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  1. Content type: Short genome report

    Members of the genus Geobacillus have been isolated from a wide variety of habitats worldwide and are the subject for targeted enzyme utilization in various industrial applications. Here we report the isolation a...

    Authors: Juliane Wissuwa, Runar Stokke, Anita-Elin Fedøy, Kjersti Lian, Arne Oskar Smalås and Ida Helene Steen

    Citation: Standards in Genomic Sciences 2016 11:16

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  2. Content type: Short genome report

    Sphingomonas paucimobilis strain LCT-SP1 is a glucose-nonfermenting Gram-negative, chemoheterotrophic, strictly aerobic bacterium. The major feature of strain LCT-SP1, isolated from the C...

    Authors: Lei Pan, Hong Zhou, Jia Li, Bing Huang, Jun Guo, Xue-Lin Zhang, Long-Cheng Gao, Chou Xu and Chang-Ting Liu

    Citation: Standards in Genomic Sciences 2016 11:18

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  3. Content type: Standard operating procedure

    The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) syst...

    Authors: Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, H. James Tripp, David Paez-Espino, Kristin Tennessen, 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 2016 11:17

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  4. Content type: Meeting report

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes fro...

    Authors: Scott Federhen, Ramon Rossello-Mora, Hans-Peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel Brown, David Labeda, David Ussery, George M. Garrity, Rita R. Colwell, Nur Hasan, Joerg Graf, Aidan Parte, Pablo Yarza, Brittany Goldberg…

    Citation: Standards in Genomic Sciences 2016 11:15

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  5. Content type: Short genome report

    Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of...

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

    Citation: Standards in Genomic Sciences 2016 11:14

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  6. Content type: Extended genome report

    The cyanobacterial genus Microcystis is well known as the main group that forms harmful blooms in water. A strain of Microcystis, M. panniformis FACHB1757, was isolated from Meiliang Bay of Lake Taihu in August 2...

    Authors: Jun-Yi Zhang, Rui Guan, Hu-Jun Zhang, Hua Li, Peng Xiao, Gong-Liang Yu, Lei Du, De-Min Cao, Bing-Chuan Zhu, Ren-Hui Li and Zu-Hong Lu

    Citation: Standards in Genomic Sciences 2016 11:11

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  7. Content type: Short genome report

    Xanthomonas arboricola is a species in genus Xanthomonas which is mainly comprised of plant pathogens. Among the members of this taxon, X. arboricola pv. pruni, the causal agent of bacter...

    Authors: Jerson Garita-Cambronero, Ana Palacio-Bielsa, María M. López and Jaime Cubero

    Citation: Standards in Genomic Sciences 2016 11:12

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  8. Content type: Short genome report

    Avian pathogenic Escherichia coli is an important etiological agent of avian colibacillosis, which manifests as respiratory, hematogenous, meningitic, and enteric infections in poultry. It is also a potential zoo...

    Authors: Xiangru Wang, Liuya Wei, Bin Wang, Ruixuan Zhang, Canying Liu, Dingren Bi, Huanchun Chen and Chen Tan

    Citation: Standards in Genomic Sciences 2016 11:13

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  9. Content type: Short genome report

    Paenibacillus sp. strain A2 is a Gram-negative rod-shaped bacterium isolated from a mixture of formation water and petroleum in Daqing oilfield, China. This facultative aerobic bacterium ...

    Authors: Beiwen Zheng, Fan Zhang, Hao Dong, Lujun Chai, Fuchang Shu, Shaojin Yi, Zhengliang Wang, Qingfeng Cui, Hanping Dong, Zhongzhi Zhang, Dujie Hou, Jinshui Yang and Yuehui She

    Citation: Standards in Genomic Sciences 2016 11:9

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  10. Content type: Short genome report

    The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the Arabidopsis thaliana phyllosphere. Here we describe the general physiological features of this microorganism together with the d...

    Authors: Hannes Horn, Alexander Keller, Ulrich Hildebrandt, Peter Kämpfer, Markus Riederer and Ute Hentschel

    Citation: Standards in Genomic Sciences 2016 11:8

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  11. Content type: Short genome report

    Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3...

    Authors: Rodrigo Guarischi-Sousa, Marina Puigvert, Núria S. Coll, María Inés Siri, María Julia Pianzzola, Marc Valls and João C. Setubal

    Citation: Standards in Genomic Sciences 2016 11:7

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  12. Content type: Short genome report

    Propionibacterium freudenreichii belongs to the class Actinobacteria (Gram positive with a high GC content). This “Generally Recognized As Safe” (GRAS) species is traditionally used as (i...

    Authors: Hélène Falentin, Stéphanie-Marie Deutsch, Valentin Loux, Amal Hammani, Julien Buratti, Sandrine Parayre, Victoria Chuat, Valérie Barbe, Jean-Marc Aury, Gwenaël Jan and Yves Le Loir

    Citation: Standards in Genomic Sciences 2016 11:6

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  13. Content type: Short genome report

    The Pseudomonas fluorescens strain UM270 was isolated form the rhizosphere of wild Medicago spp. A previous work has shown that this pseudomonad isolate was able to produce diverse diffusible and volatile compoun...

    Authors: Julie E. Hernández-Salmerón, Rocio Hernández-León, Ma. Del Carmen Orozco-Mosqueda, Eduardo Valencia-Cantero, Gabriel Moreno-Hagelsieb and Gustavo Santoyo

    Citation: Standards in Genomic Sciences 2016 11:5

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  14. Content type: Short genome report

    This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravel...

    Authors: Dwi Susanti, Eric F. Johnson, Alla Lapidus, James Han, T. B. K. Reddy, Manoj Pilay, Natalia N. Ivanova, Victor M. Markowitz, Tanja Woyke, Nikos C. Kyrpides and Biswarup Mukhopadhyay

    Citation: Standards in Genomic Sciences 2016 11:3

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  15. Content type: Short genome report

    Phaseolibacter flectens strain ATCC 12775T (Halpern et al., Int J Syst Evol Microbiol 63:268–273, 2013) is a Gram-negative, rod shaped, motile, aerobic, chemoorganotroph bacterium. Ph. fl...

    Authors: Yana Aizenberg-Gershtein, Ido Izhaki, Alla Lapidus, Alex Copeland, TBK Reddy, Marcel Huntemann, Manoj Pillay, Victor Markowitz, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Nikos C. Kyrpides and Malka Halpern

    Citation: Standards in Genomic Sciences 2016 11:4

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  16. Content type: Short genome report

    Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type species of the genus Methanospirillum, which belongs to the family Methanospirillaceae withi...

    Authors: Robert P. Gunsalus, Lauren E. Cook, Bryan Crable, Lars Rohlin, Erin McDonald, Housna Mouttaki, Jessica R. Sieber, Nicole Poweleit, Hong Zhou, Alla L. Lapidus, Hajnalka Erzsebet Daligault, Miriam Land, Paul Gilna, Natalia Ivanova, Nikos Kyrpides, David E. Culley…

    Citation: Standards in Genomic Sciences 2016 11:2

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  17. Content type: Short genome report

    Myxobacteria, phylogenetically located in the delta division of the Proteobacteria, are well known for characterized social behaviors and large genomes of more than 9 Mb in size. Myxococcus fulvus is a typical sp...

    Authors: Xiao-jing Chen, Kui Han, Jing Feng, Li Zhuo, Ya-jie Li and Yue-zhong Li

    Citation: Standards in Genomic Sciences 2016 11:1

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  18. Content type: Short genome report

    Escherichia coli lab strains K-12 GM4792 Lac+ and GM4792 Lac- carry opposite lactose markers, which are useful for distinguishing evolved lines as they produce different colored colonies....

    Authors: Yan-Cong Zhang, Yan Zhang, Bi-Ru Zhu, Bo-Wen Zhang, Chuan Ni, Da-Yong Zhang, Ying Huang, Erli Pang and Kui Lin

    Citation: Standards in Genomic Sciences 2015 10:125

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  19. Content type: Short genome report

    Halopiger salifodinae strain KCY07-B2T, isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic,...

    Authors: Wei-Yan Zhang, Jing Hu, Jie Pan, Cong Sun, Min Wu and Xue-Wei Xu

    Citation: Standards in Genomic Sciences 2015 10:124

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  20. Content type: Short genome report

    Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolate...

    Authors: Julie Ardley, Rui Tian, Graham O’Hara, Rekha Seshadri, T. B. K. Reddy, Amrita Pati, Tanja Woyke, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, John Howieson and Wayne Reeve

    Citation: Standards in Genomic Sciences 2015 10:126

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  21. Content type: Short genome report

    Bacillus subtilis LM 4–2, a Gram-positive bacterium was isolated from a molybdenum mine in Luoyang city. Due to its strong resistance to molybdate and potential utilization in bioremediat...

    Authors: Xiao-Yan You, Hui Wang, Guang-Yue Ren, Jing-Jing Li, Xu Duan, Hua-Jun Zheng and Zheng-Qiang Jiang

    Citation: Standards in Genomic Sciences 2015 10:127

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  22. Content type: Short genome report

    A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the ...

    Authors: Stepan V. Toshchakov, Aleksei A. Korzhenkov, Nazar I. Samarov, Ilia O. Mazunin, Oleg I. Mozhey, Ilya S. Shmyr, Ksenia S. Derbikova, Evgeny A. Taranov, Irina N. Dominova, Elizaveta A. Bonch-Osmolovskaya, Maxim V. Patrushev, Olga A. Podosokorskaya and Ilya V. Kublanov

    Citation: Standards in Genomic Sciences 2015 10:122

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  23. Content type: Short genome report

    Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type strain of L. dokdonensis. In this...

    Authors: Min-Jung Kwak, Soon-Kyeong Kwon, Jung-Hoon Yoon and Jihyun F. Kim

    Citation: Standards in Genomic Sciences 2015 10:123

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  24. Content type: Short genome report

    Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N2-fixing microsymbiont of white clover (Trifolium repens L.). The bacterium has been widely used in both Austral...

    Authors: Clément Delestre, Aurélie Laugraud, Hayley Ridgway, Clive Ronson, Maureen O’Callaghan, Brent Barrett, Ross Ballard, Andrew Griffiths, Sandra Young, Celine Blond, Emily Gerard and Steve Wakelin

    Citation: Standards in Genomic Sciences 2015 10:121

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  25. Content type: Short genome report

    Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in France, using a new culture medium. It is an aerobic microorganism with optimal growth at pH...

    Authors: Rita Aghnatios, Caroline Cayrou, Marc Garibal, Catherine Robert, Said Azza, Didier Raoult and Michel Drancourt

    Citation: Standards in Genomic Sciences 2015 10:120

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  26. Content type: Extended genome report

    Strain GSS01T (=KCTC 4545=MCCC 1 K00269) is the type strain of the species Geobacter soli. G. soli strain GSS01T is of interest due to its ability to reduce insoluble Fe(III) oxides with a wide range of electron ...

    Authors: Guiqin Yang, Shanshan Chen, Shungui Zhou and Yongfeng Liu

    Citation: Standards in Genomic Sciences 2015 10:118

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  27. Content type: Meeting report

    Next-generation sequencing (NGS) is not routinely used in applied settings due to lack of confidence in results. This workshop convened experts to identify measurement challenges impeding NGS implementation an...

    Authors: Nathan D. Olson, Scott A. Jackson and Nancy J. Lin

    Citation: Standards in Genomic Sciences 2015 10:119

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  28. Content type: Short genome report

    Strain UFB2 was isolated from a soybean field soil in Mississippi and identified as a member of Pseudomonas chlororaphis. Strain UFB2 has a broad-spectrum antimicrobial activity against common soil-borne pathogen...

    Authors: Peng Deng, Xiaoqiang Wang, Sonya M. Baird and Shi-En Lu

    Citation: Standards in Genomic Sciences 2015 10:117

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  29. Content type: Meeting report

    In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computatio...

    Authors: Shakuntala Baichoo, Gerrit Botha, Yasmina Jaufeerally-Fakim, Zahra Mungloo-Dilmohamud, Daniel Lundin, Nicola Mulder, Vasilis J. Promponas and Christos A. Ouzounis

    Citation: Standards in Genomic Sciences 2015 10:115

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  30. Content type: Short genome report

    Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos....

    Authors: Ravi Tiwari, John Howieson, Ron Yates, Rui Tian, Britanny Held, Roxanne Tapia, Cliff Han, Rekha Seshadri, T. B. K. Reddy, Marcel Huntemann, Amrita Pati, Tanja Woyke, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides and Wayne Reeve

    Citation: Standards in Genomic Sciences 2015 10:113

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  31. Content type: Extended genome report

    Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment with antimicrobial and antitumor properties. Janthinobacterium lividum colonizes the skin of so...

    Authors: Natalia Valdes, Paola Soto, Luis Cottet, Paula Alarcon, Alex Gonzalez, Antonio Castillo, Gino Corsini and Mario Tello

    Citation: Standards in Genomic Sciences 2015 10:110

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  32. Content type: Short genome report

    Bacteriophage P26218 is a virus that thrives in freshwater and infects Rhodoferax sp. strain IMCC26218, both of which were isolated from Soyang Lake, Korea. The bacterial host, IMCC26218, belongs to the genus Rho...

    Authors: Kira Moon, Ilnam Kang, Suhyun Kim, Jang-Cheon Cho and Sang-Jong Kim

    Citation: Standards in Genomic Sciences 2015 10:111

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  33. Content type: Extended genome report

    We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists o...

    Authors: Saima Zubair, Anne Fischer, Anne Liljander, Jochen Meens, Jan Hegerman, Hadrien Gourlé, Richard P. Bishop, Ina Roebbelen, Mario Younan, Mudassir Imran Mustafa, Mamoona Mushtaq, Erik Bongcam-Rudloff and Joerg Jores

    Citation: Standards in Genomic Sciences 2015 10:109

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  34. Content type: Extended genome report

    Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest so...

    Authors: Andrew F. Billings, Julian L. Fortney, Terry C. Hazen, Blake Simmons, Karen W. Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke and Kristen M. DeAngelis

    Citation: Standards in Genomic Sciences 2015 10:106

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  35. Content type: Commentary

    The function annotation process in computational biology has increasingly shifted from the traditional characterization of individual biochemical roles of protein molecules to the system-wide detection of enti...

    Authors: Vasilis J. Promponas, Ioannis Iliopoulos and Christos A. Ouzounis

    Citation: Standards in Genomic Sciences 2015 10:108

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  36. Content type: Short genome report

    Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae. According to the phylogenetic analysis based on 16S rRNA gene sequence of the N. pentaromativorans U...

    Authors: Dong Hee Choi, Yong Min Kwon, Kae Kyoung Kwon and Sang-Jin Kim

    Citation: Standards in Genomic Sciences 2015 10:107

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  37. Content type: Short genome report

    Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkalin...

    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 10:105

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  38. Content type: Short genome report

    Most Cellulomonas strains are cellulolytic and this feature may be applied in straw degradation and bioremediation. In this study, Cellulomonas carbonis T26T, Cellulomonas bogoriensis DSM 16987T and Cellulomonas ...

    Authors: Weiping Zhuang, Shengzhe Zhang, Xian Xia and Gejiao Wang

    Citation: Standards in Genomic Sciences 2015 10:104

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  39. 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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  40. Content type: Extended genome report

    Strain K22T is the type species of the recently- described genus Pyrinomonas, in subdivision 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014; 64(1):220–7). It was isolated from geothermally-heated soil ...

    Authors: Kevin C. Y. Lee, Xochitl C. Morgan, Jean F. Power, Peter F. Dunfield, Curtis Huttenhower and Matthew B. Stott

    Citation: Standards in Genomic Sciences 2015 10:101

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  41. Content type: Short genome report

    A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl c...

    Authors: Yoshihito Uchino, Takamasa Miura, Akira Hosoyama, Shoko Ohji, Atsushi Yamazoe, Masako Ito, Yoh Takahata, Ken-ichiro Suzuki and Nobuyuki Fujita

    Citation: Standards in Genomic Sciences 2015 10:102

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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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