Articles

High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolate...

Authors: Julie Ardley, Rui Tian, Graham O’Hara, Rekha Seshadri, T. B. K. Reddy, Amrita Pati, Tanja Woyke, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, John Howieson and Wayne Reeve

Genome sequences of two closely related strains of Escherichia coli K-12 GM4792

Escherichia coli lab strains K-12 GM4792 Lac⁺ and GM4792 Lac^- carry opposite lactose markers, which are useful for distinguishing evolved lines as they produce different colored colonies....

Authors: Yan-Cong Zhang, Yan Zhang, Bi-Ru Zhu, Bo-Wen Zhang, Chuan Ni, Da-Yong Zhang, Ying Huang, Erli Pang and Kui Lin

Draft genome sequence of Halopiger salifodinae KCY07-B2^T, an extremly halophilic archaeon isolated from a salt mine

Halopiger salifodinae strain KCY07-B2^T, isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic,...

Authors: Wei-Yan Zhang, Jing Hu, Jie Pan, Cong Sun, Min Wu and Xue-Wei Xu

Genome sequence of Lysobacter dokdonensis DS-58^T, a gliding bacterium isolated from soil in Dokdo, Korea

Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type strain of L. dokdonensis. In this...

Authors: Min-Jung Kwak, Soon-Kyeong Kwon, Jung-Hoon Yoon and Jihyun F. Kim

Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum

A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the ...

Authors: Stepan V. Toshchakov, Aleksei A. Korzhenkov, Nazar I. Samarov, Ilia O. Mazunin, Oleg I. Mozhey, Ilya S. Shmyr, Ksenia S. Derbikova, Evgeny A. Taranov, Irina N. Dominova, Elizaveta A. Bonch-Osmolovskaya, Maxim V. Patrushev, Olga A. Podosokorskaya and Ilya V. Kublanov

Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e

Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N₂-fixing microsymbiont of white clover (Trifolium repens L.). The bacterium has been widely used in both Austral...

Authors: Clément Delestre, Aurélie Laugraud, Hayley Ridgway, Clive Ronson, Maureen O’Callaghan, Brent Barrett, Ross Ballard, Andrew Griffiths, Sandra Young, Celine Blond, Emily Gerard and Steve Wakelin

Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants

Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in France, using a new culture medium. It is an aerobic microorganism with optimal growth at pH...

Authors: Rita Aghnatios, Caroline Cayrou, Marc Garibal, Catherine Robert, Said Azza, Didier Raoult and Michel Drancourt

Report from the Standards for Pathogen Identification via Next-Generation Sequencing (SPIN) Workshop

Next-generation sequencing (NGS) is not routinely used in applied settings due to lack of confidence in results. This workshop convened experts to identify measurement challenges impeding NGS implementation an...

Authors: Nathan D. Olson, Scott A. Jackson and Nancy J. Lin

Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01^T

Strain GSS01^T (=KCTC 4545=MCCC 1 K00269) is the type strain of the species Geobacter soli. G. soli strain GSS01^T is of interest due to its ability to reduce insoluble Fe(III) oxides with a wide range of electron ...

Authors: Guiqin Yang, Shanshan Chen, Shungui Zhou and Yongfeng Liu

Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato

Strain UFB2 was isolated from a soybean field soil in Mississippi and identified as a member of Pseudomonas chlororaphis. Strain UFB2 has a broad-spectrum antimicrobial activity against common soil-borne pathogen...

Authors: Peng Deng, Xiaoqiang Wang, Sonya M. Baird and Shi-En Lu

Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China

Salinicoccus halodurans H3B36 is a moderately halophilic bacterium isolated from a sediment sample of Qaidam Basin at 3.2 m vertical depth. Strain H3B36 accumulate N ...

Authors: Kai Jiang, Yanfen Xue and Yanhe Ma

H3ABioNet computational metagenomics workshop in Mauritius: training to analyse microbial diversity for Africa

In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computatio...

Authors: Shakuntala Baichoo, Gerrit Botha, Yasmina Jaufeerally-Fakim, Zahra Mungloo-Dilmohamud, Daniel Lundin, Nicola Mulder, Vasilis J. Promponas and Christos A. Ouzounis

Complete genome sequence and characterization of the haloacid–degrading Burkholderia caribensis MBA4

Burkholderia caribensis MBA4 was isolated from soil for its capability to grow on haloacids. This bacterium has a genome size of 9,482,704 bp. Here we report the genome sequences and anno...

Authors: Yanling Pan, Ka Fai Kong and Jimmy S. H. Tsang

Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos

Bradyrhizobium sp. WSM1253 is a novel N₂-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos....

Authors: Ravi Tiwari, John Howieson, Ron Yates, Rui Tian, Britanny Held, Roxanne Tapia, Cliff Han, Rekha Seshadri, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Tanja Woyke, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides and Wayne Reeve

Erratum to: An updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

Authors: Adam R. Rivers, Christa B. Smith and Mary Ann Moran

Complete genome sequence of bacteriophage P26218 infecting Rhodoferax sp. strain IMCC26218

Bacteriophage P26218 is a virus that thrives in freshwater and infects Rhodoferax sp. strain IMCC26218, both of which were isolated from Soyang Lake, Korea. The bacterial host, IMCC26218, belongs to the genus Rho...

Authors: Kira Moon, Ilnam Kang, Suhyun Kim, Jang-Cheon Cho and Sang-Jong Kim

Draft genome sequence of Janthinobacterium lividum strain MTR reveals its mechanism of capnophilic behavior

Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment with antimicrobial and antitumor properties. Janthinobacterium lividum colonizes the skin of so...

Authors: Natalia Valdes, Paola Soto, Luis Cottet, Paula Alarcon, Alex Gonzalez, Antonio Castillo, Gino Corsini and Mario Tello

Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel

We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists o...

Authors: Saima Zubair, Anne Fischer, Anne Liljander, Jochen Meens, Jan Hegerman, Hadrien Gourlé, Richard P. Bishop, Ina Roebbelen, Mario Younan, Mudassir Imran Mustafa, Mamoona Mushtaq, Erik Bongcam-Rudloff and Joerg Jores

Annotation inconsistencies beyond sequence similarity-based function prediction – phylogeny and genome structure

The function annotation process in computational biology has increasingly shifted from the traditional characterization of individual biochemical roles of protein molecules to the system-wide detection of enti...

Authors: Vasilis J. Promponas, Ioannis Iliopoulos and Christos A. Ouzounis

Complete genome sequence of Novosphingobium pentaromativorans US6-1^T

Novosphingobium pentaromativorans US6-1^T is a species in the family Sphingomonadaceae. According to the phylogenetic analysis based on 16S rRNA gene sequence of the N. pentaromativorans U...

Authors: Dong Hee Choi, Yong Min Kwon, Kae Kyoung Kwon and Sang-Jin Kim

Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

Tolumonas lignolytica BRL6-1^T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest so...

Authors: Andrew F. Billings, Julian L. Fortney, Terry C. Hazen, Blake Simmons, Karen W. Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke and Kristen M. DeAngelis

Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1^T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake

Thioalkalivibrio paradoxus strain ARh 1^T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkalin...

Authors: Tom Berben, Dimitry Y. Sorokin, Natalia Ivanova, Amrita Pati, Nikos Kyrpides, Lynne A. Goodwin, Tanja Woyke and Gerard Muyzer

Draft genome sequence of Cellulomonas carbonis T26^T and comparative analysis of six Cellulomonas genomes

Most Cellulomonas strains are cellulolytic and this feature may be applied in straw degradation and bioremediation. In this study, Cellulomonas carbonis T26^T, Cellulomonas bogoriensis DSM 16987^T and Cellulomonas ...

Authors: Weiping Zhuang, Shengzhe Zhang, Xian Xia and Gejiao Wang

Genome sequence and description of Pantoea septica strain FF5

Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This strain was identified as belonging to the species Pantoea septica based on rpoB sequence identity of 99.7 % with Pantoea...

Authors: Cheikh Ibrahima Lo, Roshan Padhmanabhan, Oleg Mediannikov, Thi Tien Nguyen, Didier Raoult, Pierre-Edouard Fournier and Florence Fenollar

Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method

A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl c...

Authors: Yoshihito Uchino, Takamasa Miura, Akira Hosoyama, Shoko Ohji, Atsushi Yamazoe, Masako Ito, Yoh Takahata, Ken-ichiro Suzuki and Nobuyuki Fujita

Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22^T

Strain K22^T is the type species of the recently- described genus Pyrinomonas, in subdivision 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014; 64(1):220–7). It was isolated from geothermally-heated soil ...

Authors: Kevin C. Y. Lee, Xochitl C. Morgan, Jean F. Power, Peter F. Dunfield, Curtis Huttenhower and Matthew B. Stott

Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna

The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft genome is arranged into 93 contigs containing 3311 p...

Authors: Anja Poehlein, Rolf Daniel and Diliana D. Simeonova

Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mes...

Authors: Shahid Manzoor, Bettina Müller, Adnan Niazi, Anna Schnürer and Erik Bongcam-Rudloff

High-quality draft genome sequence of Gracilimonas tropica CL-CB462^T (DSM 19535^T), isolated from a Synechococcus culture

Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a...

Authors: Dong Han Choi, Chisang Ahn, Gwang Il Jang, Alla Lapidus, James Han, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Natalia Ivanova, Victor Markowitz, Manfred Rohde, Brian Tindall, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides…

Complete genome sequence of Bacillus cereus FORC_005, a food-borne pathogen from the soy sauce braised fish-cake with quail-egg

Due to abundant contamination in various foods, the pathogenesis of Bacillus cereus has been widely studied in physiological and molecular level. B. cereus FORC_005 was isolated from a Korean side dish, soy sauce...

Authors: Dong-Hoon Lee, Hye Rim Kim, Han Young Chung, Jong Gyu Lim, Suyeon Kim, Se Keun Kim, Hye-Jin Ku, Heebal Kim, Sangryeol Ryu, Sang Ho Choi and Ju-Hoon Lee

Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia

Bacteriophage P8625 is a lytic bacteriophage that infects the verrucomicrobial strain IMCC8625, a marine bacterium affiliated with Verrucomicrobia subdivision 4. Both the bacteriophage and the host bacterial stra...

Authors: Ahyoung Choi, Ilnam Kang, Seung-Jo Yang and Jang-Cheon Cho

High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1

Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its po...

Authors: Aliya D. Suleimanova, Anna A. Toymentseva, Eugenia A. Boulygina, Sergey V. Kazakov, Ayslu M. Mardanova, Nelly P. Balaban and Margarita R. Sharipova

Complete genome sequence of Paracoccus marcusii phage vB_PmaS-R3 isolated from the South China Sea

Paracoccus spp. are isolated from both terrestrial and aquatic habitats, indicating their ubiquitous existence in the environment. Here we present the first phage isolated from this genus...

Authors: Yongle Xu, Rui Zhang and Nianzhi Jiao

High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32^T and comparison among Pontibacillus genomes

Pontibacillus yanchengensis Y32^T is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the fe...

Authors: Jing Huang, Zi xu Qiao, Jing wei Tang and Gejiao Wang

High quality draft genomic sequence of Flavobacterium enshiense DK69^T and comparison among Flavobacterium genomes

Flavobacterium enshiense DK69^T is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated bacterium that belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. ...

Authors: Zhipeng Zeng, Chong Chen, Hailun Du, Gejiao Wang and Mingshun Li

Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut

Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus pic...

Authors: Jean-Christophe Lagier, Saber Khelaifia, Esam Ibraheem Azhar, Olivier Croce, Fehmida Bibi, Asif Ahmad Jiman-Fatani, Muhammad Yasir, Huda Ben Helaby, Catherine Robert, Pierre-Edouard Fournier and Didier Raoult

Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01^T

Azoarcus sp. strain PA01^T belongs to the genus Azoarcus, of the family Rhodocyclaceae within the class Betaproteobacteria. It is a facultatively anaerobic, mesophilic, non-motile, Gram-st...

Authors: Madan Junghare, Yogita Patil and Bernhard Schink

High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afadé and B237

Members of the Mycoplasma mycoides cluster’ represent important livestock pathogens worldwide. Mycoplasma mycoides subsp. mycoides is the etiologic agent of contagious bovine pleuropneumonia (CBPP), which is sti...

Authors: Anne Fischer, Ivette Santana-Cruz, Jan Hegerman, Hadrien Gourlé, Elise Schieck, Mathieu Lambert, Suvarna Nadendla, Hezron Wesonga, Rachel A. Miller, Sanjay Vashee, Johann Weber, Jochen Meens, Joachim Frey and Joerg Jores

Genomic information of the arsenic-resistant bacterium Lysobacter arseniciresistens type strain ZS79^T and comparison of Lysobacter draft genomes

Lysobacter arseniciresistens ZS79^T is a highly arsenic-resistant,rod-shaped, motile, non-spore-forming, aerobic, Gram-negative bacterium. In this study, four Lysobacter type strains were ...

Authors: Lin Liu, Shengzhe Zhang, Meizhong Luo and Gejiao Wang

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743...

Authors: Leila Eshraghi, Sofie E. De Meyer, Rui Tian, Rekha Seshadri, Natalia Ivanova, Amrita Pati, Victor Markowitz, Tanja Woyke, Nikos C. Kyrpides, Ravi Tiwari, Ron Yates, John Howieson and Wayne Reeve

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. M...

Authors: Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, H. James Tripp, David Paez-Espino, Krishnaveni Palaniappan, Ernest Szeto, Manoj Pillay, I-Min A. Chen, Amrita Pati, Torben Nielsen, Victor M. Markowitz and Nikos C. Kyrpides

Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2^T

Thioalkalivibrio thiocyanoxidans strain ARh 2^T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Rema...

Authors: Tom Berben, Dimitry Y. Sorokin, Natalia Ivanova, Amrita Pati, Nikos Kyrpides, Lynne A. Goodwin, Tanja Woyke and Gerard Muyzer

Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1^T, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1^T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth ...

Authors: Tom Berben, Dimitry Y. Sorokin, Natalia Ivanova, Amrita Pati, Nikos Kyrpides, Lynne A. Goodwin, Tanja Woyke and Gerard Muyzer

Complete genome sequence of Propionibacterium freudenreichii DSM 20271^T

Propionibacterium freudenreichii subsp. freudenreichii DSM 20271^T is the type strain of species Propionibacterium freudenreichii that has a long history of safe use in the production dair...

Authors: Patrik Koskinen, Paulina Deptula, Olli-Pekka Smolander, Fitsum Tamene, Juhana Kammonen, Kirsi Savijoki, Lars Paulin, Vieno Piironen, Petri Auvinen and Pekka Varmanen

Complete genome sequences of bacteriophages P12002L and P12002S, two lytic phages that infect a marine Polaribacter strain

The bacterial genus Polaribacter is distributed widely in marine environments; however, there have been no reports of phages infecting Polaribacter strains. Here, we describe the isolation and genome sequencing o...

Authors: Ilnam Kang, Hani Jang and Jang-Cheon Cho

Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park

Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, a...

Authors: Phillip Brumm, Miriam L. Land, Loren J. Hauser, Cynthia D. Jeffries, Yun-Juan Chang and David A. Mead

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Re...

Authors: Sofie E. De Meyer, Matthew Parker, Peter Van Berkum, Rui Tian, Rekha Seshadri, T.B.K. Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, John Howieson and Wayne Reeve

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N₂-fixing root nodule of Lebeckia ambigua collected in Nieu...

Authors: Sofie E. De Meyer, Rui Tian, Rekha Seshadri, TBK Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, Ron Yates, John Howieson and Wayne Reeve

Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family

Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as the most prevalent genotype in South Korea among clinical isolates of M. tuberculosis from hi...

Authors: Seung Jung Han, Taeksun Song, Yong-Joon Cho, Jong-Seok Kim, Soo Young Choi, Hye-Eun Bang, Jongsik Chun, Gill-Han Bai, Sang-Nae Cho and Sung Jae Shin

The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon “Geoglobus ahangari” strain 234^T

“Geoglobus ahangari” strain 234^T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal syst...

Authors: Michael P. Manzella, Dawn E. Holmes, Jessica M. Rocheleau, Amanda Chung, Gemma Reguera and Kazem Kashefi