The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae , the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for ≈80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata-driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal ‘Workbenches’ for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N 2 fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.

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.

Sulfate-reducing bacteria (SRB) are anaerobic prokaryotes found ubiquitously in nature. SRB were the first nonphotosynthetic, anaerobic bacteria shown to generate energy (ATP) through electron transfer-coupled phosphorylation. For this process, the SRB typically use sulfate as the terminal electron acceptor for respiration of hydrogen or various organic acids, which results in the production of sulfide, a highly reactive and toxic end-product. Beyond their obvious function in the sulfur cycle, SRB play an important role in global cycling of numerous other elements 1 . For example, in the carbon cycle, the SRB form part of microbial consortia that completely mineralize organic carbon in anaerobic environments; polymeric materials (e.g., cellulose) are first depolymerized and metabolized by fermentative microorganisms, and the resulting organic acid and reduced gas (that is, CO and H 2 ) end-products are further fermented or oxidized by other microbes, including SRB. The latter are particularly active in sulfate-rich (e.g., marine) environments, where they effectively link the global sulfur and carbon cycles 1,2 .Beyond these ecological roles, SRB also have a major economic impact because of their involvement in biocorrosion of ferrous metals in anaerobic environments 3 , described as "industrial venereal disease-it's expensive, everybody has it, and nobody wants to talk about it" 4 . For example, because SRB are abundant in oil fields, their metabolism has many negative consequences for the petroleum industry (e.g., corrosion of drilling and pumping machinery and storage tanks, souring of oil by sulfide production, plugging of machinery and rock pores with biomass and sulfide precipitates). The SRB also contribute to bioremediation of toxic metal ions 5,6 . Their metabolism increases the pH, causing toxic metal ions like copper (II), nickel (II) and cadmium (II) to precipitate as metal sulfides in acidic aquatic environments (e.g., mine effluents). Additionally, SRB can deliver electrons directly to oxidized toxic metal ions, including uranium (VI), technetium (VII), and chromium (VI), converting these into less soluble, reduced forms. Hence, SRB-mediated reduction represents a potentially useful mechanism for the bioremediation of metal ion contaminants from anaerobic sediments 6 .Most research on the metabolism and biochemistry of SRB has been done on the genus Desulfovibrio, a member of the δ-proteobacteria The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encod...

The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and coldadapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.proteome ͉ psychrophily ͉ bioremediation ͉ astrobiology ͉ threedimensional homology modeling

Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.Pseudomonas spp. are ubiquitous inhabitants of soil, water and plant surfaces that belong to the Gamma subclass of Proteobacteria. Many pseudomonads live in a commensal relationship with plants, utilizing nutrients exuded from plant surfaces and surviving environmental stress by occupying protected sites provided by the plant's architecture. These commensal species can have profound effects on plants by suppressing pests, enhancing access to key nutrients, altering physiological processes or degrading environmental pollutants. Pseudomonads have an exceptional capacity to produce a wide variety of metabolites, including antibiotics that are toxic to plant pathogens 1,2 . Antibiotic production by plant-associated Pseudomonas spp. enhances the fitness of the producing strain 3 and suppresses pathogens that would otherwise jeopardize plant health 1,2,4 . Certain antibiotic-producing strains of Pseudomonas spp. function as biological control agents; their capacity to protect plants from disease distinguishes them as microorganisms with immense effects on agricultural productivity.Among the plant commensals, P. fluorescens Pf-5 is notable as a biological control organism, for its rhizosphere competence and the spectrum of antibiotics and other secondary metabolites that it produces. P. fluorescens Pf-5 inhabits the rhizosphere of many plants and suppresses plant diseases caused by soilborne plant pathogens [5][6][7][8][9][10][11] . P. fluorescens Pf-5 produces a suite of antibiotics including pyrrolnitrin 5 , pyoluteorin 11 and 2,4-diacetylphloroglucinol 12 . It also produces hydrogen cyanide and the siderophores pyochelin and pyoverdine, which can suppress target pathogens in the rhizosphere through iron competition 13,14 . In this study, we report the complete genome sequence of P. fluorescens Pf-5, and highlight genes with a demonstrated or proposed role in biological control or rhizosphere colonization. RESULTS Genome features and comparati...