Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latt...
Authors: Axel Aigle, James I. Prosser and Cécile Gubry-Rangin
Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soi...
Authors: Barbara Cania, Gisle Vestergaard, Maike Krauss, Andreas Fliessbach, Michael Schloter and Stefanie Schulz
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 subopti...
Authors: Juan Liang, Anne Hoffrichter, Andreas Brachmann and Macarena Marín
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,...
Authors: 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…
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 resi...
Authors: Xia Fan, Jingwei Tang, Li Nie, Jing Huang and Gejiao 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 ge...
Authors: Yi Li, Xiao-Han Guo, Yan-Ru Dang, Lin-Lin Sun, Xi-Ying Zhang, Xiu-Lan Chen, Qi-Long Qin and Peng Wang
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 phyloge...
Authors: Dimitra Sakoula, Boris Nowka, Eva Spieck, Holger Daims and Sebastian Lücker
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 se...
Authors: Jong-Hyun Jung, Min-Ho Joe, Dong-Ho Kim, Hyun Park, Jong-il Choi and Sangyong Lim
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 phytop...
Authors: Cátia Pinto, Susana Sousa, Hugo Froufe, Conceição Egas, Christophe Clément, Florence Fontaine and Ana C Gomes
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 meta...
Authors: Xian Xia, Jiahong Li, Zijie Zhou, Dan Wang, Jing Huang and Gejiao Wang
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 sho...
Authors: Zhen Yu, Guiqin Yang, Xiaoming Liu, Yueqiang Wang, Li Zhuang and Shungui Zhou
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, ...
Authors: Pierre Faye, Claire Bertrand, Jacques Pédron and Marie-Anne Barny
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 Urugu...
Authors: Juan J Fuentes-Valdés, Katia Soto-Liebe, Danilo Pérez-Pantoja, Javier Tamames, Lucy Belmar, Carlos Pedrós-Alió, Daniel Garrido and Mónica Vásquez
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...
Authors: Mohamed Seghir Daas, Albert Remus R. Rosana, Jeella Z. Acedo, Malika Douzane, Farida Nateche, Salima Kebbouche-Gana and John C. Vederas
‘Candidatus Chloroploca asiatica’ B7–9 and ‘Candidatus Viridilinea mediisalina’ Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became availa...
Authors: Denis S. Grouzdev, Maria S. Rysina, Irina A. Bryantseva, Vladimir M. Gorlenko and Vasil A. Gaisin
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 seq...
Authors: Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang and Sijing Chang
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, m...
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. pseud...
Authors: 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 and Vasco A C Azevedo
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 dr...
Authors: Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas and Adrian Ochoa-Leyva
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 provid...
Authors: Ji-Hyun Yun, Hojun Sung, Hyun Sik Kim, Euon Jung Tak, Woorim Kang, June-Young Lee, Dong-Wook Hyun, Pil Soo Kim and Jin-Woo Bae
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...
Authors: Xinye Wang, Yantao Luo, Dongying Liu, Jiamei Wang, Shi Wei and Liang Zhao
Following publication of the original article [1], the author requested this addition to the ‘Acknowledgements’ section of the article: “DW is funded by the German Federal Ministry of Education and Research (e...
Authors: 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…
Citation:Standards in Genomic Sciences
2018
13:17
Published on: 9 August 2018
The
original article was published in Standards in Genomic Sciences
2014
9:9031285
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 o...
Authors: Samuel C. Epstein, Louise K. Charkoudian and Marnix H. Medema
“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 fr...
Authors: Samuel M. Luedin, Joël F. Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer and Mauro Tonolla
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 Betaproteobac...
Authors: Joaquin Bernal-Bayard, Laura Gomez-Valero, Aimee Wessel, Varun Khanna, Christiane Bouchier and Jean-Marc Ghigo
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 ...
Authors: David Alvarez-Ponce, Chava L. Weitzman, Richard L. Tillett, Franziska C. Sandmeier and C. Richard Tracy
A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clusteri...
Authors: Rakshak Kumar, Vishal Acharya, Dharam Singh and Sanjay Kumar
Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph isolated from Hardangervidda national park (Norway). This strain represents the second of the two validly published specie...
Authors: Alejandro Mateos-Rivera, Tajul Islam, Ian P. G. Marshall, Lars Schreiber and Lise Øvreås
Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease in desert tortoises, Gopherus agassizii. We sequenced the genome of M. testudineum BH29T (ATCC 700618T = MCCM 03231T),...
Authors: Chava L. Weitzman, Richard L. Tillett, Franziska C. Sandmeier, C. Richard Tracy and David Alvarez-Ponce
We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy...
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619–24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobac...
Authors: Insa Bakenhus, Sonja Voget, Anja Poehlein, Thorsten Brinkhoff, Rolf Daniel and Meinhard Simon
This genome report describes the draft genome and physiological characteristics of Bosea sp. WAO (=DSM 102914), a novel strain of the genus Bosea in the family Bradyrhizobiaceae. Bosea sp. WAO was isolated from p...
Authors: Alexandra B. Walczak, Nathan Yee and Lily Y. Young
The gut microbiome is increasingly recognized as integral to human health, and is emerging as a mediator of human physical and cognitive performance. This has led to the recognition that US Department of Defen...
Authors: Steven Arcidiacono, Jason W. Soares, J. Philip Karl, Linda Chrisey, C. P. T. Blair C. R. Dancy, Michael Goodson, Fredrick Gregory, Rasha Hammamieh, Nancy Kelley Loughnane, Robert Kokoska, C. A. P. T. Mark Riddle, Keith Whitaker and Kenneth Racicot
After publication of the original article [1] it was identified that an incorrect version of the manuscript has been published. This was caused by a technical error which led to a discrepancy between the edito...
Authors: Anish K. Pandey, David W. Cleary, Jay R. Laver, Martin C. J. Maiden, Xavier Didelot, Andrew Gorringe and Robert C. Read
Citation:Standards in Genomic Sciences
2018
13:4
Published on: 16 February 2018
The
original article was published in Standards in Genomic Sciences
2017
12:41
In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain...
Authors: Jakub Ridl, Jachym Suman, Serena Fraraccio, Miluse Hradilova, Michal Strejcek, Tomas Cajthaml, Andrea Zubrova, Tomas Macek, Hynek Strnad and Ondrej Uhlik
Streptomyces hyaluromycini MB-PO13T (=NBRC 110483T = DSM 100105T) is type strain of the species, which produces a hyaluronidase inhibitor, hyaluromycin. Here, we report the draft genome sequence of this strain to...
Mycobacterium simiae (Karassova V, Weissfeiler J, Kraszanay E, Acta Microbiol Acad Sci Hung 12:275-82, 1965) is a slow-growing nontuberculous Mycobacterium species found in environmental niches, and recently evid...
Authors: José L. Steffani-Vallejo, Marion E. Brunck, Erika Y. Acosta-Cruz, Rafael Montiel and Francisco Barona-Gómez
Acuticoccus yangtzensis JL1095T is a proteobacterium from a genus belonging to the family Rhodobacteraceae; it was isolated from surface waters of the Yangtze Estuary, China. This strain displays...
Authors: Lei Hou, Jia Sun, Xiabing Xie, Nianzhi Jiao and Yao Zhang
Although the hemipterans (Aphididae) are comprised of roughly 50,000 extant insect species, only four have sequenced genomes that are publically available, n...
Authors: Nicolaas Francois Visser Burger and Anna-Maria Botha
Brucellosis is a commonly diagnosed zoonosis that causes infertility and abortion in cattle, it is acquired from handling of infected animals or consuming contaminated milk or milk products. In Colombia, it be...
Authors: Mauricio Pacheco-Montealegre, Rocío E. Patiño, Ligia Torres, Sabrina Jiménez, José Luis Rodríguez and Alejandro Caro-Quintero
Croceicoccus marinus E4A9Twas isolated from deep-sea sediment collected from the East Pacific polymetallic nodule area. The strain is able to produce esterase, which is widely used in the...
Authors: Yue-Hong Wu, Hong Cheng, Ying-Yi Huo, Lin Xu, Qian Liu, Chun-Sheng Wang and Xue-Wei Xu
Bacteria of the genus Pectobacterium are economically important plant pathogens that cause soft rot disease on a wide variety of plant species. Here, we report the genome sequence of Pectobacterium carotovorum st...
Authors: Outi Niemi, Pia Laine, Patrik Koskinen, Miia Pasanen, Ville Pennanen, Heidi Harjunpää, Johanna Nykyri, Liisa Holm, Lars Paulin, Petri Auvinen, E. Tapio Palva and Minna Pirhonen
A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565
...
Authors: Carolina Díaz-Cárdenas, Gina López, José David Alzate-Ocampo, Laura N. González, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides, Silvia Restrepo and Sandra Baena
Phage ST0 lysing Escherichia coli H8 was isolated from wastewater and sequenced using an Illumina HiSeq system. Genomic analyses revealed that it was virulent phages and contained a circular double-stranded DNA g...
Authors: Raquel Quatrini, Lorena V. Escudero, Ana Moya-Beltrán, Pedro A. Galleguillos, Francisco Issotta, Mauricio Acosta, Juan Pablo Cárdenas, Harold Nuñez, Karina Salinas, David S. Holmes and Cecilia Demergasso
Due to significant declines in the price of genome sequencing technology, the bioinformatics sciences are experiencing a massive upswing in data generation resulting in an increasing need for data distribution...
Authors: Kathryn Petersen Mace, Daniel Jacobson, Brooklin Gore, Lauren Rotman, Jennifer Schopf, Mary Hester, Predrag Radulovic and William Barnett
A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic ph...
Authors: Ananda Shankar Bhattacharjee, Amir Mohaghegh Motlagh, Eddie B. Gilcrease, Md Imdadul Islam, Sherwood R. Casjens and Ramesh Goel
