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1. Biological and Environmental Research Network Requirements Review Final Report

Author

Zurawski, Jason, Dart, eli, Harlan, Zach, Hawk, Carol, Hess, John, Hnilo, Justin, MacAuley, John, Madupu, Ramana, Miller, Ken, Tracy, Chris, and Wiedlea, Andrew

Abstract

The Energy Sciences Network (ESnet) is the high-performance network user facility for the US Department of Energy (DOE) Office of Science (SC) and delivers highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the DOE science mission by connecting all its laboratories and facilities in the US and abroad. ESnet is funded and stewardedby the Advanced Scientific Computing Research (ASCR) program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education (R&E) networking community.Between August 2022 and April 2023, ESnet and the Office of Biological and Environmental Research (BER) of the DOE SC organized an ESnet requirements review of BER-supported activities. Preparation for these events included identification of key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare formal case study documents about its relationshipto the BER ESS program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward. A series of pre-planning meetings better prepared case study authors for this task, along with guidance on how the review would proceed in a virtual fashion.

Published
2023

3. Co-occurrence of Anaerobes in Human Chronic Wounds

Author

Choi, Yongwook, Banerjee, Anirban, McNish, Sean, Couch, Kara S., Torralba, Manolito G., Lucas, Sarah, Tovchigrechko, Andrey, Madupu, Ramana, Yooseph, Shibu, Nelson, Karen E., Shanmugam, Victoria K., and Chan, Agnes P.

Published
2019

4. Biological and Environmental Research Network Requirements Review 2015 - Final Report:

Author

Dart, Eli, Bell, Greg, Benton, David, Canon, Shane, Cowley, David, Dattoria, Vince, Fagnan
, Kjiersten, Foster, Ian, Giuntoli, Patricia, Hester, Mary, Hettich, Robert, Hnilo, Jay, Howe, Adina, Jacob, Robert, Jacobsen, Daniel, Love, Lisa, Madupu, Ramana, Metzger, Joseph, Palinisamy, Giri, Rabinowicz, Pablo, Rotman, Lauren, Sears, Robert, Strand, Gary, Wehner, Michael, Williams, Dean, and Zurawski, Jason

Abstract

The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 25 years. In September 2015, ESnet and the Office of Biological and Environmental Research (BER), of the DOE Office of Science, organized a review to characterize the networking requirements of the programs funded by the BER program office. BER advances world-class biological and environmental research programs and scientific user facilities to support DOE’s energy, environment, and basic research missions. This report of the review contains a Findings section and documents Case Studies discussed during the Requirements Review.

Published
2015

5. Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae)

Author

Bhatnagar, Srijak, Badger, Jonathan H, Madupu, Ramana, Khouri, Hoda M, O’Connor, Elizabeth M, Robb, Frank T, Ward, Naomi L, and Eisen, Jonathan A

Subjects
Microbiology, Biological Sciences, Genetics, Biochemistry and Cell Biology
Abstract

Here, we present the complete 2,003,803-bp genome of a sulfate-reducing thermophilic bacterium, Thermodesulfovibrio yellowstonii strain DSM 11347(T).

Published
2015

6. Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria)

Author

Bhatnagar, Srijak, Badger, Jonathan H, Madupu, Ramana, Khouri, Hoda M, O’Connor, Elizabeth M, Robb, Frank T, Ward, Naomi L, and Eisen, Jonathan A

Subjects
Microbiology, Biological Sciences, Genetics, Biochemistry and Cell Biology
Abstract

Here, we present the complete genome sequence of Thermodesulfobacterium commune DSM 2178(T) of the phylum Thermodesulfobacteria.

Published
2015

7. Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.

Author

Ma, Yingfei, Madupu, Ramana, Karaoz, Ulas, Nossa, Carlos W, Yang, Liying, Yooseph, Shibu, Yachimski, Patrick S, Brodie, Eoin L, Nelson, Karen E, and Pei, Zhiheng

Subjects
Humans, Papillomaviridae, Papillomavirus Infections, Prevalence, Sequence Analysis, DNA, Female, Metagenomics, Coinfection, Healthy Volunteers, Microbiota, Clinical Research, Cervical Cancer, HIV/AIDS, Cancer, Infectious Diseases, Sexually Transmitted Infections, Aetiology, 2.2 Factors relating to the physical environment, Infection, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology
Abstract

UnlabelledHuman papillomavirus (HPV) causes a number of neoplastic diseases in humans. Here, we show a complex normal HPV community in a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data generated from the NIH Human Microbiome Project. The overall HPV prevalence was 68.9% and was highest in the skin (61.3%), followed by the vagina (41.5%), mouth (30%), and gut (17.3%). Of the 109 HPV types as well as additional unclassified types detected, most were undetectable by the widely used commercial kits targeting the vaginal/cervical HPV types. These HPVs likely represent true HPV infections rather than transitory exposure because of strong organ tropism and persistence of the same HPV types in repeat samples. Coexistence of multiple HPV types was found in 48.1% of the HPV-positive samples. Networking between HPV types, cooccurrence or exclusion, was detected in vaginal and skin samples. Large contigs assembled from short HPV reads were obtained from several samples, confirming their genuine HPV origin. This first large-scale survey of HPV using a shotgun sequencing approach yielded a comprehensive map of HPV infections among different body sites of healthy human subjects.ImportanceThis nonbiased survey indicates that the HPV community in healthy humans is much more complex than previously defined by widely used kits that are target selective for only a few high- and low-risk HPV types for cervical cancer. The importance of nononcogenic viruses in a mixed HPV infection could be for stimulating or inhibiting a coexisting oncogenic virus via viral interference or immune cross-reaction. Knowledge gained from this study will be helpful to guide the designing of epidemiological and clinical studies in the future to determine the impact of nononcogenic HPV types on the outcome of HPV infections.

Published
2014

8. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12

Author

Coil, David A., Badger, Jonathan H., Forberger, Heather C., Riggs, Florenta, Madupu, Ramana, Fedorova, Nadia, Ward, Naomi, Robb, Frank T., and Eisen, Jonathan A.

Abstract

Here, we present the complete genome of the extreme thermophile, Dictyoglomus thermophilum H-6-12 (phylum Dictyoglomi), which consists of 1,959,987 bp.

Published
2014

9. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

Author

Bogdanove, Adam J, Koebnik, Ralf, Lu, Hong, Furutani, Ayako, Angiuoli, Samuel V, Patil, Prabhu B, Van Sluys, Marie-Anne, Ryan, Robert P, Meyer, Damien F, Han, Sang-Wook, Aparna, Gudlur, Rajaram, Misha, Delcher, Arthur L, Phillippy, Adam M, Puiu, Daniela, Schatz, Michael C, Shumway, Martin, Sommer, Daniel D, Trapnell, Cole, Benahmed, Faiza, Dimitrov, George, Madupu, Ramana, Radune, Diana, Sullivan, Steven, Jha, Gopaljee, Ishihara, Hiromichi, Lee, Sang-Won, Pandey, Alok, Sharma, Vikas, Sriariyanun, Malinee, Szurek, Boris, Vera-Cruz, Casiana M, Dorman, Karin S, Ronald, Pamela C, Verdier, Valérie, Dow, J Maxwell, Sonti, Ramesh V, Tsuge, Seiji, Brendel, Volker P, Rabinowicz, Pablo D, Leach, Jan E, White, Frank F, and Salzberg, Steven L

Abstract

Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.

Published
2011

10. Genome Analysis of Multiple Pathogenic Isolates of Streptococcus agalactiae: Implications for the Microbial "Pan-Genome"

Author

Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., Angiuoli, Samuel V., Crabtree, Jonathan, Jones, Amanda L., Durkin, A. Scott, DeBoy, Robert T., Davidsen, Tanja M., Mora, Marirosa, Scarselli, Maria, Peterson, Jeremy D., Hauser, Christopher R., Sundaram, Jaideep P., Nelson, William C., Madupu, Ramana, Brinkac, Lauren M., Dodson, Robert J., Rosovitz, Mary J., Sullivan, Steven A., Daugherty, Sean C., Haft, Daniel H., Selengut, Jeremy, Gwinn, Michelle L., Zhou, Liwei, Zafar, Nikhat, Khouri, Hoda, Radune, Diana, Dimitrov, George, Watkins, Kisha, Smith, Shannon, Utterback, Teresa R., White, Owen, Rubens, Craig E., Grandi, Guido, Madoff, Lawrence C., Kasper, Dennis L., Telford, John L., Wessels, Michael R., Rappuoli, Rino, and Fraser, Claire M.

Published
2005

11. The Psychrophilic Lifestyle as Revealed by the Genome Sequence of Colwellia psychrerythraea 34H through Genomic and Proteomic Analyses

Author

Methé, Barbara A., Nelson, Karen E., Deming, Jody W., Momen, Bahram, Melamud, Eugene, Zhang, Xijun, Moult, John, Madupu, Ramana, Nelson, William C., Dodson, Robert J., Brinkac, Lauren M., Daugherty, Sean C., Durkin, Anthony S., DeBoy, Robert T., Kolonay, James F., Sullivan, Steven A., Zhou, Liwei, Davidsen, Tanja M., Wu, Martin, Huston, Adrienne L., Lewis, Matthew, Weaver, Bruce, Weidman, Janice F., Khouri, Hoda, Utterback, Terry R., Feldblyum, Tamara V., and Fraser, Claire M.

Published
2005

12. Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes

Author

Seshadri, Rekha, Adrian, Lorenz, Fouts, Derrick E., Eisen, Jonathan A., Phillippy, Adam M., Methe, Barbara A., Ward, Naomi L., Nelson, William C., Deboy, Robert T., Khouri, Hoda M., Kolonay, James F., Dodson, Robert J., Daugherty, Sean C., Brinkac, Lauren M., Sullivan, Steven A., Madupu, Ramana, Nelson, Karen E., Kang, Katherine H., Impraim, Marjorie, Tran, Kevin, Robinson, Jeffrey M., Forberger, Heather A., Fraser, Claire M., Zinder, Stephen H., and Heidelberg, John F.

Published
2005

13. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.

Author

Davidsen, Tanja, Madupu, Ramana, Sterk, Peter, Field, Dawn, Garrity, George, Gilbert, Jack, Glöckner, Frank Oliver, Hirschman, Lynette, Kolker, Eugene, Kottmann, Renzo, Kyrpides, Nikos, Meyer, Folker, Morrison, Norman, Schriml, Lynn, Tatusova, Tatiana, and Wooley, John

Subjects
Biochemistry and Cell Biology, Genetics
Abstract

This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platform for next-generation collaborative computational infrastructures, building ties with the biodiversity research community and two discussion panels with government and industry participants. Progress was made on all fronts, and major outcomes included the completion of the MIENS specification for publication and the formation of the Biodiversity working group.

Published
2010

14. The complete genome sequence of Haloferax volcanii DS2, a model archaeon.

Author

Hartman, Amber L, Norais, Cédric, Badger, Jonathan H, Delmas, Stéphane, Haldenby, Sam, Madupu, Ramana, Robinson, Jeffrey, Khouri, Hoda, Ren, Qinghu, Lowe, Todd M, Maupin-Furlow, Julie, Pohlschroder, Mecky, Daniels, Charles, Pfeiffer, Friedhelm, Allers, Thorsten, and Eisen, Jonathan A

Subjects
Archaea, Haloferax volcanii, Amino Acids, Codon, Chromosome Mapping, Sequence Analysis, DNA, Computational Biology, Phylogeny, Signal Transduction, Gene Library, Open Reading Frames, Genome, Genome, Archaeal, Isoelectric Point, Sequence Analysis, DNA, Archaeal, General Science & Technology
Abstract

BackgroundHaloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general.Methodology/principal findingsWe report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb).Conclusions/significanceThe completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.

Published
2010

15. Structural Flexibility in the Burkholderia mallei Genome

Author

Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, Ulrich, Ricky L., Ronning, Catherine M., Brinkac, Lauren M., Daugherty, Sean C., Davidsen, Tanja D., Deboy, Robert T., Dimitrov, George, Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle L., Haft, Daniel H., Khouri, Hoda, Kolonay, James F., Madupu, Ramana, Mohammoud, Yasmin, Nelson, William C., Radune, Diana, Romero, Claudia M., Sarria, Saul, Selengut, Jeremy, Shamblin, Christine, Sullivan, Steven A., White, Owen, Yu, Yan, Zafar, Nikhat, Zhou, Liwei, Fraser, Claire M., and Greenberg, E. Peter

Published
2004

16. Comparison of the Genome of the Oral Pathogen Treponema denticola with Other Spirochete Genomes

Author

Seshadri, Rekha, Tettelin, Hervé, Eisen, Jonathan A., Heidelberg, John F., Dodson, Robert J., Davidsen, Tanja M., DeBoy, Robert T., Fouts, Derrick E., Haft, Dan H., Selengut, Jeremy, Ren, Qinghu, Brinkac, Lauren M., Madupu, Ramana, Kolonay, Jamie, Durkin, Scott A., Daugherty, Sean C., Shetty, Jyoti, Shvartsbeyn, Alla, Gebregeorgis, Elizabeth, Geer, Keita, Tsegaye, Getahun, Malek, Joel, Ayodeji, Bola, Shatsman, Sofiya, McLeod, Michael P., Šmajs, David, Howell, Jerrilyn K., Pal, Sangita, Amin, Anita, Vashisth, Pankaj, McNeill, Thomas Z., Xiang, Qin, Sodergren, Erica, Baca, Ernesto, Weinstock, George M., Norris, Steven J., Fraser, Claire M., Paulsen, Ian T., and Haselkorn, Robert

Published
2004

17. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).

Author

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

Subjects
Animals, Proteobacteria, Nitrogen, Polysaccharides, Spectrometry, Mass, Electrospray Ionization, Computational Biology, Marine Biology, Phylogeny, Symbiosis, Genome, Bacterial, Wood, Bivalvia, Tandem Mass Spectrometry, Quorum Sensing, General Science & Technology
Abstract

Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2-40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.

Published
2009

18. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.

Author

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

Subjects
Flagella, Bacteria, Aerobic, Chloroflexi, Gram-Negative Bacteria, Carbon Monoxide, DNA, Circular, Sequence Analysis, DNA, Hot Springs, Phylogeny, Chemotaxis, Photosynthesis, Genome, Bacterial, Metabolic Networks and Pathways, General Science & Technology
Abstract

In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.

Published
2009

19. The Complete Genome Sequence of the Arabidopsis and Tomato Pathogen Pseudomonas syringae pv. tomato DC3000

Author

Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., Dodson, Robert J., Deboy, Robert T., Durkin, A. Scott, Kolonay, James F., Madupu, Ramana, Daugherty, Sean, Brinkac, Lauren, Beanan, Maureen J., Haft, Daniel H., Nelson, William C., Davidsen, Tanja, Zafar, Nikhat, Zhou, Liwei, Liu, Jia, Yuan, Qiaoping, Khouri, Hoda, Fedorova, Nadia, Tran, Bao, Russell, Daniel, Berry, Kristi, Utterback, Teresa, Van Aken, Susan E., Feldblyum, Tamara V., D'Ascenzo, Mark, Deng, Wen-Ling, Ramos, Adela R., Alfano, James R., Cartinhour, Samuel, Chatterjee, Arun K., Delaney, Terrence P., Lazarowitz, Sondra G., Martin, Gregory B., Schneider, David J., Tang, Xiaoyan, Bender, Carol L., White, Owen, Fraser, Claire M., and Collmer, Alan

Published
2003

20. Complete Genome Sequence of the Q-Fever Pathogen Coxiella burnetii

Author

Seshadri, Rekha, Paulsen, Ian T., Eisen, Jonathan A., Read, Timothy D., Nelson, Karen E., Nelson, William C., Ward, Naomi L., Tettelin, Hervé, Davidsen, Tanja M., Beanan, Maureen J., Deboy, Robert T., Daugherty, Sean C., Brinkac, Lauren M., Madupu, Ramana, Dodson, Robert J., Khouri, Hoda M., Lee, Kathy H., Carty, Heather A., Scanlan, David, Heinzen, Robert A., Thompson, Herbert A., Samuel, James E., Fraser, Claire M., and Heidelberg, John F.

Published
2003

21. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

Author

Salzberg, Steven L, Sommer, Daniel D, Schatz, Michael C, Phillippy, Adam M, Rabinowicz, Pablo D, Tsuge, Seiji, Furutani, Ayako, Ochiai, Hirokazu, Delcher, Arthur L, Kelley, David, Madupu, Ramana, Puiu, Daniela, Radune, Diana, Shumway, Martin, Trapnell, Cole, Aparna, Gudlur, Jha, Gopaljee, Pandey, Alok, Patil, Prabhu B, Ishihara, Hiromichi, Meyer, Damien F, Szurek, Boris, Verdier, Valerie, Koebnik, Ralf, Dow, J Maxwell, Ryan, Robert P, Hirata, Hisae, Tsuyumu, Shinji, Won Lee, Sang, Seo, Young-Su, Sriariyanum, Malinee, Ronald, Pamela C, Sonti, Ramesh V, Van Sluys, Marie-Anne, Leach, Jan E, White, Frank F, and Bogdanove, Adam J

Abstract

Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another.The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus.Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.

Published
2008

22. The Brucella suis Genome Reveals Fundamental Similarities between Animal and Plant Pathogens and Symbionts

Author

Paulsen, Ian T., Seshadri, Rekha, Nelson, Karen E., Eisen, Jonathan A., Heidelberg, John F., Read, Timothy D., Dodson, Robert J., Umayam, Lowell, Brinkac, Lauren M., Beanan, Maureen J., Daugherty, Sean C., Deboy, Robert T., Durkin, A. Scott, Kolonay, James F., Madupu, Ramana, Nelson, William C., Ayodeji, Bola, Kraul, Margaret, Shetty, Jyoti, Malek, Joel, van Aken, Susan E., Riedmuller, Steven, Tettelin, Herve, Gill, Steven R., White, Owen, Salzberg, Steven L., Hoover, David L., Lindler, Luther E., Halling, Shirley M., Boyle, Stephen M., and Fraser, Claire M.

Published
2002

23. Complete Genome Sequence and Comparative Genomic Analysis of an Emerging Human Pathogen, Serotype V Streptococcus agalactiae

Author

Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Eisen, Jonathan A., Peterson, Scott, Wessels, Michael R., Paulsen, Ian T., Nelson, Karen E., Margarit, Immaculada, Read, Timothy D., Madoff, Lawrence C., Wolf, Alex M., Beanan, Maureen J., Brinkac, Lauren M., Daugherty, Sean C., DeBoy, Robert T., Durkin, A. Scott, Kolonay, James F., Madupu, Ramana, Lewis, Matthew R., Radune, Diana, Fedorova, Nadezhda B., Scanlan, David, Khouri, Hoda, Mulligan, Stephanie, Carty, Heather A., Cline, Robin T., Van Aken, Susan E., Gill, John, Scarselli, Maria, Mora, Marirosa, Iacobini, Emilia T., Brettoni, Cecilia, Galli, Giuliano, Mariani, Massimo, Vegni, Filippo, Maione, Domenico, Rinaudo, Daniela, Rappuoli, Rino, Telford, John L., Kasper, Dennis L., Grandi, Guido, and Fraser, Claire M.

Published
2002

24. Comparative Genomics of Emerging Human Ehrlichiosis Agents

Author

Hotopp, Julie C Dunning, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, Seshadri, Rekha, Ren, Qinghu, Wu, Martin, Utterback, Teresa R, Smith, Shannon, Lewis, Matthew, Khouri, Hoda, Zhang, Chunbin, Niu, Hua, Lin, Quan, Ohashi, Norio, Zhi, Ning, Nelson, William, Brinkac, Lauren M, Dodson, Robert J, Rosovitz, MJ, Sundaram, Jaideep, Daugherty, Sean C, Davidsen, Tanja, Durkin, Anthony S, Gwinn, Michelle, Haft, Daniel H, Selengut, Jeremy D, Sullivan, Steven A, Zafar, Nikhat, Zhou, Liwei, Benahmed, Faiza, Forberger, Heather, Halpin, Rebecca, Mulligan, Stephanie, Robinson, Jeffrey, White, Owen, Rikihisa, Yasuko, and Tettelin, Hervé

Subjects
Infectious Diseases, Rare Diseases, Genetics, Biotechnology, Vector-Borne Diseases, Prevention, Emerging Infectious Diseases, Infection, Good Health and Well Being, Animals, Biotin, DNA Repair, Ehrlichia, Ehrlichiosis, Genome, Genomics, Humans, Models, Biological, Phylogeny, Rickettsia, Ticks, Developmental Biology
Abstract

Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. © 2006 Dunning Hotopp.

Published
2006

25. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Author

Wu, Martin, Ren, Qinghu, Durkin, A Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, Madupu, Ramana, Sullivan, Steven A, Kolonay, James F, Haft, Daniel H, Nelson, William C, Tallon, Luke J, Jones, Kristine M, Ulrich, Luke E, Gonzalez, Juan M, Zhulin, Igor B, Robb, Frank T, and Eisen, Jonathan A

Subjects
Peptococcaceae, Carbon Monoxide, Sequence Analysis, DNA, Genomics, Base Sequence, Oxidative Stress, Genes, Bacterial, Genome, Bacterial, Models, Biological, Molecular Sequence Data, Hot Temperature, Genes, Bacterial, Genome, Models, Biological, Sequence Analysis, DNA, Genetics, Developmental Biology
Abstract

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Published
2005

26. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.

Author

Wu, Martin, Sun, Ling V, Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C, McGraw, Elizabeth A, Martin, William, Esser, Christian, Ahmadinejad, Nahal, Wiegand, Christian, Madupu, Ramana, Beanan, Maureen J, Brinkac, Lauren M, Daugherty, Sean C, Durkin, A Scott, Kolonay, James F, Nelson, William C, Mohamoud, Yasmin, Lee, Perris, Berry, Kristi, Young, M Brook, Utterback, Teresa, Weidman, Janice, Nierman, William C, Paulsen, Ian T, Nelson, Karen E, Tettelin, Hervé, O'Neill, Scott L, and Eisen, Jonathan A

Subjects
Animals, Drosophila melanogaster, Parasites, Wolbachia, Purines, DNA, DNA Primers, Adenosine Triphosphate, Polymerase Chain Reaction, Genomics, Evolution, Molecular, Phylogeny, Gene Duplication, Gene Deletion, Interspersed Repetitive Sequences, Protein Structure, Tertiary, Glycolysis, Cell Lineage, Gene Library, Genes, Bacterial, Genome, Bacterial, Open Reading Frames, Genome, Models, Genetic, Molecular Sequence Data, Evolution, Molecular, Protein Structure, Tertiary, Genes, Bacterial, Models, Genetic, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.

Published
2004

28. Genomic analysis of a large set of currently—and historically—important human adenovirus pathogens

Author

Ismail, Ashrafali M., Cui, Tiange, Dommaraju, Kalpana, Singh, Gurdeep, Dehghan, Shoaleh, Seto, Jason, Shrivastava, Susmita, Fedorova, Nadia B., Gupta, Neha, Stockwell, Timothy B., Halpin, Rebecca, Madupu, Ramana, Heim, Albert, Kajon, Adriana E., Romanowski, Eric G., Kowalski, Regis P., Malathi, Jambulingam, Therese, Kuzhanthai L., Madhavan, Hajib Narahari, Zhang, Qiwei, Ferreyra, Leonardo J., Jones, Morris S., Rajaiya, Jaya, Dyer, David W., Chodosh, James, and Seto, Donald

Published
2018
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29. Author Correction: Genomic analysis of a large set of currently—and historically—important human adenovirus pathogens

Author

Ismail, Ashrafali M., Cui, Tiange, Dommaraju, Kalpana, Singh, Gurdeep, Dehghan, Shoaleh, Seto, Jason, Shrivastava, Susmita, Fedorova, Nadia B., Gupta, Neha, Stockwell, Timothy B., Halpin, Rebecca, Madupu, Ramana, Heim, Albert, Kajon, Adriana E., Romanowski, Eric G., Kowalski, Regis P., Malathi, Jambulingam, Therese, Kuzhanthai L., Madhavan, Hajib Narahari, Zhang, Qiwei, Ferreyra, Leonardo J., Jones, Morris S., Rajaiya, Jaya, Dyer, David W., Chodosh, James, and Seto, Donald

Published
2018
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30. Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...)

Author

Denroche, Robert, Madupu, Ramana, Yooseph, Shibu, Sutton, Granger, Shatkay, Hagit, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Blaschke, Christian, editor, and Shatkay, Hagit, editor

Published
2010
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35. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus

Author

Myers, Garry S A, Parker, Dane, Al-Hasani, Keith, Kennan, Ruth M, Seemann, Torsten, Ren, Qinghu, Badger, Jonathan H, Selengut, Jeremy D, DeBoy, Robert T, Tettelin, Hervé, Boyce, John D, McCarl, Victoria P, Han, Xiaoyan, Nelson, William C, Madupu, Ramana, Mohamoud, Yasmin, Holley, Tara, Fedorova, Nadia, Khouri, Hoda, Bottomley, Steven P, Whittington, Richard J, Adler, Ben, Songer, J Glenn, Rood, Julian I, and Paulsen, Ian T

Published
2007
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37. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Author

Paulsen, Ian T, Press, Caroline M, Ravel, Jacques, Kobayashi, Donald Y, Myers, Garry S A, Mavrodi, Dmitri V, DeBoy, Robert T, Seshadri, Rekha, Ren, Qinghu, Madupu, Ramana, Dodson, Robert J, Durkin, A Scott, Brinkac, Lauren M, Daugherty, Sean C, Sullivan, Stephen A, Rosovitz, Mary J, Gwinn, Michelle L, Zhou, Liwei, Schneider, Davd J, Cartinhour, Samuel W, Nelson, William C, Weidman, Janice, Watkins, Kisha, Tran, Kevin, Khouri, Hoda, Pierson, Elizabeth A, Pierson, III, Leland S, Thomashow, Linda S, and Loper, Joyce E

Published
2005
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38. Genome sequence of Aeromonas hydrophila ATCC [7966.sup.T]: jack of all trades

Author

Seshadri, Rekha, Joseph, Sam W., Chopra, Ashok K., Sha, Jian, Shaw, Jonathan, Graf, Joerg, Haft, Daniel, Wu, Martin, Ren, Qinghu, Rosovitz, M.J., Madupu, Ramana, Tallon, Luke, Kim, Mary, Jin, Shaohua, Vuong, Hue, Stine, O. Colin, Ali, Afsar, Horneman, Amy J., and Heidelberg, John F.

Subjects
Virulence (Microbiology) -- Research, Genetic markers -- Research, Genetic research, Biological sciences
Abstract

The complete genome of Aeromonas hydrophila ATCC [7966.sup.T] was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate List because of its potential to cause human disease. The 4.7-Mb genome of this emerging pathogen shows a physiologically adroit organism with broad metabolic capabilities and considerable virulence potential. A large array of virulence genes, including some identified in clinical isolates of Aeromonas spp. or Vibrio spp., may confer upon this organism the ability to infect a wide range of hosts. However, two recognized virulence markers, a type III secretion system and a lateral flagellum, that are reported in other A. hydrophila strains are not identified in the sequenced isolate, ATCC [7966.sup.T]. Given the ubiquity and free-living lifestyle of this organism, there is relatively little evidence of fluidity in terms of mobile elements in the genome of this particular strain. Notable aspects of the metabolic repertoire of A. hydrophila include dissimilatory sulfate reduction and resistance mechanisms (such as thiopurine reductase, arsenate reductase, and phosphonate degradation enzymes) against toxic compounds encountered in polluted waters. These enzymes may have bioremediative as well as industrial potential. Thus, the A. hydrophila genome sequence provides valuable insights into its ability to flourish in both aquatic and host environments.

Published
2006

39. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus

Author

Badger, Jonathan H., Hoover, Timothy R., Brun, Yves V., Weiner, Ronald M., Laub, Michael T., Alexandre, Gladys, Mrazek, Jan, Ren, Qinghu, Paulsen, Ian T., Nelson, Karen E., Khouri, Hoda M., Radune, Diana, Sosa, Julia, Dodson, Robert J., Sullivan, Steven A., Rosovitz, M.J., Madupu, Ramana, Brinkac, Lauren M., Durkin, A. Scott, Daugherty, Sean C., Kothari, Sagar P., Giglio, Michelle Gwinn, Zhou, Liwei, Haft, Daniel H., Selengut, Jeremy D., Davidsen, Tanja M., Yang, Qi, Zafar, Nikhat, and Ward, Naomi L.

Subjects
Caulobacter -- Genetic aspects, Chemotaxis -- Research, Biological sciences
Abstract

The dimorphic prosthecate bacteria (DPB) are [alpha]-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.

Published
2006

40. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition

Author

Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., Daugherty, Sean C., DeBoy, Robert, Durkin, A. Scott, Giglio, Michelle Gwinn, Madupu, Ramana, Nelson, William C., Rosovitz, M.J., Sullivan, Steven, Crabtree, Jonathan, Creasy, Todd, Davidsen, Tanja, Haft, Dan H., Zafar, Nikhat, Zhou, Liwei, Halpin, Rebecca, Holley, Tara, Khouri, Hoda, Feldblyum, Tamara, White, Owen, Fraser, Claire M., Chatterjee, Arun K., Cartinhour, Sam, Schneider, David J., Mansfield, John, Collmer, Alan, and Buell, C. Robin

Subjects
Genomics -- Comparative analysis, Genetic research -- Comparative analysis, Biological sciences
Abstract

Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.

Published
2005

41. Insights on evolution Of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain

Author

Gill, Steven R., Fouts, Derrick E., Archer, Gordon L., Mongodin, Emmanuel F., DeBoy, Robert T., Ravel, Jacques, Paulsen, Ian T., Kolonay, James F., Brinkac, Lauren, Beanan, Mauren, Dodson, Robert J., Daugherty, Sean C., Madupu, Ramana, Angiuoli, Samuel V., Durkin, A. Scott, Haft, Daniel H., Vamathevan, Jessica, Khouri, Hoda, Utterback, Terry, Lee, Chris, Dimitrov, George, Jiang, Lingxia, Qin, Haiying, Weidman, Jan, Tran, Kevin, Kang, Kathy, Hance, Ioana R., Nelson, Karen E., and Fraser, Claire M.

Subjects
Bacterial genetics -- Research, Bacteriology -- Research, Staphylococcus aureus -- Research, Staphylococcus aureus -- Genetic aspects, Drug resistance in microorganisms -- Research, Drug resistance in microorganisms -- Genetic aspects, Biological sciences
Abstract

Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the ~2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the ~2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.

Published
2005

42. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Author

Moran, Mary Ann, Buchan, Alison, Gonzalez, Jose M., Heidelberg, John F., Whitman, William B., Kiene, Ronald P., Henriksen, James R., King, Gary M., Belas, Robert, Fuqua, Clay, Brinkac, Lauren, Lewis, Matt, Johri, Shivani, Weaver, Bruce, Pai, Grace, Eisen, Jonathan A., Rahe, Elisha, Sheldon, Wade M., Ye, Wenying, Miller, Todd R., Carlton, Jane, Rasko, David A., Paulsen, Ian T., Ren, Qinghu, Daugherty, Sean C., Deboy, Robert T., Dodson, Robert J., Durkin, A. Scott, Madupu, Ramana, Nelson, William C., Sullivan, Steven A., Rosovitz, M. J., Haft, Daniel H., Selengut, Jeremy, and Ward, Naomi

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mary Ann Moran (corresponding author) [1]; Alison Buchan [3]; José M. González [4]; John F. Heidelberg [5]; William B. Whitman [2]; Ronald P. Kiene [6]; James R. Henriksen [2]; [...]

Published
2004
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44. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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45. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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47. Pathema: a clade-specific bioinformatics resource center for pathogen research

Author

Brinkac, Lauren M., Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Caler, Elisabet, Dodson, Robert J., Durkin, A. Scott, Harkins, Derek M., Lorenzi, Hernan, Madupu, Ramana, Sebastian, Yinong, Shrivastava, Susmita, Thiagarajan, Mathangi, Orvis, Joshua, Sundaram, Jaideep P., Crabtree, Jonathon, Galens, Kevin, Zhao, Yongmei, Inman, Jason M., Montgomery, Robert, Schobel, Seth, Galinsky, Kevin, Tanenbaum, David M., Resnick, Adam, Zafar, Nikhat, White, Owen, and Sutton, Granger

Published
2010
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48. The comprehensive microbial resource

Author

Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Montgomery, Robert, Zafar, Nikhat, Yang, Qi, Madupu, Ramana, Goetz, Phil, Galinsky, Kevin, White, Owen, and Sutton, Granger

Published
2010
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49. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species

Author

Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., Rasko, David A., Angiuoli, Samuel V., Gill, Steven R., Paulsen, Ian T., Peterson, Jeremy, White, Owen, Nelson, William C., Nierman, William, Beanan, Maureen J., Brinkac, Lauren M., Daugherty, Sean C., Dodson, Robert J., Durkin, A. Scott, Madupu, Ramana, Haft, Daniel H., Selengut, Jeremy, Van Aken, Susan, Khouri, Hoda, Fedorova, Nadia, Forberger, Heather, Tran, Bao, Kathariou, Sophia, Wonderling, Laura D., Uhlich, Gaylen A., Bayles, Darrell O., Luchansky, John B., and Fraser, Claire M.

Published
2004

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