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  1. Content type: Short genome report

    Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This strain was identified as belonging to the species Pantoea septica based on rpoB sequence identity of 99.7 % with Pantoea...

    Authors: Cheikh Ibrahima Lo, Roshan Padhmanabhan, Oleg Mediannikov, Thi Tien Nguyen, Didier Raoult, Pierre-Edouard Fournier and Florence Fenollar

    Citation: Standards in Genomic Sciences 2015 10:103

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  2. Content type: Short genome report

    The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft genome is arranged into 93 contigs containing 3311 p...

    Authors: Anja Poehlein, Rolf Daniel and Diliana D. Simeonova

    Citation: Standards in Genomic Sciences 2015 10:100

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  3. Content type: Short genome report

    Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mes...

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

    Citation: Standards in Genomic Sciences 2015 10:99

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  4. Content type: Short genome report

    Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a...

    Authors: Dong Han Choi, Chisang Ahn, Gwang Il Jang, Alla Lapidus, James Han, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Natalia Ivanova, Victor Markowitz, Manfred Rohde, Brian Tindall, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides…

    Citation: Standards in Genomic Sciences 2015 10:98

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  5. Content type: Short genome report

    Due to abundant contamination in various foods, the pathogenesis of Bacillus cereus has been widely studied in physiological and molecular level. B. cereus FORC_005 was isolated from a Korean side dish, soy sauce...

    Authors: Dong-Hoon Lee, Hye Rim Kim, Han Young Chung, Jong Gyu Lim, Suyeon Kim, Se Keun Kim, Hye-Jin Ku, Heebal Kim, Sangryeol Ryu, Sang Ho Choi and Ju-Hoon Lee

    Citation: Standards in Genomic Sciences 2015 10:97

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  6. Content type: Short genome report

    Bacteriophage P8625 is a lytic bacteriophage that infects the verrucomicrobial strain IMCC8625, a marine bacterium affiliated with Verrucomicrobia subdivision 4. Both the bacteriophage and the host bacterial stra...

    Authors: Ahyoung Choi, Ilnam Kang, Seung-Jo Yang and Jang-Cheon Cho

    Citation: Standards in Genomic Sciences 2015 10:96

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  7. Content type: Extended genome report

    Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its po...

    Authors: Aliya D. Suleimanova, Anna A. Toymentseva, Eugenia A. Boulygina, Sergey V. Kazakov, Ayslu M. Mardanova, Nelly P. Balaban and Margarita R. Sharipova

    Citation: Standards in Genomic Sciences 2015 10:95

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  8. Content type: Short genome report

    Pontibacillus yanchengensis Y32T is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the fe...

    Authors: Jing Huang, Zi xu Qiao, Jing wei Tang and Gejiao Wang

    Citation: Standards in Genomic Sciences 2015 10:93

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  9. Content type: Short genome report

    Flavobacterium enshiense DK69T is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated bacterium that belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. ...

    Authors: Zhipeng Zeng, Chong Chen, Hailun Du, Gejiao Wang and Mingshun Li

    Citation: Standards in Genomic Sciences 2015 10:92

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  10. Content type: Short genome report

    Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus pic...

    Authors: Jean-Christophe Lagier, Saber Khelaifia, Esam Ibraheem Azhar, Olivier Croce, Fehmida Bibi, Asif Ahmad Jiman-Fatani, Muhammad Yasir, Huda Ben Helaby, Catherine Robert, Pierre-Edouard Fournier and Didier Raoult

    Citation: Standards in Genomic Sciences 2015 10:91

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  11. Content type: Short genome report

    Members of the Mycoplasma mycoides cluster’ represent important livestock pathogens worldwide. Mycoplasma mycoides subsp. mycoides is the etiologic agent of contagious bovine pleuropneumonia (CBPP), which is sti...

    Authors: Anne Fischer, Ivette Santana-Cruz, Jan Hegerman, Hadrien Gourlé, Elise Schieck, Mathieu Lambert, Suvarna Nadendla, Hezron Wesonga, Rachel A. Miller, Sanjay Vashee, Johann Weber, Jochen Meens, Joachim Frey and Joerg Jores

    Citation: Standards in Genomic Sciences 2015 10:89

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  12. Content type: Short genome report

    Lysobacter arseniciresistens ZS79T is a highly arsenic-resistant,rod-shaped, motile, non-spore-forming, aerobic, Gram-negative bacterium. In this study, four Lysobacter type strains were ...

    Authors: Lin Liu, Shengzhe Zhang, Meizhong Luo and Gejiao Wang

    Citation: Standards in Genomic Sciences 2015 10:88

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  13. Content type: Short genome report

    Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743...

    Authors: Leila Eshraghi, Sofie E. De Meyer, Rui Tian, Rekha Seshadri, Natalia Ivanova, Amrita Pati, Victor Markowitz, Tanja Woyke, Nikos C. Kyrpides, Ravi Tiwari, Ron Yates, John Howieson and Wayne Reeve

    Citation: Standards in Genomic Sciences 2015 10:87

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  14. Content type: Standard operating procedure

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. M...

    Authors: Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, H. James Tripp, David Paez-Espino, Krishnaveni Palaniappan, Ernest Szeto, Manoj Pillay, I-Min A. Chen, Amrita Pati, Torben Nielsen, Victor M. Markowitz and Nikos C. Kyrpides

    Citation: Standards in Genomic Sciences 2015 10:86

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    The Erratum to this article has been published in Standards in Genomic Sciences 2016 11:27

  15. Content type: Short genome report

    Thioalkalivibrio thiocyanoxidans strain ARh 2T is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Rema...

    Authors: Tom Berben, Dimitry Y. Sorokin, Natalia Ivanova, Amrita Pati, Nikos Kyrpides, Lynne A. Goodwin, Tanja Woyke and Gerard Muyzer

    Citation: Standards in Genomic Sciences 2015 10:85

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  16. Content type: Short genome report

    Thioalkalivibrio thiocyanodenitrificans strain ARhD 1T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth ...

    Authors: Tom Berben, Dimitry Y. Sorokin, Natalia Ivanova, Amrita Pati, Nikos Kyrpides, Lynne A. Goodwin, Tanja Woyke and Gerard Muyzer

    Citation: Standards in Genomic Sciences 2015 10:84

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  17. Content type: Short genome report

    Propionibacterium freudenreichii subsp. freudenreichii DSM 20271T is the type strain of species Propionibacterium freudenreichii that has a long history of safe use in the production dair...

    Authors: Patrik Koskinen, Paulina Deptula, Olli-Pekka Smolander, Fitsum Tamene, Juhana Kammonen, Kirsi Savijoki, Lars Paulin, Vieno Piironen, Petri Auvinen and Pekka Varmanen

    Citation: Standards in Genomic Sciences 2015 10:83

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  18. Content type: Short genome report

    The bacterial genus Polaribacter is distributed widely in marine environments; however, there have been no reports of phages infecting Polaribacter strains. Here, we describe the isolation and genome sequencing o...

    Authors: Ilnam Kang, Hani Jang and Jang-Cheon Cho

    Citation: Standards in Genomic Sciences 2015 10:82

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  19. Content type: Short genome report

    Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, a...

    Authors: Phillip Brumm, Miriam L. Land, Loren J. Hauser, Cynthia D. Jeffries, Yun-Juan Chang and David A. Mead

    Citation: Standards in Genomic Sciences 2015 10:81

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    The Erratum to this article has been published in Standards in Genomic Sciences 2016 11:10

  20. Content type: Short genome report

    Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Re...

    Authors: Sofie E. De Meyer, Matthew Parker, Peter Van Berkum, Rui Tian, Rekha Seshadri, T.B.K. Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, John Howieson and Wayne Reeve

    Citation: Standards in Genomic Sciences 2015 10:80

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  21. Content type: Short genome report

    Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieu...

    Authors: Sofie E. De Meyer, Rui Tian, Rekha Seshadri, TBK Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, Ron Yates, John Howieson and Wayne Reeve

    Citation: Standards in Genomic Sciences 2015 10:79

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  22. Content type: Short genome report

    Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as the most prevalent genotype in South Korea among clinical isolates of M. tuberculosis from hi...

    Authors: Seung Jung Han, Taeksun Song, Yong-Joon Cho, Jong-Seok Kim, Soo Young Choi, Hye-Eun Bang, Jongsik Chun, Gill-Han Bai, Sang-Nae Cho and Sung Jae Shin

    Citation: Standards in Genomic Sciences 2015 10:78

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  23. Content type: Extended Genome Report

    “Geoglobus ahangari” strain 234T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal syst...

    Authors: Michael P. Manzella, Dawn E. Holmes, Jessica M. Rocheleau, Amanda Chung, Gemma Reguera and Kazem Kashefi

    Citation: Standards in Genomic Sciences 2015 10:77

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  24. Content type: Short genome report

    Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological mode...

    Authors: Beng Soon Teh, Nyok-Sean Lau, Fui Ling Ng, Ahmad Yamin Abdul Rahman, Xuehua Wan, Jennifer A. Saito, Shaobin Hou, Aik-Hong Teh, Nazalan Najimudin and Maqsudul Alam

    Citation: Standards in Genomic Sciences 2015 10:76

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  25. Content type: Short genome report

    Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microb...

    Authors: Julie L. Meyer, Brian A. Dillard, John M. Rodgers, Kim B. Ritchie, Valerie J. Paul and Max Teplitski

    Citation: Standards in Genomic Sciences 2015 10:75

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  26. Content type: Genome report

    Thermoanaerobacter thermohydrosulfuricus BSB-33 is a thermophilic gram positive obligate anaerobe isolated from a hot spring in West Bengal, India. Unlike other T. thermohydrosulfuricus s...

    Authors: Pamela Bhattacharya, Adam Barnebey, Marcin Zemla, Lynne Goodwin, Manfred Auer and Steven M. Yannone

    Citation: Standards in Genomic Sciences 2015 10:74

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  27. Content type: Short genome report

    Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the Nationa...

    Authors: Phillip J. Brumm, Miriam L. Land and David A. Mead

    Citation: Standards in Genomic Sciences 2015 10:73

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  28. Content type: Short genome report

    Fervidobacterium islandicum AW-1 (KCTC 4680) is an extremely thermophilic anaerobe isolated from a hot spring in Indonesia. This bacterium could degrade native chicken feathers completely...

    Authors: Yong-Jik Lee, Haeyoung Jeong, Gun-Seok Park, Yunyoung Kwak, Sang-Jae Lee, Sang Jun Lee, Min-Kyu Park, Ji-Yeon Kim, Hwan Ku Kang, Jae-Ho Shin and Dong-Woo Lee

    Citation: Standards in Genomic Sciences 2015 10:71

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  29. Content type: Short genome report

    Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many biotechnological applications. Anoxybacillus ayderensis AB04T (= NCIMB 13972T = NCCB 100050T) was isolated from the Ay...

    Authors: Ali Osman Belduz, Sabriye Canakci, Kok-Gan Chan, Ummirul Mukminin Kahar, Chia Sing Chan, Amira Suriaty Yaakop and Kian Mau Goh

    Citation: Standards in Genomic Sciences 2015 10:70

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  30. Content type: Short genome report

    Plant necrotrophic Dickeya spp. are among the top ten most devastating bacterial plant pathogens able to infect a number of different plant species worldwide including economically important crops. Little is know...

    Authors: Robert Czajkowski, Zofia Ozymko, Joanna Siwinska, Adam Ossowicki, Victor de Jager, Magdalena Narajczyk and Ewa Łojkowska

    Citation: Standards in Genomic Sciences 2015 10:68

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  31. Content type: Short genome report

    ‘Treponema phagedenis’ is considered to be a key agent in the pathogenesis of bovine digital dermatitis, an infectious foot condition of economic and animal welfare importance. We hereby ...

    Authors: Mamoona Mushtaq, Shahid Manzoor, Märit Pringle, Anna Rosander and Erik Bongcam-Rudloff

    Citation: Standards in Genomic Sciences 2015 10:67

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  32. Content type: Short genome report

    Flavihumibacter solisilvae 3-3T (= KACC 17917T = JCM 19891T) represents a type strain of the genus Flavihumibacter within the family Chitinophagaceae. This strain can use various sole car...

    Authors: Gang Zhou, Chong Chen, Che Ok Jeon, Gejiao Wang and Mingshun Li

    Citation: Standards in Genomic Sciences 2015 10:66

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  33. Content type: Metagenome report

    Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system...

    Authors: Bonnie L. Brown, Rebecca V. LePrell, Rima B. Franklin, Maria C. Rivera, Francine M. Cabral, Hugh L. Eaves, Vicki Gardiakos, Kevin P. Keegan and Timothy L. King

    Citation: Standards in Genomic Sciences 2015 10:65

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  34. Content type: Short genome report

    Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected...

    Authors: Sofie E. De Meyer, Rui Tian, Rekha Seshadri, Natalia Ivanova, Amrita Pati, Victor Markowitz, Tanja Woyke, Ron Yates, John Howieson, Nikos Kyrpides and Wayne Reeve

    Citation: Standards in Genomic Sciences 2015 10:64

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  35. Content type: Short genome report

    Clostridium ihumii strain AP5T sp. nov. is a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the stool sample of a 21-year-old Fre...

    Authors: Vicky Merhej, Anne Pfleiderer, Dhamodharan Ramasamy, Jean-Christophe Lagier, Caroline Michelle, Didier Raoult and Pierre-Edouard Fournier

    Citation: Standards in Genomic Sciences 2015 10:63

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  36. Content type: Extended genome report

    Bacillus thuringiensis is the most widely used biological pesticide in the world. It belongs to the Bacillus cereus sensu lato group, which contains six species. Among these six species,

    Authors: Qiao Li, Li Z. Xu, Ting Zou, Peng Ai, Gang H. Huang, Ping Li and Ai P. Zheng

    Citation: Standards in Genomic Sciences 2015 10:62

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  37. Content type: Short genome report

    The actinobacterium Rhodococcus sp. JG-3 is an aerobic, eurypsychrophilic, soil bacterium isolated from permafrost in the hyper arid Upper Dry Valleys of Antarctica. It is yellow pigmented, gram positive, moderat...

    Authors: Jacqueline Goordial, Isabelle Raymond-Bouchard, Jennifer Ronholm, Nicole Shapiro, Tanja Woyke, Lyle Whyte and Corien Bakermans

    Citation: Standards in Genomic Sciences 2015 10:61

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  38. Content type: Extended genome report

    Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a Gr...

    Authors: Kåre Olav Holm, Kristina Nilsson, Erik Hjerde, Nils-Peder Willassen and Debra L. Milton

    Citation: Standards in Genomic Sciences 2015 10:60

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  39. Content type: Extended genome report

    Streptomyces sp. TP-A0598, isolated from seawater, produces lydicamycin, structurally unique type I polyketide bearing two nitrogen-containing five-membered rings, and four congeners TPU-...

    Authors: Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Nobuyuki Fujita and Yasuhiro Igarashi

    Citation: Standards in Genomic Sciences 2015 10:58

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  40. Content type: Short genome report

    Methanosarcina species are the most metabolically versatile of the methanogenic Archaea and can obtain energy for growth by producing methane via the hydrogenotrophic, acetoclastic or met...

    Authors: Suzanne C. Lambie, William J. Kelly, Sinead C. Leahy, Dong Li, Kerri Reilly, Tim A. McAllister, Edith R. Valle, Graeme T. Attwood and Eric Altermann

    Citation: Standards in Genomic Sciences 2015 10:57

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  41. Content type: Extended Genome Report

    The tenacious association between strains of the heterotrophic alphaproteobacterial genus Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this context the genome of the heterotr...

    Authors: Sophie R. Ullrich, Anja Poehlein, Sonja Voget, Michael Hoppert, Rolf Daniel, Andreas Leimbach, Judith S. Tischler, Michael Schlömann and Martin Mühling

    Citation: Standards in Genomic Sciences 2015 10:56

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  42. Content type: Extended genome report

    Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delft...

    Authors: Ameesha R. Shetty, Vidya de Gannes, Chioma C. Obi, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne A. Goodwin, Samuel Pitluck, Linda Peters, Natalia Mikhailova, Hazuki Teshima, Cliff Han, Roxanne Tapia, Miriam Land, Loren J. Hauser, Nikos Kyrpides…

    Citation: Standards in Genomic Sciences 2015 10:55

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  43. Content type: Short genome report

    Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICEMlSymR7A, also known as the R7A symbiosis island, in a laboratory ma...

    Authors: Wayne Reeve, John Sullivan, Clive Ronson, Rui Tian, Christine Munk, Cliff Han, T.B.K. Reddy, Rekha Seshadri, Tanja Woyke, Amrita Pati, Victor Markowitz, Natalia Ivanova and Nikos Kyrpides

    Citation: Standards in Genomic Sciences 2015 10:54

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  44. Content type: Short genome report

    An extremely halophilic archaeon, Haladaptatus cibarius D43T, was isolated from traditional Korean salt-rich fermented seafood. Strain D43T shows the highest 16S rRNA gene sequence similarity (98.7 %) with Halada...

    Authors: Hae-Won Lee, Dae-Won Kim, Mi-Hwa Lee, Byung-Yong Kim, Yong-Joon Cho, Kyung June Yim, Hye Seon Song, Jin-Kyu Rhee, Myung-Ji Seo, Hak-Jong Choi, Jong-Soon Choi, Dong-Gi Lee, Changmann Yoon, Young-Do Nam and Seong Woon Roh

    Citation: Standards in Genomic Sciences 2015 10:53

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  45. Content type: Short genome report

    Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the deg...

    Authors: Spyridon Ntougias, Alla Lapidus, Alex Copeland, T. B. K. Reddy, Amrita Pati, Natalia N. Ivanova, Victor M. Markowitz, Hans-Peter Klenk, Tanja Woyke, Constantinos Fasseas, Nikos C. Kyrpides and Georgios I. Zervakis

    Citation: Standards in Genomic Sciences 2015 10:52

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