Skip to content

Advertisement

Articles

Page 1 of 17

  1. Content type: Correction

    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:

    The original article was published in Standards in Genomic Sciences 2014 9:9031285

  2. Content type: Standard operating procedure

    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

    Citation: Standards in Genomic Sciences 2018 13:16

    Published on:

  3. Content type: Report

    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

    Citation: Standards in Genomic Sciences 2018 13:14

    Published on:

  4. Content type: Short genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:13

    Published on:

  5. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:12

    Published on:

  6. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:11

    Published on:

  7. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:10

    Published on:

  8. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:7

    Published on:

  9. Content type: Short genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:9

    Published on:

  10. Content type: Extended genome report

    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...

    Authors: Mamadou Beye, Sofiane Bakour, Sory Ibrahima Traore, Jaishriram Rathored, Noémie Labas, Didier Raoult and Pierre-Edouard Fournier

    Citation: Standards in Genomic Sciences 2018 13:8

    Published on:

  11. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:6

    Published on:

  12. Content type: Meeting report

    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

    Citation: Standards in Genomic Sciences 2018 13:5

    Published on:

  13. Content type: Correction

    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:

    The original article was published in Standards in Genomic Sciences 2017 12:41

  14. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:3

    Published on:

  15. Content type: Short genome report

    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...

    Authors: Enjuro Harunari, Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Akane Kimura, Moriyuki Hamada and Yasuhiro Igarashi

    Citation: Standards in Genomic Sciences 2018 13:2

    Published on:

  16. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2018 13:1

    Published on:

  17. Content type: Short genome report

    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

    Citation: Standards in Genomic Sciences 2017 12:91

    Published on:

  18. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2017 12:89

    Published on:

  19. Content type: Short genome report

    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

    Citation: Standards in Genomic Sciences 2017 12:88

    Published on:

  20. Content type: Extended genome report

    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

    Citation: Standards in Genomic Sciences 2017 12:86

    Published on:

  21. Content type: Short genome report

    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

    Citation: Standards in Genomic Sciences 2017 12:87

    Published on:

  22. Content type: Meeting report

    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

    Citation: Standards in Genomic Sciences 2017 12:83

    Published on:

  23. Content type: Short genome report

    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: Honghui Liu, Xinchun Liu and Jinqing Li

    Citation: Standards in Genomic Sciences 2017 12:85

    Published on:

    The Correction to this article has been published in Standards in Genomic Sciences 2018 13:15

  24. Content type: Extended genome report

    Acidithiobacillus thiooxidans CLST is an extremely acidophilic gamma-proteobacteria that was...

    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

    Citation: Standards in Genomic Sciences 2017 12:84

    Published on:

  25. Content type: Short genome report

    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

    Citation: Standards in Genomic Sciences 2017 12:82

    Published on:

  26. Content type: Short genome report

    Paraburkholderia caballeronis is a plant-associated bacterium. Stra...

    Authors: Fernando Uriel Rojas-Rojas, Erika Yanet Tapia-García, Maskit Maymon, Ethan Humm, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke…

    Citation: Standards in Genomic Sciences 2017 12:80

    Published on:

  27. Content type: Extended genome report

    Archaeoglobus fulgidus is the type species of genus Archaeoglobus Stetter 1998, a hyperthermophilic sulfate reducing group within the Archaeoglobi class of the euryarchaeota phylum. Membe...

    Authors: Nils-Kåre Birkeland, Peter Schönheit, Lianna Poghosyan, Anne Fiebig and Hans-Peter Klenk

    Citation: Standards in Genomic Sciences 2017 12:79

    Published on:

  28. Content type: Extended genome report

    Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, a...

    Authors: Gina López, Carolina Diaz-Cárdenas, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides, J. David Alzate, Laura N. González, Silvia Restrepo and Sandra Baena

    Citation: Standards in Genomic Sciences 2017 12:78

    Published on:

  29. Content type: Report

    Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first d...

    Authors: Matías Castro, Ana Moya-Beltrán, Paulo C. Covarrubias, Mónica Gonzalez, Juan Pablo Cardenas, Francisco Issotta, Harold Nuñez, Lillian G. Acuña, Gonzalo Encina, David S. Holmes, D. Barrie Johnson and Raquel Quatrini

    Citation: Standards in Genomic Sciences 2017 12:77

    Published on:

  30. Content type: Extended genome report

    Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing bacterium isolated from the nodules of the legume Medicago arborea L. in the Maamora Forest, Morocco. The strain form...

    Authors: Marianna Nagymihály, Bálint M. Vásarhelyi, Quentin Barrière, Teik-Min Chong, Balázs Bálint, Péter Bihari, Kar-Wai Hong, Balázs Horváth, Jamal Ibijbijen, Mohammed Amar, Attila Farkas, Éva Kondorosi, Kok-Gan Chan, Véronique Gruber, Pascal Ratet, Peter Mergaert…

    Citation: Standards in Genomic Sciences 2017 12:75

    Published on:

  31. Content type: Extended genome report

    A Bacillus velezensis strain from the rhizosphere of Sporobolus airoides (Torr.) Torr., a grass in central-north México, was isolated during a biocontrol of phytopathogens scrutiny study. The 2A-2B strain exhibit...

    Authors: Inés Martínez-Raudales, Yumiko De La Cruz-Rodríguez, Alejandro Alvarado-Gutiérrez, Julio Vega-Arreguín, Ahuitz Fraire-Mayorga, Miguel Alvarado-Rodríguez, Victor Balderas-Hernández and Saúl Fraire-Velázquez

    Citation: Standards in Genomic Sciences 2017 12:73

    Published on:

  32. Content type: Extended genome report

    Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allo...

    Authors: Laura T. Morales, Laura N. González-García, María C. Orozco, Silvia Restrepo and Martha J. Vives

    Citation: Standards in Genomic Sciences 2017 12:71

    Published on:

  33. Content type: Extended genome report

    Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents from a pasture-grazed New Zealand dairy cow, and was selected for genome sequencing in order t...

    Authors: Nikola Palevich, William J. Kelly, Sinead C. Leahy, Eric Altermann, Jasna Rakonjac and Graeme T. Attwood

    Citation: Standards in Genomic Sciences 2017 12:72

    Published on:

  34. Content type: Extended genome report

    Candida boidinii is an Ascomycota yeast with important biotechnological applications. In this paper we present the genome sequencing and annotation of eight strains of this species isolat...

    Authors: Salvatore Camiolo, Cinzia Porru, Antonio Benítez-Cabello, Francisco Rodríguez-Gómez, Beatríz Calero-Delgado, Andrea Porceddu, Marilena Budroni, Ilaria Mannazzu, Rufino Jiménez-Díaz and Francisco Noé Arroyo-López

    Citation: Standards in Genomic Sciences 2017 12:70

    Published on:

  35. Content type: Metagenome report

    Cyanobacterial mats are laminated microbial ecosystems which occur in highly diverse environments and which may provide a possible model for early life on Earth. Their ability to produce hydrogen also makes th...

    Authors: Patrik D’haeseleer, Jackson Z. Lee, Leslie Prufert-Bebout, Luke C. Burow, Angela M. Detweiler, Peter K. Weber, Ulas Karaoz, Eoin L. Brodie, Tijana Glavina del Rio, Susannah G. Tringe, Brad M. Bebout and Jennifer Pett-Ridge

    Citation: Standards in Genomic Sciences 2017 12:67

    Published on:

  36. Content type: Short genome report

    The genus Marinobacterium belongs to the family Alteromonadaceae within the class Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium contains 16 species. Marinobacterium rhizophilum

    Authors: Dong Han Choi, Gwang II Jang, Alla Lapidus, Alex Copeland, T. B. K. Reddy, Supratim Mukherjee, Marcel Huntemann, Neha Varghese, Natalia Ivanova, Manoj Pillay, Brian J. Tindall, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Nikos C. Kyrpides and Byung Cheol Cho

    Citation: Standards in Genomic Sciences 2017 12:65

    Published on:

  37. Content type: Extended genome report

    The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and ...

    Authors: Emilie E. L. Muller, Shaman Narayanasamy, Myriam Zeimes, Cédric C. Laczny, Laura A. Lebrun, Malte Herold, Nathan D. Hicks, John D. Gillece, James M. Schupp, Paul Keim and Paul Wilmes

    Citation: Standards in Genomic Sciences 2017 12:64

    Published on:

  38. Content type: Short genome report

    This article reports the full genome sequence of Paenibacillus yonginensis DCY84T (KCTC33428, JCM19885), which is a Gram-positive rod-shaped bacterium isolated from humus soil of Yongin Forest in Gyeonggi Provinc...

    Authors: Yeon-Ju Kim, Johan Sukweenadhi, Ji Woong Seok, Chang Ho Kang, Eul-Su Choi, Sathiyamoorthy Subramaniyam and Deok Chun Yang

    Citation: Standards in Genomic Sciences 2017 12:63

    Published on:

  39. Content type: Extended genome report

    Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales. It is a Gram negative, hyperthermophilic, and strictly anaerobic bacterium. It grows on dive...

    Authors: Zhaohui Xu, Rutika Puranik, Junxi Hu, Hui Xu and Dongmei Han

    Citation: Standards in Genomic Sciences 2017 12:62

    Published on:

  40. Content type: Extended genome report

    Escherichia coli is the most abundant facultative anaerobic bacteria in the gastro-intestinal tract of mammals but can be responsible for intestinal infection due to acquisition of virule...

    Authors: Audrey Segura, Pauline Auffret, Christophe Klopp, Yolande Bertin and Evelyne Forano

    Citation: Standards in Genomic Sciences 2017 12:61

    Published on:

  41. Content type: Short genome report

    Paenibacillus ferrarius CY1T (= KCTC 33419T = CCTCC AB2013369T) is a Gram-positive, aerobic, endospore-forming, motile and rod-shaped bacterium isolated from iron mineral soil. This bacte...

    Authors: Jingxin Li, Wei Guo, Manman Shi, Yajing Cao and Gejiao Wang

    Citation: Standards in Genomic Sciences 2017 12:60

    Published on: