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Standards in Genomic Sciences

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 a wide range of Lotus hosts. To investigate the basis of this phenotype, we sequenced the complete genome of Rl Norway and compared it to the genome of the closely related strain R...
2018: Standards in Genomic Sciences
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 the USA, the Middle East, China, and the Republic of Korea. The average genome size of the C. sakazakii genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56...
2018: Standards in Genomic Sciences
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 features make it a great potential to bioremediate heavy metal contamination and biotechnical application. Here we describe the genome sequence and annotation of strain TBZ30T ...
2018: Standards in Genomic Sciences
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 with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome...
2018: Standards in Genomic Sciences
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 this biotechnologically important genus, we analyzed the high quality draft genome of " Nitrospira lenta " strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany...
2018: Standards in Genomic Sciences
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 Planococcus sp. PAMC21323 possesses chromosomal DNA (3,196,500-bp) with plasmid DNA (3364-bp). The complete 3,199,864-bp of the genome consists of 3171 genes including 60 transfer RNAs and 24 ribosomal RNAs...
2018: Standards in Genomic Sciences
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 subsp. plantarum Fito_F321, isolated from the leaf of Vitis vinifera cv. Merlot at Bairrada appellation (Cantanhede, Portugal). The genome size is 3,856,229 bp, with a GC content of 46...
2018: Standards in Genomic Sciences
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 contribute to metal remove/adsorption. Thus, strain JH-7T shows a great potential in bioremediation of heavy metal-contaminated environment. In this study, we report the draft genomic sequence of P...
2018: Standards in Genomic Sciences
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 of A. humicireducens SgZ-5T , which consists of a circular chromosome and six plasmids with the total genome size of 6,834,379 bp and the average GC content of 67.55%...
2018: Standards in Genomic Sciences
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 strains belonging to " P. peruviense " isolated from river water in France indicating that the geographic distribution of this specie is likely to be larger than previously anticipated...
2018: Standards in Genomic Sciences
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 C. raciborskii strains using the assembly of reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508 (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs)...
2018: Standards in Genomic Sciences
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 Algeria, has strong antibacterial, antifungal and biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of B. thuringiensis DNG9. The genome encodes several gene inventories for the biosynthesis of bioactive compounds such as zwittermycin A, petrobactin, insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins...
2018: Standards in Genomic Sciences
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. Viridilinea mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures with a fold coverage 86.3× and 163.8×, respectively...
2018: Standards in Genomic Sciences
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 Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium...
2018: Standards in Genomic Sciences
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 on strains and on food matrix. Several B. thermosphacta genome sequences have been reported, all issued from meat isolates. Here, we report four genome sequences, one complete and three as drafts...
2018: Standards in Genomic Sciences
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 sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software...
2018: Standards in Genomic Sciences
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 analysis of the functions encoded in the metagenome showed enrichment of characteristic features of soil and root-associated bacteria such as ABC-transporters and hydrolase enzymes. Additionally, we found antibiotic resistances genes principally for spectinomycin, tetracycline, and aminoglycosides...
2018: Standards in Genomic Sciences
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 of X49T to hypersaline environments. Due to resistance to high salt concentrations, genome research of K. konosiri X49T will contribute to the improvement of environmental and biotechnological usage by enhancing understanding of the osmotic equilibrium in the cytoplasm...
2018: Standards in Genomic Sciences
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. The 7,374,589 bp long genome which encodes 7136 protein-coding genes and 63 RNA coding genes, contains one chromosome and four plasmids...
2018: Standards in Genomic Sciences
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.].
2018: Standards in Genomic Sciences
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