Skip to main content

Articles

Page 3 of 18

  1. 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

    Content type: Metagenome report

    Published on:

  2. 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

    Content type: Short genome report

    Published on:

  3. 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

    Content type: Extended genome report

    Published on:

  4. 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

    Content type: Short genome report

    Published on:

  5. 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

    Content type: Extended genome report

    Published on:

  6. 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

    Content type: Extended genome report

    Published on:

  7. 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

    Content type: Short genome report

    Published on:

  8. Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000

    Authors: Wan Adnawani Meor Osman, Peter van Berkum, Milagros León-Barrios, Encarna Velázquez, Patrick Elia, Rui Tian, Julie Ardley, Margaret Gollagher, Rekha Seshadri, T. B. K. Reddy, Natalia Ivanova, Tanja Woyke, Amrita Pati, Victor Markowitz, Mohamed N. Baeshen, Naseebh Nabeeh Baeshen…

    Citation: Standards in Genomic Sciences 2017 12:58

    Content type: Extended genome report

    Published on:

  9. Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern M...

    Authors: Emily Denise Melton, Dimitry Y. Sorokin, Lex Overmars, Alla L. Lapidus, Manoj Pillay, Natalia Ivanova, Tijana Glavina del Rio, Nikos C. Kyrpides, Tanja Woyke and Gerard Muyzer

    Citation: Standards in Genomic Sciences 2017 12:57

    Content type: Extended genome report

    Published on:

  10. Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated fr...

    Authors: Shicheng Chen, Marty Soehnlen, Frances P. Downes and Edward D. Walker

    Citation: Standards in Genomic Sciences 2017 12:56

    Content type: Extended genome report

    Published on:

  11. Irpex lacteus, a cosmopolitan white-rot fungus, degrades lignin and lignin-derived aromatic compounds. In this study, we report the high-quality draft genome sequence of I. lacteus F17, i...

    Authors: Mengwei Yao, Wenman Li, Zihong Duan, Yinliang Zhang and Rong Jia

    Citation: Standards in Genomic Sciences 2017 12:55

    Content type: Short genome report

    Published on:

  12. A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKTT, isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO2 bio-mitigation owing to its ability...

    Authors: Wooyoung Jeon, Lia Priscilla, Gyuyeon Park, Heeseok Lee, Narae Lee, Dongyup Lee, Hyuksung Kwon, Iksung Ahn, Changha Lee, Hongweon Lee and Jungoh Ahn

    Citation: Standards in Genomic Sciences 2017 12:54

    Content type: Short genome report

    Published on:

  13. Here we report the draft genome sequence of Chitinophaga costai A37T2T (=CIP 110584T, =LMG 27458T), which was isolated from the endophytic community of Pinus pinaster tree. The total genome size of C. costaii A37...

    Authors: Diogo N. Proença, William B. Whitman, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides and Paula V. Morais

    Citation: Standards in Genomic Sciences 2017 12:53

    Content type: Short genome report

    Published on:

  14. Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was s...

    Authors: Wah-Seng See-Too, Robson Ee, Yan-Lue Lim, Peter Convey, David A. Pearce, Taznim Begam Mohd Mohidin, Wai-Fong Yin and Kok Gan Chan

    Citation: Standards in Genomic Sciences 2017 12:52

    Content type: Short genome report

    Published on:

  15. Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagna...

    Authors: Amir Ktari, Imen Nouioui, Teal Furnholm, Erik Swanson, Faten Ghodhbane-Gtari, Louis S. Tisa and Maher Gtari

    Citation: Standards in Genomic Sciences 2017 12:51

    Content type: Extended genome report

    Published on:

  16. Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gil...

    Authors: Ruby Ponnudurai, Lizbeth Sayavedra, Manuel Kleiner, Stefan E. Heiden, Andrea Thürmer, Horst Felbeck, Rabea Schlüter, Stefan M. Sievert, Rolf Daniel, Thomas Schweder and Stephanie Markert

    Citation: Standards in Genomic Sciences 2017 12:50

    Content type: Extended genome report

    Published on:

  17. Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in...

    Authors: Soraya Mendoza-Olazarán, José F. Garcia-Mazcorro, Rayo Morfín-Otero, Licet Villarreal-Treviño, Adrián Camacho-Ortiz, Eduardo Rodríguez-Noriega, Paola Bocanegra-Ibarias, Héctor J. Maldonado-Garza, Scot E. Dowd and Elvira Garza-González

    Citation: Standards in Genomic Sciences 2017 12:49

    Content type: Extended genome report

    Published on:

  18. Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (4...

    Authors: Lucas M. Demey, Caitlin R. Miller, Michael P Manzella, Rachel R. Spurbeck, Sukhinder K. Sandhu, Gemma Reguera and Kazem Kashefi

    Citation: Standards in Genomic Sciences 2017 12:47

    Content type: Extended genome report

    Published on:

  19. The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We...

    Authors: Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova…

    Citation: Standards in Genomic Sciences 2017 12:46

    Content type: Extended genome report

    Published on:

  20. Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequ...

    Authors: Sijing Chang, Gaosen Zhang, Ximing Chen, Haozhi Long, Yilin Wang, Tuo Chen and Guangxiu Liu

    Citation: Standards in Genomic Sciences 2017 12:45

    Content type: Extended genome report

    Published on:

  21. Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile....

    Authors: Antonio E. Serrano, Lorena V. Escudero, Cinthya Tebes-Cayo, Mauricio Acosta, Olga Encalada, Sebastián Fernández-Moroso and Cecilia Demergasso

    Citation: Standards in Genomic Sciences 2017 12:43

    Content type: Extended genome report

    Published on:

  22. Xanthomonas citri pv. malvacearum is a major pathogen of cotton, Gossypium hirsutum L.. In this study we report the complete genome of the X. citri pv. malvacearum strain MSCT1 assembled ...

    Authors: Kurt C. Showmaker, Mark A. Arick II, Chuan-Yu Hsu, Brigitte E. Martin, Xiaoqiang Wang, Jiayuan Jia, Martin J. Wubben, Robert L. Nichols, Tom W. Allen, Daniel G. Peterson and Shi-En Lu

    Citation: Standards in Genomic Sciences 2017 12:42

    Content type: Extended genome report

    Published on:

  23. We present the high quality, complete genome assembly of Neisseria lactamica Y92–1009 used to manufacture an outer membrane vesicle (OMV)-based vaccine, and a member of the Neisseria genus. The strain is availabl...

    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 2017 12:41

    Content type: Extended genome report

    Published on:

    The Correction to this article has been published in Standards in Genomic Sciences 2018 13:4

  24. Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understand...

    Authors: Björn E. Olsson, Ekaterina S. Korsakova, Lyudmila N. Anan’ina, Anna A. Pyankova, Olga V. Mavrodi, Elena G. Plotnikova and Dmitri V. Mavrodi

    Citation: Standards in Genomic Sciences 2017 12:39

    Content type: Extended genome report

    Published on:

  25. The genome of Leuconostoc suionicum DSM 20241T (=ATCC 9135T = LMG 8159T = NCIMB 6992T) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative propertie...

    Authors: Byung Hee Chun, Se Hee Lee, Hye Hee Jeon, Dong-Woon Kim and Che Ok Jeon

    Citation: Standards in Genomic Sciences 2017 12:38

    Content type: Short genome report

    Published on:

  26. Filamentous fungus Aspergillus niger has high industrial value due to their lignocellulolytic enzyme activities and ATCC 10864 is one of the few type strains of A. niger which has a unique biofilm forming capabil...

    Authors: Sujay Paul, Yvette Ludeña, Gretty K. Villena, Fengan Yu, David H. Sherman and Marcel Gutiérrez-Correa

    Citation: Standards in Genomic Sciences 2017 12:37

    Content type: Short genome report

    Published on:

  27. Microbulbifer sp. CCB-MM1 is a halophile isolated from estuarine sediment of Matang Mangrove Forest, Malaysia. Based on 16S rRNA gene sequence analysis, strain CCB-MM1 is a potentially...

    Authors: Tsu Horng Moh, Nyok-Sean Lau, Go Furusawa and Al-Ashraf Abdullah Amirul

    Citation: Standards in Genomic Sciences 2017 12:36

    Content type: Genome report

    Published on:

  28. Planktothricoides is a free-living filamentous cyanobacterium belonging to the order Oscillatoriales and the family Phormidiaceae, capable of forming bloom in fresh and brackish waters. A...

    Authors: Shu Harn Te, Boon Fei Tan, Chek Yin Boo, Janelle Renee Thompson and Karina Yew-Hoong Gin

    Citation: Standards in Genomic Sciences 2017 12:35

    Content type: Extended genome report

    Published on:

  29. Desulfoplanes formicivorans strain Pf12BT is the type strain of the type species in the genus Desulfoplanes, which is the one of the genera in the family Desulfomicrobiaceae within the or...

    Authors: Miho Watanabe, Hisaya Kojima and Manabu Fukui

    Citation: Standards in Genomic Sciences 2017 12:34

    Content type: Short genome report

    Published on:

  30. Escherichia coli causing infection outside the gastrointestinal system are referred to as extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a subgroup of extra-intestinal p...

    Authors: Steffen L. Jørgensen, Egle Kudirkiene, Lili Li, Jens P. Christensen, John E. Olsen, Lisa Nolan and Rikke H. Olsen

    Citation: Standards in Genomic Sciences 2017 12:33

    Content type: Short genome report

    Published on:

  31. The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bac...

    Authors: Qian Liu, Yue-Hong Wu, Hong Cheng, Lin Xu, Chun-Sheng Wang and Xue-Wei Xu

    Citation: Standards in Genomic Sciences 2017 12:32

    Content type: Short genome report

    Published on:

  32. Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotrop...

    Authors: Sivan Laviad-Shitrit, Markus Göker, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke, Hans-Peter Klenk…

    Citation: Standards in Genomic Sciences 2017 12:31

    Content type: Short genome report

    Published on:

  33. A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was isolated from soil samples from the botanical garden of Ulm University, Ulm, Germany. Here, the isolation procedure, id...

    Authors: Vanessa Jag, Anja Poehlein, Frank R. Bengelsdorf, Rolf Daniel and Peter Dürre

    Citation: Standards in Genomic Sciences 2017 12:30

    Content type: Short genome report

    Published on:

  34. Ralstonia solanacearum is an extremely destructive pathogen able to cause disease in a wide range of host plants. Here we report the draft genome sequences of the strains FJAT-91, FJAT-45...

    Authors: Yidan Sun, Keke Wang, Carlos Caceres-Moreno, Wei Jia, Aojun Chen, Heng Zhang, Renyi Liu and Alberto P. Macho

    Citation: Standards in Genomic Sciences 2017 12:29

    Content type: Extended genome report

    Published on:

  35. Strain Ola 51T (=LMG 24251T = CGMCC 1.7012T) is the type strain of the species Kosakonia oryzae and was isolated from surface-sterilized roots of the wild rice species Oryza latifolia grown in Guangdong, China. H...

    Authors: Yuanyuan Li, Shuying Li, Mingyue Chen, Guixiang Peng, Zhiyuan Tan and Qianli An

    Citation: Standards in Genomic Sciences 2017 12:28

    Content type: Short genome report

    Published on:

  36. 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

    Content type: Standard operating procedure

    Published on:

  37. 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

    Content type: Extended genome report

    Published on:

  38. 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

    Content type: Short genome report

    Published on:

  39. 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

    Content type: Short genome report

    Published on:

  40. 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

    Content type: Extended genome report

    Published on:

  41. 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

    Content type: Short genome report

    Published on:

  42. 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

    Content type: Short genome report

    Published on:

  43. 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

    Content type: Extended genome report

    Published on:

  44. 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

    Content type: Short genome report

    Published on:

\