Skip to content

Advertisement

Articles

Page 3 of 17

  1. Content type: Standard operating procedure

    The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomi...

    Authors: Nguyet Kong, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin and Bart C. Weimer

    Citation: Standards in Genomic Sciences 2017 12:27

    Published on:

  2. Content type: Extended genome report

    Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an e...

    Authors: Wayne Reeve, Peter van Berkum, Julie Ardley, Rui Tian, Margaret Gollagher, Dora Marinova, Patrick Elia, T. B. K. Reddy, Manoj Pillay, Neha Varghese, Rekha Seshadri, Natalia Ivanova, Tanja Woyke, Mohamed N. Baeshen, Nabih A. Baeshen and Nikos Kyrpides

    Citation: Standards in Genomic Sciences 2017 12:26

    Published on:

  3. Content type: Short genome report

    Anaerobium acetethylicum strain GluBS11T belongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated ...

    Authors: Yogita Patil, Nicolai Müller, Bernhard Schink, William B. Whitman, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides…

    Citation: Standards in Genomic Sciences 2017 12:24

    Published on:

  4. Content type: Short genome report

    Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr...

    Authors: Romy Chakraborty, Hannah Woo, Paramvir Dehal, Robert Walker, Marcin Zemla, Manfred Auer, Lynne A. Goodwin, Alexey Kazakov, Pavel Novichkov, Adam P. Arkin and Terry C. Hazen

    Citation: Standards in Genomic Sciences 2017 12:23

    Published on:

  5. Content type: Extended genome report

    Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, T...

    Authors: Christian Schäfers, Saskia Blank, Sigrid Wiebusch, Skander Elleuche and Garabed Antranikian

    Citation: Standards in Genomic Sciences 2017 12:22

    Published on:

  6. Content type: Short genome report

    Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soi...

    Authors: Jian-Yu Jiao, Lorena Carro, Lan Liu, Xiao-Yang Gao, Xiao-Tong Zhang, Wael N. Hozzein, Alla Lapidus, Marcel Huntemann, T. B. K. Reddy, Neha Varghese, Michalis Hadjithomas, Natalia N. Ivanova, Markus Göker, Manoj Pillay, Jonathan A. Eisen, Tanja Woyke…

    Citation: Standards in Genomic Sciences 2017 12:21

    Published on:

  7. Content type: Short genome report

    Pseudoalteromonas phage vB_PspS-H40/1 is a lytic phage that infects Pseudoalteromonas sp. strain H40. Both, the phage and its host were isolated in the 1970s from seawater samples collect...

    Authors: René Kallies, Bärbel Kiesel, Matthias Schmidt, Johannes Kacza, Nawras Ghanem, Anja Narr, Jakob Zopfi, Lukas Y. Wick, Jörg Hackermüller, Hauke Harms and Antonis Chatzinotas

    Citation: Standards in Genomic Sciences 2017 12:20

    Published on:

  8. Content type: Extended genome report

    The article provides an overview of the genomic features of Lactobacillus fermentum strain 3872. The genomic sequence reported here is one of three L. fermentum genome sequences completed to date. Comparative gen...

    Authors: Burhan Lehri, Alan M. Seddon and Andrey V. Karlyshev

    Citation: Standards in Genomic Sciences 2017 12:19

    Published on:

  9. Content type: Extended genome report

    Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the ...

    Authors: Voula Alexandraki, Maria Kazou, Jochen Blom, Bruno Pot, Effie Tsakalidou and Konstantinos Papadimitriou

    Citation: Standards in Genomic Sciences 2017 12:18

    Published on:

  10. Content type: Extended genome report

    We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling ...

    Authors: Despoina S. Lymperopoulou, David A. Coil, Denise Schichnes, Steven E. Lindow, Guillaume Jospin, Jonathan A. Eisen and Rachel I. Adams

    Citation: Standards in Genomic Sciences 2017 12:17

    Published on:

  11. Content type: Short genome report

    The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content ...

    Authors: Rafael A. Baraúna, Rommel T. J. Ramos, Adonney A. O. Veras, Pablo H. C. G. de Sá, Luís C. Guimarães, Diego A. das Graças, Adriana R. Carneiro, Judy M. Edman, Sharon J. Spier, Vasco Azevedo and Artur Silva

    Citation: Standards in Genomic Sciences 2017 12:16

    Published on:

  12. Content type: Extended genome report

    Probiotic Lactobacillus species offer various health benefits, thus have been employed in treatment and prevention of various diseases. Due to the differences in the isolation source and the site of action, most ...

    Authors: Mangesh V. Suryavanshi, Dhiraj Paul, Swapnil P. Doijad, Shrikant S. Bhute, Tejashri B. Hingamire, Rahul P. Gune and Yogesh S. Shouche

    Citation: Standards in Genomic Sciences 2017 12:15

    Published on:

  13. Content type: Extended genome report

    Rhizobium aethiopicum sp. nov. is a newly proposed species within the genus Rhizobium. This species includes six rhizobial strains; which were isolated from root nodules of the legume pla...

    Authors: Aregu Amsalu Aserse, Tanja Woyke, Nikos C. Kyrpides, William B. Whitman and Kristina Lindström

    Citation: Standards in Genomic Sciences 2017 12:14

    Published on:

  14. Content type: Short genome report

    Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium, isolated from the arsenic-contaminated aquifer sediment in the Datong basin, China. This strain displays...

    Authors: Linghua Xu, Wanxia Shi, Xian-Chun Zeng, Ye Yang, Lingli Zhou, Yao Mu and Yichen Liu

    Citation: Standards in Genomic Sciences 2017 12:11

    Published on:

  15. Content type: Extended genome report

    Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dep...

    Authors: Connor B. Driscoll, Timothy G. Otten, Nathan M. Brown and Theo W. Dreher

    Citation: Standards in Genomic Sciences 2017 12:9

    Published on:

  16. Content type: Short genome report

    Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the work...

    Authors: Lee P. Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke and Rich Boden

    Citation: Standards in Genomic Sciences 2017 12:10

    Published on:

  17. Content type: Short genome report

    Strain S3-2T, isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus Janthinobacterium. Strain S3-2T is a facultative anaerobe that lacks the abil...

    Authors: Xianzhe Gong, Stig Skrivergaard, Benjamin Smed Korsgaard, Lars Schreiber, Ian P. G. Marshall, Kai Finster and Andreas Schramm

    Citation: Standards in Genomic Sciences 2017 12:8

    Published on:

  18. Content type: Extended genome report

    Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing ...

    Authors: Agnieszka Klonowska, Aline López-López, Lionel Moulin, Julie Ardley, Margaret Gollagher, Dora Marinova, Rui Tian, Marcel Huntemann, T.B.K. Reddy, Neha Varghese, Tanja Woyke, Victor Markowitz, Natalia Ivanova, Rekha Seshadri, Mohamed N. Baeshen, Nabih A. Baeshen…

    Citation: Standards in Genomic Sciences 2017 12:7

    Published on:

  19. Content type: Short genome report

    Pseudomonas brassicacearum strain L13-6-12 is a rhizosphere colonizer of potato, lettuce and sugar beet. Previous studies have shown that this motile, Gram-negative, non-sporulating bacte...

    Authors: Christin Zachow, Henry Müller, Jana Monk and Gabriele Berg

    Citation: Standards in Genomic Sciences 2017 12:6

    Published on:

  20. Content type: Short genome report

    Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki’s Castle vent field, located on the A...

    Authors: Juliane Wissuwa, Sven Le Moine Bauer, Ida Helene Steen and Runar Stokke

    Citation: Standards in Genomic Sciences 2017 12:5

    Published on:

  21. Content type: Short genome report

    Nakamurella lactea DLS-10T , isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality dra...

    Authors: Imen Nouioui, Markus Göker, Lorena Carro, Maria del Carmen Montero-Calasanz, Manfred Rohde, Tanja Woyke, Nikos C. Kyrpides and Hans-Peter Klenk

    Citation: Standards in Genomic Sciences 2017 12:4

    Published on:

  22. Content type: Short genome report

    Agromyces aureus AR33T is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead...

    Authors: Erika Corretto, Livio Antonielli, Angela Sessitsch, Stéphane Compant, Christoph Höfer, Markus Puschenreiter and Günter Brader

    Citation: Standards in Genomic Sciences 2017 12:2

    Published on:

  23. Content type: Short genome report

    Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermo...

    Authors: Lijing Jiang, Stéphane L’Haridon, Mohamed Jebbar, Hongxiu Xu, Karine Alain and Zongze Shao

    Citation: Standards in Genomic Sciences 2017 12:3

    Published on:

  24. Content type: Short genome report

    Salmonella enterica serovar Enteritidis is one of the most common causes of Salmonellosis worldwide. Utilization of bacteriophages as prophylactic agents is a practical solution to preven...

    Authors: Javier Santander, Jose I. Vasquez, Cristopher Segovia, Leonardo Santos, Gabriel Turra, Karen Huber and James Robeson

    Citation: Standards in Genomic Sciences 2017 12:1

    Published on:

  25. Content type: Short genome report

    Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment producing and spore-forming actinomycete, which forms branching vegetative hyphae and was iso...

    Authors: Lena Schaffert, Andreas Albersmeier, Anika Winkler, Jörn Kalinowski, Sergey B. Zotchev and Christian Rückert

    Citation: Standards in Genomic Sciences 2016 11:91

    Published on:

  26. Content type: Short genome report

    The emergence of antibiotic-resistant foodborne bacteria is a global health problem that requires immediate attention. Bacteriophages are a promising biotechnological alternative approach against bacterial pat...

    Authors: Luis Amarillas, Cristobal Chaidez, Arturo González-Robles and Josefina León-Félix

    Citation: Standards in Genomic Sciences 2016 11:89

    Published on:

  27. Content type: Short genome report

    Oligoflexus tunisiensis Shr3T is the first strain described in the newest (eighth) class Oligoflexia of the phylum Proteobacteria. This strain was isolated from the 0.2-μm filtrate of a s...

    Authors: Ryosuke Nakai, Takatomo Fujisawa, Yasukazu Nakamura, Tomoya Baba, Miyuki Nishijima, Fatma Karray, Sami Sayadi, Hiroko Isoda, Takeshi Naganuma and Hironori Niki

    Citation: Standards in Genomic Sciences 2016 11:90

    Published on:

  28. Content type: Metagenome report

    Chlorinated solvent contamination of potable water supplies is a serious problem worldwide. Biostimulation protocols can successfully remediate chlorinated solvent contamination through enhanced reductive dech...

    Authors: Rebecca A. Reiss, Peter Guerra and Oleg Makhnin

    Citation: Standards in Genomic Sciences 2016 11:88

    Published on:

  29. Content type: Short genome report

    Several species of the genus Dickeya provoke soft rot and blackleg diseases on a wide range of plants and crops. Dickeya solani has been identified as the causative agent of diseases outbreaks on potato culture i...

    Authors: Slimane Khayi, Pauline Blin, Teik Min Chong, Kok-Gan Chan and Denis Faure

    Citation: Standards in Genomic Sciences 2016 11:87

    Published on:

  30. Content type: Short genome report

    Pseudomonas jessenii C2 and Pseudomonas jessenii H16 were isolated from low-Cu and high-Cu industrially contaminated soil, respectively. P. jessenii H16 displayed significant resistance t...

    Authors: Yanan Qin, Dan Wang, Kristian K. Brandt and Christopher Rensing

    Citation: Standards in Genomic Sciences 2016 11:86

    Published on:

  31. Content type: Short genome report

    Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated alchivemycins A and B. Here, we report the draft genome sequence of this strain together with...

    Authors: Hisayuki Komaki, Natsuko Ichikawa, Akio Oguchi, Moriyuki Hamada, Enjuro Harunari, Shinya Kodani, Nobuyuki Fujita and Yasuhiro Igarashi

    Citation: Standards in Genomic Sciences 2016 11:85

    Published on:

  32. Content type: Short genome report

    Here, we report the draft genome sequence of Micromonospora sp. DSW705 (=NBRC 110037), a producer of antitumor cyclic depsipeptides rakicidins A and B, together with the features of this strain and generation, an...

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

    Citation: Standards in Genomic Sciences 2016 11:84

    Published on:

  33. Content type: Short genome report

    Streptomyces sp. MWW064 (=NBRC 110611) produces an antitumor cyclic depsipeptide rakicidin D. Here, we report the draft genome sequence of this strain together with features of the organi...

    Authors: Hisayuki Komaki, Arisa Ishikawa, Natsuko Ichikawa, Akira Hosoyama, Moriyuki Hamada, Enjuro Harunari, Takuya Nihira, Watanalai Panbangred and Yasuhiro Igarashi

    Citation: Standards in Genomic Sciences 2016 11:83

    Published on:

  34. Content type: Short genome report

    Prochlorothrix hollandica is filamentous non-heterocystous cyanobacterium which possesses the chlorophyll a/b light-harvesting complexes. Despite the growing interest in unusual green-pig...

    Authors: Natalia Velichko, Mikhail Rayko, Ekaterina Chernyaeva, Alla Lapidus and Alexander Pinevich

    Citation: Standards in Genomic Sciences 2016 11:82

    Published on:

  35. Content type: Extended genome report

    The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the u...

    Authors: Helge-Ansgar Giebel, Franziska Klotz, Sonja Voget, Anja Poehlein, Katrin Grosser, Andreas Teske and Thorsten Brinkhoff

    Citation: Standards in Genomic Sciences 2016 11:81

    Published on:

  36. Content type: Commentary

    Here we introduce a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources. The proposed MIxS-HCR package incorporates the core features of the MIx...

    Authors: Nicolas Tsesmetzis, Pelin Yilmaz, Peter C. Marks, Nikos C. Kyrpides, Ian M. Head and Bart P. Lomans

    Citation: Standards in Genomic Sciences 2016 11:78

    Published on:

  37. Content type: Short genome report

    The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition ...

    Authors: Travis K. Price, Arya Mehrtash, Laurynas Kalesinskas, Kema Malki, Evann E. Hilt, Catherine Putonti and Alan J. Wolfe

    Citation: Standards in Genomic Sciences 2016 11:79

    Published on:

  38. Content type: Short genome report

    Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermo...

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

    Citation: Standards in Genomic Sciences 2016 11:80

    Published on:

  39. Content type: Short genome report

    A new plant commensal Pseudomonas veronii isolate (strain R4) was identified from a Xiphinema index biocontrol screen. Isolated from grapevine roots from vineyards in central Chile, the strain R4 exhibited a slow...

    Authors: Christian Montes, Fabiola Altimira, Hayron Canchignia, Álvaro Castro, Evelyn Sánchez, María Miccono, Eduardo Tapia, Álvaro Sequeida, Jorge Valdés, Paz Tapia, Carolina González and Humberto Prieto

    Citation: Standards in Genomic Sciences 2016 11:76

    Published on:

  40. Content type: Erratum

    Authors: Rich Boden, Lee P. Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke…

    Citation: Standards in Genomic Sciences 2016 11:77

    Published on:

    The original article was published in Standards in Genomic Sciences 2016 11:74

  41. Content type: Extended genome report

    Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosp...

    Authors: Mitja N.P. Remus-Emsermann, Michael Schmid, Maria-Theresia Gekenidis, Cosima Pelludat, Jürg E. Frey, Christian H. Ahrens and David Drissner

    Citation: Standards in Genomic Sciences 2016 11:75

    Published on:

  42. Content type: Short genome report

    Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and ...

    Authors: Rich Boden, Lee P. Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke…

    Citation: Standards in Genomic Sciences 2016 11:74

    Published on:

    The Erratum to this article has been published in Standards in Genomic Sciences 2016 11:77

  43. Content type: Short genome report

    Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of inhibition of a broad range of plant pathogenic fungi. The strain has the potential to be developed...

    Authors: Shumei Zhang, Wei Jiang, Jing Li, Liqiang Meng, Xu Cao, Jihua Hu, Yushuai Liu, Jingyu Chen and Changqing Sha

    Citation: Standards in Genomic Sciences 2016 11:73

    Published on:

  44. Content type: Short genome report

    Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, Lipoptena cervi (Diptera: Hippoboscidae). ...

    Authors: Eva Nováková, Václav Hypša, Petr Nguyen, Filip Husník and Alistair C. Darby

    Citation: Standards in Genomic Sciences 2016 11:72

    Published on:

  45. Content type: Short genome report

    Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria belonging to the family Acidiferrobacteraceae in the order Acidiferrobacterales. The type str...

    Authors: Kazuhiro Umezawa, Tomohiro Watanabe, Aya Miura, Hisaya Kojima and Manabu Fukui

    Citation: Standards in Genomic Sciences 2016 11:71

    Published on:

  46. Content type: Short genome report

    Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogen...

    Authors: Iain J. Anderson, Priya DasSarma, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Hope Tice, Eileen Dalin, David C. Bruce, Lynne Goodwin, Sam Pitluck, David Sims, Thomas S. Brettin, John C. Detter, Cliff S. Han, Frank Larimer…

    Citation: Standards in Genomic Sciences 2016 11:70

    Published on:

  47. Content type: Short genome report

    The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in ...

    Authors: Oliver K. I. Bezuidt, Mohamed A. Gomri, Rian Pierneef, Marc W. Van Goethem, Karima Kharroub, Don A. Cowan and Thulani P. Makhalanyane

    Citation: Standards in Genomic Sciences 2016 11:68

    Published on: