Nikos Kyrpides

Publications of Nikos Kyrpides

• Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09.

  Authors: Rich Boden, Michael Cunliffe, Julie Scanlan, Hélène Moussard, K Dimitri Kits, Martin G Klotz, Mike S M Jetten, Stéphane Vuilleumier, James Han, Lin Peters [......] Lynne Goodwin, Cliff Han, Loren Hauser, Miriam L Land, Alla Lapidus, Susan Lucas, Sam Pitluck, Tanja Woyke, Lisa Stein, J Colin Murrell

  Journal of bacteriology. 12/2011; 193(24):7001-2.

  Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence ofMethylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.

• Complete genome sequence of Staphylothermus hellenicus P8.

  Authors: Iain Anderson, Reinhard Wirth, Susan Lucas, Alex Copeland, Alla Lapidus, Jan-Fang Cheng, Lynne Goodwin, Samuel Pitluck, Karen Davenport, John C Detter, Cliff Han, Roxanne Tapia, Miriam Land, Loren Hauser, Amrita Pati, Natalia Mikhailova, Tanja Woyke, Hans-Peter Klenk, Nikos Kyrpides, Natalia Ivanova

  Standards in genomic sciences. 10/2011; 5(1):12-20.

  Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. Strain P8(T) is the type strain of the species and was isolated from a shallow hydrothermalStaphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. Strain P8(T) is the type strain of the species and was isolated from a shallow hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein-coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) Laboratory Sequencing Program (LSP) project.

• Complete genome sequence of Ferroglobus placidus AEDII12DO.

  Authors: Iain Anderson, Carla Risso, Dawn Holmes, Susan Lucas, Alex Copeland, Alla Lapidus, Jan-Fang Cheng, David Bruce, Lynne Goodwin, Samuel Pitluck [......] John C Detter, Cliff Han, Roxanne Tapia, Frank Larimer, Miriam Land, Loren Hauser, Tanja Woyke, Derek Lovley, Nikos Kyrpides, Natalia Ivanova

  Standards in genomic sciences. 10/2011; 5(1):50-60.

  Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marineFerroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.

• Engineering Escherichia coli for biodiesel production utilizing a bacterial fatty acid methyltransferase.

  Authors: Parwez Nawabi, Stefan Bauer, Nikos Kyrpides, Athanasios Lykidis

  Applied and environmental microbiology. 09/2011; 77(22):8052-61.

  The production of low-cost biofuels in engineered microorganisms is of great interest due to the continual increase in the world's energy demands. Biodiesel is a renewable fuel that can potentiallyThe production of low-cost biofuels in engineered microorganisms is of great interest due to the continual increase in the world's energy demands. Biodiesel is a renewable fuel that can potentially be produced in microbes cost-effectively. Fatty acid methyl esters (FAMEs) are a common component of biodiesel and can be synthesized from either triacylglycerol or free fatty acids (FFAs). Here we report the identification of a novel bacterial fatty acid methyltransferase (FAMT) that catalyzes the formation of FAMEs and 3-hydroxyl fatty acid methyl esters (3-OH-FAMEs) from the respective free acids and S-adenosylmethionine (AdoMet). FAMT exhibits a higher specificity toward 3-hydroxy free fatty acids (3-OH-FFAs) than FFAs, synthesizing 3-hydroxy fatty acid methyl esters (3-OH-FAMEs) in vivo. We have also identified bacterial members of the fatty acyl-acyl carrier protein (ACP) thioesterase (FAT) enzyme family with distinct acyl chain specificities. These bacterial FATs exhibit increased specificity toward 3-hydroxyacyl-ACP, generating 3-OH-FFAs, which can subsequently be utilized by FAMTs to produce 3-OH-FAMEs. PhaG (3-hydroxyacyl ACP:coenzyme A [CoA] transacylase) constitutes an alternative route to 3-OH-FFA synthesis; the coexpression of PhaG with FAMT led to the highest level of accumulation of 3-OH-FAMEs and FAMEs. The availability of AdoMet, the second substrate for FAMT, is an important factor regulating the amount of methyl esters produced by bacterial cells. Our results indicate that the deletion of the global methionine regulator metJ and the overexpression of methionine adenosyltransferase result in increased methyl ester synthesis.

• The Genomic Standards Consortium.

  Authors: Dawn Field, Linda Amaral-Zettler, Guy Cochrane, James R Cole, Peter Dawyndt, George M Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi [......] Nikos Kyrpides, Folker Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M Schriml, Peter Sterk, Tatiana Tatusova, David W Ussery, Owen White, John Wooley

  PLoS biology. 06/2011; 9(6):e1001088.

  A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise itsA vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

  Authors: Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane [......] James M Tiedje, Doyle V Ward, George M Weinstock, Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer R Wortman, Tanya Yatsunenko, Frank Oliver Glöckner

  Nature biotechnology. 05/2011; 29(5):415-20.

  Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce aHere we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

• Meeting report of the RNA Ontology Consortium January 8-9, 2011.

  Authors: Amanda Birmingham, Jose C Clemente, Narayan Desai, Jack Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel, Neocles B Leontis, Craig Zirbel, Rob Knight, Alain Laederach

  Standards in genomic sciences. 04/2011; 4(2):252-6.

  This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop toThis report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-related software, and those performing genome annotation and standardization. The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the second to discuss standardization and benchmarking of existing RNA annotation pipelines. These working groups have subsequently pursued concrete implementation of actions suggested during the discussion. Further information about the ROC and its activities can be found at http://roc.bgsu.edu/.

• Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

  Authors: Norman Morrison, David Hancock, Lynette Hirschman, Peter Dawyndt, Bert Verslyppe, Nikos Kyrpides, Renzo Kottmann, Pelin Yilmaz, Frank Oliver Glöckner, Jeff Grethe, Tim Booth, Peter Sterk, Goran Nenadic, Dawn Field

  Standards in genomic sciences. 04/2011; 4(2):286-92.

  In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that mustIn the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources.

• Alive and well at 100.

  Authors: George M Garrity, Dawn Field, Nikos Kyrpides

  Standards in genomic sciences. 01/2011; 4(1):1.

• Proposal for Open Discussion - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments.

  Authors: Folker Meyer, Nikos Kyrpides

  BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Rome, Italy, 26-29 January, 2011; 01/2011

• The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.

  Authors: Bettina Siebers, Melanie Zaparty, Guenter Raddatz, Britta Tjaden, Sonja-Verena Albers, Steve D Bell, Fabian Blombach, Arnulf Kletzin, Nikos Kyrpides, Christa Lanz, André Plagens, Markus Rampp, Andrea Rosinus, Mathias von Jan, Kira S Makarova, Hans-Peter Klenk, Stephan C Schuster, Reinhard Hensel

  PloS one. 01/2011; 6(10):e24222.

  Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. ItsHere, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is strictly anaerobic and sulfur-dependent with optimal growth at 86°C and pH 5.6. One particular feature is the great metabolic versatility, which is not accompanied by a distinct increase of genome size or information density as compared to other Crenarchaeota. T. tenax is able to grow chemolithoautotrophically (CO₂/H₂) as well as chemoorganoheterotrophically in presence of various organic substrates. All pathways for synthesizing the 20 proteinogenic amino acids are present. In addition, two presumably complete gene sets for NADH:quinone oxidoreductase (complex I) were identified in the genome and there is evidence that either NADH or reduced ferredoxin might serve as electron donor. Beside the typical archaeal A₀A₁-ATP synthase, a membrane-bound pyrophosphatase is found, which might contribute to energy conservation. Surprisingly, all genes required for dissimilatory sulfate reduction are present, which is confirmed by growth experiments. Mentionable is furthermore, the presence of two proteins (ParA family ATPase, actin-like protein) that might be involved in cell division in Thermoproteales, where the ESCRT system is absent, and of genes involved in genetic competence (DprA, ComF) that is so far unique within Archaea.

• Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.

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

  PloS one. 01/2011; 6(5):e20237.

  The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing anThe extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis. We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses. These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.

• Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.

  Authors: Christopher L Hemme, Housna Mouttaki, Yong-Jin Lee, Gengxin Zhang, Lynne Goodwin, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina del Rio, Hope Tice [......] Nanqi Ren, Aijie Wang, Raymond L Huhnke, Jonathan R Mielenz, Shi-You Ding, Michael E Himmel, Safiyh Taghavi, Daniël van der Lelie, Edward M Rubin, Jizhong Zhou

  Journal of bacteriology. 10/2010; 192(24):6494-6.

  Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidatesModern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae. Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.

• A catalog of reference genomes from the human microbiome.

  Authors: Karen E Nelson, George M Weinstock, Sarah K Highlander, Kim C Worley, Heather Huot Creasy, Jennifer Russo Wortman, Douglas B Rusch, Makedonka Mitreva, Erica Sodergren, Asif T Chinwalla [......] Sandra W Clifton, Emma Allen-Vercoe, Ashlee M Earl, Candace N Farmer, Konstantinos Liolios, Michael G Surette, Qiang Xu, Craig Pohl, Katarzyna Wilczek-Boney, Dianhui Zhu

  Science (New York, N.Y.). 05/2010; 328(5981):994-9.

  The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched anThe human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.

• Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

  Authors: Sean D. Hooper, Daniel Dalevi, Amrita Pati, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides

  Bioinformatics. 01/2010; 26:295-301.

• The integrated microbial genomes system: an expanding comparative analysis resource.

  Authors: Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides

  Nucleic Acids Research. 01/2010; 38:382-390.

• Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8.

  Authors: Nikos Kyrpides, Dawn Field, Peter Sterk, Renzo Kottmann, Frank Oliver Glöckner, Lynette Hirschman, George M Garrity, Guy Cochrane, John Wooley

  Standards in genomic sciences. 01/2010; 3(1):93-6.

  This report summarizes the proceedings of the 8th meeting of the Genomic Standards Consortium held at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA on September 9-11, 2009.This report summarizes the proceedings of the 8th meeting of the Genomic Standards Consortium held at the Department of Energy Joint Genome Institute in Walnut Creek, CA, USA on September 9-11, 2009. This three-day workshop marked the maturing of Genomic Standards Consortium from an informal gathering of researchers interested in developing standards in the field of genomic and metagenomics to an established community with a defined governance mechanism, its own open access journal, and a family of established standards for describing genomes, metagenomes and marker studies (i.e. ribosomal RNA gene surveys). There will be increased efforts within the GSC to reach out to the wider scientific community via a range of new projects. Further information about the GSC and its activities can be found at http://gensc.org/.

• Meeting Report: Towards a Critical Assessment of Functional Annotation Experiment (CAFAE) for bacterial genome annotation.

  Authors: Owen White, Nikos Kyrpides

  Standards in genomic sciences. 01/2010; 3(3):240-2.

  It is widely recognized that, with the advent of very high throughput, short read, and highly parallelized sequencing technologies, the generation of new DNA sequences from microbes, plants,It is widely recognized that, with the advent of very high throughput, short read, and highly parallelized sequencing technologies, the generation of new DNA sequences from microbes, plants, metagenomes is outpacing the ability to assign functions to ("annotate") all this data. To begin to try to address this, on May 18 and 19, 2010, a team of roughly fifty people met to define and scope the possibility of a first Critical Assessment of Functional Annotation Experiment (CAFAE) for bacterial genome annotation in Crystal City, Virginia. Due to the fundamental importance of genomic data to its mission, the Department of Energy (DOE) BER program hosted this workshop, funding the attendance of all invitees. The workshop was co-organized by Dan Drell and Susan Gregurick (DOE), Owen White and Nikos Kyripides.

• Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010.

  Authors: Jack A Gilbert, Folker Meyer, Rob Knight, Dawn Field, Nikos Kyrpides, Pelin Yilmaz, John Wooley

  Standards in genomic sciences. 01/2010; 3(3):235-9.

  This report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting inThis report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA August 22-27, 2010. The Genomic Standards Consortium (GSC) hosted this meeting as a community engagement exercise to describe the GSC to the microbial ecology community during this important international meeting. The roundtable included five talks given by members of the GSC, and was followed by audience participation in the form of a roundtable discussion. This report summarizes this event. Further information on the GSC and its range of activities can be found at http://www.gensc.org.

• Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum.

  Authors: Wayne Reeve, Graham O'Hara, Patrick Chain, Julie Ardley, Lambert Bräu, Kemanthi Nandesena, Ravi Tiwari, Stephanie Malfatti, Hajnalka Kiss, Alla Lapidus [......] Matt Nolan, Miriam Land, Natalia Ivanova, Konstantinos Mavromatis, Victor Markowitz, Nikos Kyrpides, Vanessa Melino, Matthew Denton, Ron Yates, John Howieson

  Standards in genomic sciences. 01/2010; 2(1):66-76.

  Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile,Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.