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PLoS ONE: Prokaryotic Genome Collection

The PLoS ONE Prokaryotic Genome Collection is an attempt to present and highlight a number of important articles that describe whole genome sequence and/or comparative genomics of important prokaryotic organisms. We believe that this collection will be able to facilitate understanding of the biology and lifestyle of the underlying organisms not only through the content of the Research Articles, but also from the external information sources which are linked to from the original articles.

Editorial oversight and coordination of the peer-review for most of the articles was provided by Niyaz Ahmed, PLoS ONE Section Editor for Genomics and Microbiology. Articles are presented in order of publication date and new articles will be added to the collection as they are published. We welcome submissions in this field.

Image Credit: William G. Miller (see Miller et al., doi:10.1371/journal.pone.0001358).

Overview Top

A Flood of Microbial Genomes–Do We Need More?

Niyaz Ahmed

PLoS ONE:
Published 09 Jun 2009 | info:doi/10.1371/journal.pone.0005831

Research Articles Top

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

Sinead C. Leahy, William J. Kelly, Eric Altermann, Ron S. Ronimus, Carl J. Yeoman, Diana M. Pacheco, Dong Li, Zhanhao Kong, Sharla McTavish, Carrie Sang, Suzanne C. Lambie, Peter H. Janssen, Debjit Dey, Graeme T. Attwood

PLoS ONE: published 28 Jan 2010 | info:doi/10.1371/journal.pone.0008926

Complete Genome Sequence of the Multiresistant Taxonomic Outlier Pseudomonas aeruginosa PA7

Paul H. Roy, Sasha G. Tetu, André Larouche, Liam Elbourne, Simon Tremblay, Qinghu Ren, Robert Dodson, Derek Harkins, Ryan Shay, Kisha Watkins, Yasmin Mahamoud, Ian T. Paulsen

PLoS ONE:
Published 22 Jan 2010 | info:doi/10.1371/journal.pone.0008842

Complete Genome Sequence and Comparative Metabolic Profiling of the Prototypical Enteroaggregative Escherichia coli Strain 042

Roy R. Chaudhuri, Mohammed Sebaihia, Jon L. Hobman, Mark A. Webber, Denisse L. Leyton, Martin D. Goldberg, Adam F. Cunningham, Anthony Scott-Tucker, Paul R. Ferguson, Christopher M. Thomas, Gad Frankel, Christoph M. Tang, Edward G. Dudley, Ian S. Roberts, David A. Rasko, Mark J. Pallen, Julian Parkhill, James P. Nataro, Nicholas R. Thomson, Ian R. Henderson

PLoS ONE:
Published 20 Jan 2010 | info:doi/10.1371/journal.pone.0008801

Genome Sequence of the Endosymbiont Rickettsia peacockii and Comparison with Virulent Rickettsia rickettsii: Identification of Virulence Factors

Roderick F. Felsheim, Timothy J. Kurtti, Ulrike G. Munderloh

PLoS ONE:
Published 21 Dec 2009 | info:doi/10.1371/journal.pone.0008361

Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches

Qiyao Wang, Minjun Yang, Jingfan Xiao, Haizhen Wu, Xin Wang, Yuanzhi Lv, Lili Xu, Huajun Zheng, Shengyue Wang, Guoping Zhao, Qin Liu, Yuanxing Zhang

PLoS ONE:
Published 29 Oct 2009 | info:doi/10.1371/journal.pone.0007646

Complete Genome Sequence of Francisella tularensis Subspecies holarctica FTNF002-00

Ravi D. Barabote, Gary Xie, Thomas S. Brettin, Steven H. Hinrichs, Paul D. Fey, Justin J. Jay, Jennifer L. Engle, Shubhada D. Godbole, Jyothi M. Noronha, Richard H. Scheuermann, Liwei W. Zhou, Christine Lion, Michael P. Dempsey

PLoS ONE:
Published 16 Sep 2009 | info:doi/10.1371/journal.pone.0007041

Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

Margret E. Berg Miller, Dionysios A. Antonopoulos, Marco T. Rincon, Mark Band, Albert Bari, Tatsiana Akraiko, Alvaro Hernandez, Jyothi Thimmapuram, Bernard Henrissat, Pedro M. Coutinho, Ilya Borovok, Sadanari Jindou, Raphael Lamed, Harry J. Flint, Edward A. Bayer, Bryan A. White

PLoS ONE:
Published 14 Aug 2009 | info:doi/10.1371/journal.pone.0006650

The Complete Genome of Teredinibacter turnerae T7901: An Intracellular Endosymbiont of Marine Wood-Boring Bivalves (Shipworms)

Joyce C. Yang, Ramana Madupu, A. Scott Durkin, Nathan A. Ekborg, Chandra S. Pedamallu, Jessica B. Hostetler, Diana Radune, Bradley S. Toms, Bernard Henrissat, Pedro M. Coutinho, Sandra Schwarz, Lauren Field, Amaro E. Trindade-Silva, Carlos A. G. Soares, Sherif Elshahawi, Amro Hanora, Eric W. Schmidt, Margo G. Haygood, Janos Posfai, Jack Benner, Catherine Madinger, John Nove, Brian Anton, Kshitiz Chaudhary, Jeremy Foster, Alex Holman, Sanjay Kumar, Philip A. Lessard, Yvette A. Luyten, Barton Slatko, Nicole Wood, Bo Wu, Max Teplitski, Joseph D. Mougous, Naomi Ward, Jonathan A. Eisen, Jonathan H. Badger, Daniel L. Distel

PLoS ONE:
Published 01 Jul 2009 | info:doi/10.1371/journal.pone.0006085

Non Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus

Fabienne Ripoll, Sophie Pasek, Chantal Schenowitz, Carole Dossat, Valérie Barbe, Martin Rottman, Edouard Macheras, Beate Heym, Jean-Louis Herrmann, Mamadou Daffé, Roland Brosch, Jean-Loup Risler, Jean-Louis Gaillard

PLoS ONE:
Published 19 Jun 2009 | info:doi/10.1371/journal.pone.0005660

Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

Iain Anderson, Luke E. Ulrich, Boguslaw Lupa, Dwi Susanti, Iris Porat, Sean D. Hooper, Athanasios Lykidis, Magdalena Sieprawska-Lupa, Lakshmi Dharmarajan, Eugene Goltsman, Alla Lapidus, Elizabeth Saunders, Cliff Han, Miriam Land, Susan Lucas, Biswarup Mukhopadhyay, William B. Whitman, Carl Woese, James Bristow, Nikos Kyrpides

PLoS ONE:
Published 04 Jun 2009 | info:doi/10.1371/journal.pone.0005797

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Stéphane Vuilleumier, Ludmila Chistoserdova, Ming-Chun Lee, Françoise Bringel, Aurélie Lajus, Yang Zhou, Benjamin Gourion, Valérie Barbe, Jean Chang, Stéphane Cruveiller, Carole Dossat, Will Gillett, Christelle Gruffaz, Eric Haugen, Edith Hourcade, Ruth Levy, Sophie Mangenot, Emilie Muller, Thierry Nadalig, Marco Pagni, Christian Penny, Rémi Peyraud, David G. Robinson, David Roche, Zoé Rouy, Channakhone Saenampechek, Grégory Salvignol, David Vallenet, Zaining Wu, Christopher J. Marx, Julia A. Vorholt, Maynard V. Olson, Rajinder Kaul, Jean Weissenbach, Claudine Médigue, Mary E. Lidstrom

PLoS ONE:
Published 18 May 2009 | info:doi/10.1371/journal.pone.0005584

Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism

Renee M. Tsolis, Rekha Seshadri, Renato L. Santos, Felix J. Sangari, Juan M. García Lobo, Maarten F. de Jong, Qinghu Ren, Garry Myers, Lauren M. Brinkac, William C. Nelson, Robert T. DeBoy, Samuel Angiuoli, Hoda Khouri, George Dimitrov, Jeffrey R. Robinson, Stephanie Mulligan, Richard L. Walker, Philip E. Elzer, Karl A. Hassan, Ian T. Paulsen

PLoS ONE:
Published 13 May 2009 | info:doi/10.1371/journal.pone.0005519

Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira hyodysenteriae Reveals Adaptations to Its Lifestyle in the Porcine Large Intestine

Matthew I. Bellgard, Phatthanaphong Wanchanthuek, Tom La, Karon Ryan, Paula Moolhuijzen, Zayed Albertyn, Babak Shaban, Yair Motro, David S. Dunn, David Schibeci, Adam Hunter, Roberto Barrero, Nyree D. Phillips, David J. Hampson

PLoS ONE:
Published 05 Mar 2009 | info:doi/10.1371/journal.pone.0004641

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

Dongying Wu, Jason Raymond, Martin Wu, Sourav Chatterji, Qinghu Ren, Joel E. Graham, Donald A. Bryant, Frank Robb, Albert Colman, Luke J. Tallon, Jonathan H. Badger, Ramana Madupu, Naomi L. Ward, Jonathan A. Eisen

PLoS ONE:
Published 16 Jan 2009 | info:doi/10.1371/journal.pone.0004207

Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii

Konstantinos Mavromatis, Natalia Ivanova, Iain Anderson, Athanasios Lykidis, Sean D. Hooper, Hui Sun, Victor Kunin, Alla Lapidus, Philip Hugenholtz, Bharat Patel, Nikos C. Kyrpides

PLoS ONE:
Published 15 Jan 2009 | info:doi/10.1371/journal.pone.0004192

Survival in Nuclear Waste, Extreme Resistance, and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216

Christopher E. Bagwell, Swapna Bhat, Gary M. Hawkins, Bryan W. Smith, Tapan Biswas, Timothy R. Hoover, Elizabeth Saunders, Cliff S. Han, Oleg V. Tsodikov, Lawrence J. Shimkets

PLoS ONE:
Published 05 Dec 2008 | info:doi/10.1371/journal.pone.0003878

Genome Sequence of a Lancefield Group C Streptococcus zooepidemicus Strain Causing Epidemic Nephritis: New Information about an Old Disease

Stephen B. Beres, Ricardo Sesso, Sergio Wyton L. Pinto, Nancy P. Hoe, Stephen F. Porcella, Frank R. DeLeo, James M. Musser

PLoS ONE:
Published 21 Aug 2008 | info:doi/10.1371/journal.pone.0003026

Genome Sequence of Brucella abortus Vaccine Strain S19 Compared to Virulent Strains Yields Candidate Virulence Genes

Oswald R. Crasta, Otto Folkerts, Zhangjun Fei, Shrinivasrao P. Mane, Clive Evans, Susan Martino-Catt, Betsy Bricker, GongXin Yu, Lei Du, Bruno W. Sobral

PLoS ONE:
Published 14 May 2008 | info:doi/10.1371/journal.pone.0002193

The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria

Sara H. Thomas, Ryan D. Wagner, Adrian K. Arakaki, Jeffrey Skolnick, John R. Kirby, Lawrence J. Shimkets, Robert A. Sanford, Frank E. Löffler

PLoS ONE:
Published 07 May 2008 | info:doi/10.1371/journal.pone.0002103

Characterization of Clinically-Attenuated Burkholderia mallei by Whole Genome Sequencing: Candidate Strain for Exclusion from Select Agent Lists

Steven E. Schutzer, Linda R. K. Schlater, Catherine M. Ronning, David DeShazer, Benjamin J. Luft, John J. Dunn, Jacques Ravel, Claire M. Fraser-Liggett, William C. Nierman

PLoS ONE:
Published 30 Apr 2008 | info:doi/10.1371/journal.pone.0002058

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

David Vallenet, Patrice Nordmann, Valérie Barbe, Laurent Poirel, Sophie Mangenot, Elodie Bataille, Carole Dossat, Shahinaz Gas, Annett Kreimeyer, Patricia Lenoble, Sophie Oztas, Julie Poulain, Béatrice Segurens, Catherine Robert, Chantal Abergel, Jean-Michel Claverie, Didier Raoult, Claudine Médigue, Jean Weissenbach, Stéphane Cruveiller

PLoS ONE:
Published 19 Mar 2008 | info:doi/10.1371/journal.pone.0001805

Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis

Mathieu Picardeau, Dieter M. Bulach, Christiane Bouchier, Richard L. Zuerner, Nora Zidane, Peter J. Wilson, Sophie Creno, Elizabeth S. Kuczek, Simona Bommezzadri, John C. Davis, Annette McGrath, Matthew J. Johnson, Caroline Boursaux-Eude, Torsten Seemann, Zoé Rouy, Ross L. Coppel, Julian I. Rood, Aurélie Lajus, John K. Davies, Claudine Médigue, Ben Adler

PLoS ONE:
Published 13 Feb 2008 | info:doi/10.1371/journal.pone.0001607

Genome Biology of Actinobacillus pleuropneumoniae JL03, an Isolate of Serotype 3 Prevalent in China

Zhuofei Xu, Yan Zhou, Liangjun Li, Rui Zhou, Shaobo Xiao, Yun Wan, Sihua Zhang, Kai Wang, Wei Li, Lu Li, Hui Jin, Mingsong Kang, Baolige Dalai, Tingting Li, Lei Liu, Yangyi Cheng, Lei Zhang, Tao Xu, Huajun Zheng, Shiying Pu, Bofei Wang, Wenyi Gu, Xiang-Lin Zhang, Geng-Feng Zhu, Shengyue Wang, Guo-Ping Zhao, Huanchun Chen

PLoS ONE:
Published 16 Jan 2008 | info:doi/10.1371/journal.pone.0001450