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Journal Stand Genomic Sci

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Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont.

Juan Liang, Anne Hoffrichter, Andreas Brachmann, Macarena Marín,

Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic interaction with legume plants in which a bidirectional nutrient exchange takes place. Occasionally, this interaction is suboptimal resulting in the formation of ineffective nodules in which little or no atmospheric nitrogen fixation occurs. Rhizobium leguminosarum Norway induces ineffective nodules in ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:36]

Cited: 2 times

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High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T.

Xia Fan, Jingwei Tang, Li Nie, Jing Huang, Gejiao Wang,

Mucilaginibacter pedocola TBZ30T (= CCTCC AB 2015301T = KCTC 42833T) is a Gram- negative, rod-shaped, non-motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resistance to multiple heavy metals and can adsorb/remove Zn2+ and Cd2+ during cultivation. In addition, strain TBZ30T produces exopolysaccharides (EPS). These ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:34]

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Complete genome sequence of Arcticibacterium luteifluviistationis SM1504T, a cytophagaceae bacterium isolated from Arctic surface seawater.

Yi Li, Xiao-Han Guo, Yan-Ru Dang, Lin-Lin Sun, Xi-Ying Zhang, Xiu-Lan Chen, Qi-Long Qin, Peng Wang,

Arcticibacterium luteifluviistationis SM1504T was isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839 bp ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:33]

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Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.

Hyein Jang, Jungha Woo, Youyoung Lee, Flavia Negrete, Samantha Finkelstein, Hannah R Chase, Nicole Addy, Laura Ewing, Junia Jean Gilles Beaubrun, Isha Patel, Jayanthi Gangiredla, Athmanya Eshwar, Ziad W Jaradat, Kunho Seo, Srikumar Shabarinath, Séamus Fanning, Roger Stephan, Angelika Lehner, Ben D Tall, Gopal R Gopinath,

Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:35]

Cited: 2 times

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The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge.

Dimitra Sakoula, Boris Nowka, Eva Spieck, Holger Daims, Sebastian Lücker,

The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:32]

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Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants.

Jong-Hyun Jung, Min-Ho Joe, Dong-Ho Kim, Hyun Park, Jong-Il Choi, Sangyong Lim,

The Planococcus sp. PAMC21323 is a yellow pigment-producing bacterium isolated from King George Island in Antarctica; it has a broad growth temperature range of 5-40 °C. Herein, we describe the complete genome sequence information of the genus Planococcus with its annotated sequence, genetic features for bioremediation, and oxidative stress capacity. The ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:31]

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Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential.

Cátia Pinto, Susana Sousa, Hugo Froufe, Conceição Egas, Christophe Clément, Florence Fontaine, Ana C Gomes,

Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321 is a naturally occurring strain in vineyard, with the ability to colonise grapevine and which unveils a naturally antagonistic potential against phytopathogens of grapevine, including those responsible for the Botryosphaeria dieback, a GTD disease. Herein we report the draft genome sequence of B. amyloliquefaciens ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:30]

Cited: 1 time

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High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7T.

Xian Xia, Jiahong Li, Zijie Zhou, Dan Wang, Jing Huang, Gejiao Wang,

Pseudaminobacter manganicus JH-7T (= KCTC 52258T = CCTCC AB 2016107T) is a Gram-staining-negative, aerobic and non-motile strain that was isolated from a manganese mine. The strain JH-7T shows multiple heavy metal resistance and can effectively remove Mn2+ and Cd2+. In addition, it is able to produce exopolysaccharides (EPS), which may ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:29]

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Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T.

Zhen Yu, Guiqin Yang, Xiaoming Liu, Yueqiang Wang, Li Zhuang, Shungui Zhou,

The Azospirillum humicireducens strain SgZ-5T, belonging to the Order Rhodospirillales and the Family Rhodospirillaceae, was isolated from a microbial fuel cell inoculated with paddy soil. A previous work has shown that strain SgZ-5T was able to fix atmospheric nitrogen involved in plant growth promotion. Here we present the complete genome ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:28]

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One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.

Nassima Illikoud, Christophe Klopp, Alain Roulet, Olivier Bouchez, Nathalie Marsaud, Emmanuel Jaffrès, Monique Zagorec,

Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of chilled meat and seafood products through the production of various metabolites responsible for off-odors. However, metabolic pathways leading to meat and seafood spoilage are not all well known. The production of spoiling molecules seems to depend both ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:22]

Cited: 1 time

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First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.

Doglas Parise, Mariana T D Parise, Marcus V C Viana, Adrian V Muñoz-Bucio, Yazmin A Cortés-Pérez, Beatriz Arellano-Reynoso, Efrén Díaz-Aparicio, Fernanda A Dorella, Felipe L Pereira, Alex F Carvalho, Henrique C P Figueiredo, Preetam Ghosh, Debmalya Barh, Anne C P Gomide, Vasco A C Azevedo,

Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:21]

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Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough.

Mohamed Seghir Daas, Albert Remus R Rosana, Jeella Z Acedo, Malika Douzane, Farida Nateche, Salima Kebbouche-Gana, John C Vederas,

Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:25]

Cited: 1 time

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Draft genomes of "Pectobacterium peruviense" strains isolated from fresh water in France.

Pierre Faye, Claire Bertrand, Jacques Pédron, Marie-Anne Barny,

Bacteria belonging to the genus Pectobacterium are responsible for soft rot disease on a wide range of cultivated crops. The "Pectobacterium peruviense" specie, recently proposed inside the Pectobacterium genus, gathers strains isolated from potato tubers cultivated in Peru at high altitude. Here we report the draft genome sequence of two ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:27]

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The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.

Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang, Sijing Chang,

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:23]

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Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay.

Juan J Fuentes-Valdés, Katia Soto-Liebe, Danilo Pérez-Pantoja, Javier Tamames, Lucy Belmar, Carlos Pedrós-Alió, Daniel Garrido, Mónica Vásquez,

Members of the genus Cylindrospermopsis represent an important environmental and health concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of these ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:26]

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Functional and taxonomic classification of a greenhouse water drain metagenome.

Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas, Adrian Ochoa-Leyva,

Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by Rhizobiales and Rodobacterales. The ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:20]

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Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications.

Denis S Grouzdev, Maria S Rysina, Irina A Bryantseva, Vladimir M Gorlenko, Vasil A Gaisin,

'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:24]

Cited: 3 times

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Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus.

Ji-Hyun Yun, Hojun Sung, Hyun Sik Kim, Euon Jung Tak, Woorim Kang, June-Young Lee, Dong-Wook Hyun, Pil Soo Kim, Jin-Woo Bae,

Kushneria konosiri X49T is a member of the Halomonadaceae family within the order Oceanospirillales and can be isolated from salt-fermented larval gizzard shad. The genome of K. konosiri X49T reported here provides a genetic basis for its halophilic character. Diverse genes were involved in salt-in and -out strategies enabling adaptation ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:19]

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Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123.

Xinye Wang, Yantao Luo, Dongying Liu, Jiamei Wang, Shi Wei, Liang Zhao,

Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province, China. M. amorphae CCNWGS0123 is an aerobic, Gram-negative, non-spore-forming rod strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete genome sequence information and genome annotation. ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:18]

Cited: 1 time

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Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet,

[This corrects the article DOI: 10.4056/sigs.5279417.]. ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:17]

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A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences.

Samuel C Epstein, Louise K Charkoudian, Marnix H Medema,

Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:16]

Cited: 4 times

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Correction to: Complete genome of a novel virulent phage ST0 lysing Escherichia coli H8.

Honghui Liu, Xinchun Liu, Jinqing Li,

[This corrects the article DOI: 10.1186/s40793-017-0304-9.]. ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:15]

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Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.

Samuel M Luedin, Joël F Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla,

"Thiodictyon syntrophicum" sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:14]

Cited: 1 time

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Short genome report of cellulose-producing commensal Escherichia coli 1094.

Joaquin Bernal-Bayard, Laura Gomez-Valero, Aimee Wessel, Varun Khanna, Christiane Bouchier, Jean-Marc Ghigo,

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:13]

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High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease.

David Alvarez-Ponce, Chava L Weitzman, Richard L Tillett, Franziska C Sandmeier, C Richard Tracy,

Mycoplasma agassizii is one of the known causative agents of upper respiratory tract disease (URTD) in Mojave desert tortoises (Gopherus agassizii) and in gopher tortoises (Gopherus polyphemus). We sequenced the genomes of M. agassizii strains PS6T (ATCC 700616) and 723 (ATCC 700617) isolated from the upper respiratory tract of a ... Read more >>

Stand Genomic Sci (Standards in genomic sciences)
[2018, 13:12]

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