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Table of Contents: PLoS ONE: Prokaryotic Genome Collection

COVER

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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

Research Articles

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

Ramy K. Aziz, Scott Devoid, Terrence Disz, Robert A. Edwards, Christopher S. Henry, Gary J. Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D. Pusch, Rick L. Stevens, Veronika Vonstein, Fangfang Xia

Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage

Patrick J. Biggs, Paul Fearnhead, Grant Hotter, Vathsala Mohan, Julie Collins-Emerson, Errol Kwan, Thomas E. Besser, Adrian Cookson, Philip E. Carter, Nigel P. French

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

Alexander Mellmann, Dag Harmsen, Craig A. Cummings, Emily B. Zentz, Shana R. Leopold, Alain Rico, Karola Prior, Rafael Szczepanowski, Yongmei Ji, Wenlan Zhang, Stephen F. McLaughlin, John K. Henkhaus, Benjamin Leopold, Martina Bielaszewska, Rita Prager, Pius M. Brzoska, Richard L. Moore, Simone Guenther, Jonathan M. Rothberg, Helge Karch

Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes

Iain Anderson, Carmen Scheuner, Markus Göker, Kostas Mavromatis, Sean D. Hooper, Iris Porat, Hans-Peter Klenk, Natalia Ivanova, Nikos Kyrpides

Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence

I-Hsuan Lin, Tze-Tze Liu, Yu-Ting Teng, Hui-Lun Wu, Yen-Ming Liu, Keh-Ming Wu, Chuan-Hsiung Chang, Ming-Ta Hsu

Helicobacter pylori from Peruvian Amerindians: Traces of Human Migrations in Strains from Remote Amazon, and Genome Sequence of an Amerind Strain

Dangeruta Kersulyte, Awdhesh Kalia, Robert H. Gilman, Melissa Mendez, Phabiola Herrera, Lilia Cabrera, Billie Velapatiño, Jacqueline Balqui, Freddy Paredes Puente de la Vega, Carlos A. Rodriguez Ulloa, Jaime Cok, Catherine C. Hooper, Giedrius Dailide, Sravya Tamma, Douglas E. Berg

The Arthrobacter arilaitensis Re117 Genome Sequence Reveals Its Genetic Adaptation to the Surface of Cheese

Christophe Monnet, Valentin Loux, Jean-François Gibrat, Eric Spinnler, Valérie Barbe, Benoit Vacherie, Frederick Gavory, Edith Gourbeyre, Patricia Siguier, Michaël Chandler, Rayda Elleuch, Françoise Irlinger, Tatiana Vallaeys

Genomic Analysis of Carbon Monoxide Utilization and Butanol Production by Clostridium carboxidivorans Strain P7T

Guillaume Bruant, Marie-Josée Lévesque, Chardeen Peter, Serge R. Guiot, Luke Masson

Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82

Sylvie Miquel, Eric Peyretaillade, Laurent Claret, Amélie de Vallée, Carole Dossat, Benoit Vacherie, El Hajji Zineb, Beatrice Segurens, Valerie Barbe, Pierre Sauvanet, Christel Neut, Jean-Frédéric Colombel, Claudine Medigue, Francisco J. M. Mojica, Pierre Peyret, Richard Bonnet, Arlette Darfeuille-Michaud

Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

Pradeep Reddy Marri, Mary Paniscus, Nathan J. Weyand, María A. Rendón, Christine M. Calton, Diana R. Hernández, Dustin L. Higashi, Erica Sodergren, George M. Weinstock, Steven D. Rounsley, Magdalene So

The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications

Hélène Falentin, Stéphanie-Marie Deutsch, Gwenaël Jan, Valentin Loux, Anne Thierry, Sandrine Parayre, Marie-Bernadette Maillard, Julien Dherbécourt, Fabien J. Cousin, Julien Jardin, Patricia Siguier, Arnaud Couloux, Valérie Barbe, Benoit Vacherie, Patrick Wincker, Jean-François Gibrat, Claude Gaillardin, Sylvie Lortal

The Genome of a Bacillus Isolate Causing Anthrax in Chimpanzees Combines Chromosomal Properties of B. cereus with B. anthracis Virulence Plasmids

Silke R. Klee, Elzbieta B. Brzuszkiewicz, Herbert Nattermann, Holger Brüggemann, Susann Dupke, Antje Wollherr, Tatjana Franz, Georg Pauli, Bernd Appel, Wolfgang Liebl, Emmanuel Couacy-Hymann, Christophe Boesch, Frauke-Dorothee Meyer, Fabian H. Leendertz, Heinz Ellerbrok, Gerhard Gottschalk, Roland Grunow, Heiko Liesegang

Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium

Liang Ran, John Larsson, Theoden Vigil-Stenman, Johan A. A. Nylander, Karolina Ininbergs, Wei-Wen Zheng, Alla Lapidus, Stephen Lowry, Robert Haselkorn, Birgitta Bergman

The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes

Phatthanaphong Wanchanthuek, Matthew I. Bellgard, Tom La, Karon Ryan, Paula Moolhuijzen, Brett Chapman, Michael Black, David Schibeci, Adam Hunter, Roberto Barrero, Nyree D. Phillips, David J. Hampson

De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads

Harish Nagarajan, Jessica E. Butler, Anna Klimes, Yu Qiu, Karsten Zengler, Joy Ward, Nelson D. Young, Barbara A. Methé, Bernhard Ø. Palsson, Derek R. Lovley, Christian L. Barrett

The Waddlia Genome: A Window into Chlamydial Biology

Claire Bertelli, François Collyn, Antony Croxatto, Christian Rückert, Adam Polkinghorne, Carole Kebbi-Beghdadi, Alexander Goesmann, Lloyd Vaughan, Gilbert Greub

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments

Paul J. Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed A. Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue, Safiyh Taghavi, Sean McCorkle, John Dunn, Daniël van der Lelie, Max Mergeay

One Bacterial Cell, One Complete Genome

Tanja Woyke, Damon Tighe, Konstantinos Mavromatis, Alicia Clum, Alex Copeland, Wendy Schackwitz, Alla Lapidus, Dongying Wu, John P. McCutcheon, Bradon R. McDonald, Nancy A. Moran, James Bristow, Jan-Fang Cheng

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

Athanasios Lykidis, Danilo Pérez-Pantoja, Thomas Ledger, Kostantinos Mavromatis, Iain J. Anderson, Natalia N. Ivanova, Sean D. Hooper, Alla Lapidus, Susan Lucas, Bernardo González, Nikos C. Kyrpides

Genome Sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species

Eva Kucerova, Sandra W. Clifton, Xiao-Qin Xia, Fred Long, Steffen Porwollik, Lucinda Fulton, Catrina Fronick, Patrick Minx, Kim Kyung, Wesley Warren, Robert Fulton, Dongyan Feng, Aye Wollam, Neha Shah, Veena Bhonagiri, William E. Nash, Kymberlie Hallsworth-Pepin, Richard K. Wilson, Michael McClelland, Stephen J. Forsythe

The Genome of Streptococcus mitis B6 - What Is a Commensal?

Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, Rolf Wambutt, Regine Hakenbeck

Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp. tularensis A1 and Schu S4

Ufuk Nalbantoglu, Khalid Sayood, Michael P. Dempsey, Peter C. Iwen, Stephen C. Francesconi, Ravi D. Barabote, Gary Xie, Thomas S. Brettin, Steven H. Hinrichs, Paul D. Fey

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The Complete Genome Sequence and Analysis of the Epsilonproteobacterium Arcobacter butzleri

William G. Miller, Craig T. Parker, Marc Rubenfield, George L. Mendz, Marc M. S. M. Wösten, David W. Ussery, John F. Stolz, Tim T. Binnewies, Peter F. Hallin, Guilin Wang, Joel A. Malek, Andrea Rogosin, Larry H. Stanker, Robert E. Mandrell

Molecular Correlates of Host Specialization in Staphylococcus aureus

Lisa Herron-Olson, J. Ross Fitzgerald, James M. Musser, Vivek Kapur