and formate. This feature separates this species from most other anaerobic spirochetes. The genome of T. succinifaciens 6091(T) is only the second completed and published type strain genome from the genus Treponema in the family Spirochaetaceae. The 2,897,425 bp long genome with one plasmid harbors 2,723 protein-coding and 63 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
48. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)).
- Author
-
Huntemann, Marcel, Lu, Megan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D, Detter, John C, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Mavromatis, Konstantinos
- Subjects
Desulfurellaceae ,GEBA ,Gram-negative ,anaerobic ,marine ,moderately thermophilic ,motile ,rod-shaped ,sulfur-reducer ,Biochemistry and Cell Biology ,Genetics - Abstract
Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH(2) (T) is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
49. Complete genome sequence of Haliscomenobacter hydrossis type strain (O).
- Author
-
Daligault, Hajnalka, Lapidus, Alla, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Verbarg, Susanne, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
- Subjects
"Saprospiraceae" ,GEBA ,Gram-negative ,branching ,chemoorganotrophic ,mesophilic ,non-motile ,sheathed ,strictly aerobic ,Saprospiraceae ,Biochemistry and Cell Biology ,Genetics - Abstract
Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
50. Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL).
- Author
-
Ivanova, Natalia, Sikorski, Johannes, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kannan, K Palani, Rohde, Manfred, Tindall, Brian J, Göker, Markus, Detter, John C, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Lapidus, Alla
- Subjects
GEBA ,Gram-negative ,Halanaerobiaceae ,chemoorganotroph ,halophilic ,mesophilic ,moderate alkaliphile ,non-motile ,straight rod-shaped ,strictly anaerobic ,Biochemistry and Cell Biology ,Genetics - Abstract
Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest because it functions as a hydrolytic bacterium, fermenting complex organic matter and producing intermediary metabolites for other trophic groups such as sulfate-reducing and methanogenic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the family Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2011
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.