- Genome sequencing in microfabricated high-density picolitre reactors
454 Life Sciences Corp, 20 Commercial Street, Branford, Connecticut 06405, USA
Nature 437:376-80. 2005
..Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine...
- RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO 0027 Oslo, Norway
Nucleic Acids Res 35:3100-8. 2007
..pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute...
- Velvet: algorithms for de novo short read assembly using de Bruijn graphs
Daniel R Zerbino
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Genome Res 18:821-9. 2008
..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
- Identifying bacterial genes and endosymbiont DNA with Glimmer
Arthur L Delcher
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Bioinformatics 23:673-9. 2007
..This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host...
- Mauve: multiple alignment of conserved genomic sequence with rearrangements
Aaron C E Darling
Department of Computer Science, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Genome Res 14:1394-403. 2004
..We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution...
- The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
Nucleic Acids Res 33:5691-702. 2005
..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms...
- The complete genome sequence of Escherichia coli K-12
F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997
..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
S T Cole
Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK
Nature 393:537-44. 1998
- Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
PLoS Genet 5:e1000344. 2009
..Overall, despite a very high gene flow, genes co-exist in an organised genome...
- Metagenomic analysis of the human distal gut microbiome
Steven R Gill
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 312:1355-9. 2006
..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
- The human microbiome project
Peter J Turnbaugh
Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
Nature 449:804-10. 2007
..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...
- CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
Univ Paris Sud, Institut de Genetique et Microbiologie, UMR 8621, Orsay, F 91405, France
Nucleic Acids Res 35:W52-7. 2007
..CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php...
- Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
S D Bentley
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 417:141-7. 2002
..The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering...
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
Genome Res 18:1851-8. 2008
..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
- ISfinder: the reference centre for bacterial insertion sequences
Laboratoire de Microbiologie et Genetique Moleculaires, C N R S 118, route de Narbonne, F 31062 Toulouse Cedex, France
Nucleic Acids Res 34:D32-6. 2006
..Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication...
- Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
Nature 413:852-6. 2001
..Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets...
- Metagenomics: application of genomics to uncultured microorganisms
Department of Plant Pathology, University of Wisconsin Madison, Madison, WI 53706, USA
Microbiol Mol Biol Rev 68:669-85. 2004
..The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies...
- Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 293:498-506. 2001
..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
- The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
David A Rasko
Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
J Bacteriol 190:6881-93. 2008
..This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens...
- Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
Departement de Biochimie et de Microbiologie, Faculte des sciences et de genie, Groupe de Recherche en Ecologie Buccale, Felix d Herelle Reference Center for Bacterial Viruses, Universite Laval, Quebec City, Quebec G1V 0A6, Canada
J Bacteriol 190:1390-400. 2008
..Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1...
- An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants
Nicole T Liberati
Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
Proc Natl Acad Sci U S A 103:2833-8. 2006
..Comparison of the genes disrupted in the PA14 transposon insertion library with an independently constructed insertion library in P. aeruginosa strain PAO1 provides an estimate of the number of P. aeruginosa essential genes...
- GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
Nucleic Acids Res 29:2607-18. 2001
..These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed...
- Environmental genome shotgun sequencing of the Sargasso Sea
J Craig Venter
Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
Science 304:66-74. 2004
..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
- A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
Daniel H Haft
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Comput Biol 1:e60. 2005
..It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated...
- The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
Univ Paris Sud, Institut de Genetique et Microbiologie, UMR 8621, Orsay, France
BMC Bioinformatics 8:172. 2007
..As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations...
- Essential genes of a minimal bacterium
John I Glass
Synthetic Biology Group, J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 103:425-30. 2006
..Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth...
- Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients
Eric E Smith
Genome Center, Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 103:8487-92. 2006
..aeruginosa strains present in advanced CF infections differ systematically from those of "wild-type" P. aeruginosa and that these differences may offer new opportunities for treatment of this chronic disease...
- DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
Int J Syst Evol Microbiol 57:81-91. 2007
..It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available...
- Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
Nestle, Research Center, Vers chez les Blanc, CH 1000 Lausanne, Switzerland
Microbiol Mol Biol Rev 68:560-602, table of contents. 2004
..Prophages also contribute to the diversification of the bacterial genome architecture. In many cases, they actually represent a large fraction of the strain-specific DNA sequences...
- Comparative genomics of the lactic acid bacteria
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Proc Natl Acad Sci U S A 103:15611-6. 2006
- Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus
Binh An Diep
Department of Medicine, University of California, San Francisco General Hospital, San Francisco, CA 94143, USA
Lancet 367:731-9. 2006
..Our aim was to sequence its genome and compare it with those of other strains of S aureus to try to identify genes responsible for its distinctive epidemiological and virulence properties...
- The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Nat Genet 38:779-86. 2006
..The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism...
- The uncultured microbial majority
Michael S Rappé
Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
Annu Rev Microbiol 57:369-94. 2003
..Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory...
- A new evolutionary scenario for the Mycobacterium tuberculosis complex
Unite de Genetique Moleculaire Bacterienne, Laboratoire de Génomique des Microorganismes Pathogènes, and Centre National de Référence des Mycobactéries, Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
Proc Natl Acad Sci U S A 99:3684-9. 2002
..bovis lineage separated from the M. tuberculosis lineage. This observation suggests that the common ancestor of the tubercle bacilli resembled M. tuberculosis or M. canettii and could well have been a human pathogen already...
- Genomic insights that advance the species definition for prokaryotes
Konstantinos T Konstantinidis
Center for Microbial Ecology, and Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 102:2567-72. 2005
- Complete genome sequence of Lactobacillus plantarum WCFS1
Wageningen Centre for Food Sciences, P O Box 557, 6700 AN Wageningen, The Netherlands
Proc Natl Acad Sci U S A 100:1990-5. 2003
..These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome...
- Host-bacterial mutualism in the human intestine
Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
Science 307:1915-20. 2005
..We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ...
- A molecular view of microbial diversity and the biosphere
N R Pace
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
Science 276:734-40. 1997
- The microbial pan-genome
Immunobiological Research Institute of Siena IRIS, Chiron Vaccines, Via Fiorentina 1, 53100 Siena, Italy
Curr Opin Genet Dev 15:589-94. 2005
..Given that the number of unique genes is vast, the pan-genome of a bacterial species might be orders of magnitude larger than any single genome...
- A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
Adam M Feist
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Mol Syst Biol 3:121. 2007
..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
- Genomic islands: tools of bacterial horizontal gene transfer and evolution
Clinical Microbiology and Infectious Diseases, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
FEMS Microbiol Rev 33:376-93. 2009
..Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria...
- Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Nature 450:560-5. 2007
..Our results underscore how complex even a 1-microl environment can be...
- New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis
Michael G Smith
Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
Genes Dev 21:601-14. 2007
..The DNA sequencing approach described in this study allows the rapid elucidation of the DNA sequence of any microbe and, when combined with genetic screens, can identify many novel genes important for microbial pathogenesis...
- Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
C K Stover
PathoGenesis Corporation, Seattle, Washington 98119, USA
Nature 406:959-64. 2000
..aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance ..
- Microbial minimalism: genome reduction in bacterial pathogens
Nancy A Moran
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
Cell 108:583-6. 2002
..Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts...
- Evolutionary conservation of sequence and secondary structures in CRISPR repeats
DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Genome Biol 8:R61. 2007
..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
- The RAST Server: rapid annotations using subsystems technology
Ramy K Aziz
Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
BMC Genomics 9:75. 2008
..The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them...
- The complete genome sequence of Mycobacterium bovis
Unité de Génétique Moléculaire Bactérienne and PT4 Annotation, Genopole, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
Proc Natl Acad Sci U S A 100:7877-82. 2003
..bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis...
- Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
Microbiology 151:2551-61. 2005
..The presence of gene fragments in CRISPR structures and the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step...
- Comparisons of dN/dS are time dependent for closely related bacterial genomes
Eduardo P C Rocha
Atelier de BioInformatique, Universite Paris VI, 75005 Paris, France
J Theor Biol 239:226-35. 2006
..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...
- Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus
Danisco France SAS, BP10, F 86220 Dangé Saint Romain, France
J Bacteriol 190:1401-12. 2008
..Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes...
- Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
Genome Biol 8:R71. 2007
..This study employs comparative evolutionary analyses of 26 Streptococcus genomes to yield an improved understanding of the relative roles of recombination and positive selection in pathogen adaptation to their hosts...
- TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Jeremy D Selengut
TIGR, Bioinformatics Department, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 35:D260-4. 2007
..The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties...
- Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
Institut fur Botanik, Heinrich Heine Universitat, Universitatsstrasse 1, 40225 Dusseldorf, Germany
Proc Natl Acad Sci U S A 99:12246-51. 2002
- Genome of the bacterium Streptococcus pneumoniae strain R6
Infectious Diseases Research and Clinical Investigation, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
J Bacteriol 183:5709-17. 2001
..Among those proteins there may be new targets for vaccine and antibiotic development...
- Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
Timothy P Stinear
Department of Microbiology, Monash University, Clayton 3800, Australia
Genome Res 18:729-41. 2008
..tuberculosis. The work described herein provides a foundation for using M. marinum to better understand the determinants of pathogenesis of tuberculosis...
- Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
Nicholas R Thomson
The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
Genome Res 18:1624-37. 2008
..Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica...
- The multifarious, multireplicon Burkholderia cepacia complex
Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK
Nat Rev Microbiol 3:144-56. 2005
..Here we highlight the unique characteristics of the Bcc, focusing on the factors that determine virulence...
- Emergent properties of reduced-genome Escherichia coli
Institute of Biochemistry, Biological Research Center, H 6726 Szeged, Hungary
Science 312:1044-6. 2006
..Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties...
- Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
Gene W Tyson
Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
Environ Microbiol 10:200-7. 2008
..Results reinforce the importance of phage-host interactions in shaping microbial ecology and evolution over very short time scales...
Alan J A McBride
Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Ministry of Health, Rua Waldemar Falcao 121, 40295 001 Salvador, Bahia, Brazil
Curr Opin Infect Dis 18:376-86. 2005
..This review addresses the issues in the epidemiology, diagnosis and clinical management which confront public health responses, and highlights the progress made towards understanding the Leptospira genome, biology and pathogenesis...
- Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6
Joel A Lanie
Department of Biology, Indiana University Bloomington, Jordan Hall 142, Bloomington, IN 47405, USA
J Bacteriol 189:38-51. 2007
- Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
The Institute for Genomic Research, Rockville, Maryland, USA
PLoS Biol 2:E69. 2004
..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...
- The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode
Molecular Parasitology Division, New England Biolabs, Beverly, Massachusetts, USA
PLoS Biol 3:e121. 2005
..Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease...
- Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
K E Nelson
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Environ Microbiol 4:799-808. 2002
..Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production...
- The composite genome of the legume symbiont Sinorhizobium meliloti
UMR6061-CNRS, , , , F-35043 Rennes Cedex, France
Science 293:668-72. 2001
..The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments...
- Evolution of sensory complexity recorded in a myxobacterial genome
B S Goldman
Monsanto Company, St Louis, MO 63167, USA
Proc Natl Acad Sci U S A 103:15200-5. 2006
..Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation...
- Dynamics of Pseudomonas aeruginosa genome evolution
Department of Molecular Microbiology and Immunology, College of Medicine, School of Computing and Information Sciences, College of Engineering, Florida International University, Miami, FL 33199, USA
Proc Natl Acad Sci U S A 105:3100-5. 2008
..Consequently, this organism can survive in a wide range of environmental reservoirs that can serve as sources of the infecting organisms...
- Enzyme-specific profiles for genome annotation: PRIAM
Laboratoire de Genetique Cellulaire, INRA, INRA CNRS, BP27, 31326 Castanet Tolosan Cedex, France
Nucleic Acids Res 31:6633-9. 2003
..The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes...
- A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, MO 63110, USA
Science 299:2074-6. 2003
..These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine...
- Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
N T Perna
Genome Center of Wisconsin, and Department of Animal Health and Biomedical Sciences, University of Wisconsin, Madison 53706, USA
Nature 409:529-33. 2001
..These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance...
- Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Mark W Silby
Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA
Genome Biol 10:R51. 2009
..A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species...
- The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
Institut für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
J Biotechnol 104:5-25. 2003
..As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate...
- Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
Proc Natl Acad Sci U S A 99:14434-9. 2002
- Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W Tyson
Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
Nature 428:37-43. 2004
..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
- Prodigal: prokaryotic gene recognition and translation initiation site identification
Computational Biology and Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
BMC Bioinformatics 11:119. 2010
..Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals...
- Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 102:11064-9. 2005
..The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism...
- Massive comparative genomic analysis reveals convergent evolution of specialized bacteria
Faculty of Medicine, Unit for Research on Emergent and Tropical Infectious Diseases, CNRS IRD UMR 6236 IFR48, University of the Mediterranean, Marseilles, France
Biol Direct 4:13. 2009
..The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles...
- Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
Institut für Botanik III, Heinrich Heine Universitat Dusseldorf, Universitatsstrasse 1, 40225 Dusseldorf, Germany
Proc Natl Acad Sci U S A 105:10039-44. 2008
- Prophages and bacterial genomics: what have we learned so far?
Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132 2501, USA
Mol Microbiol 49:277-300. 2003
b>Bacterial genome nucleotide sequences are being completed at a rapid and increasing rate. Integrated virus genomes (prophages) are common in such genomes...
- The consequences of genetic drift for bacterial genome complexity
Chih Horng Kuo
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Genome Res 19:1450-4. 2009
..This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria...
- Comparative analysis of Acinetobacters: three genomes for three lifestyles
Génomique Métabolique, CNRS UMR8030, CEA Institut de Génomique Genoscope, Evry, France
PLoS ONE 3:e1805. 2008
..Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil...
- The CGView Server: a comparative genomics tool for circular genomes
Jason R Grant
Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada
Nucleic Acids Res 36:W181-4. 2008
..The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/..
- Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
Byung Kwan Cho
Department of Bioengineering, University of California San Diego, La Jolla, California 92093 0412, USA
Genome Res 18:900-10. 2008
..These novel results provide new insight into how Fis modulates DNA topology at a genome scale and thus advance our understanding of the architectural bases of the E. coli nucleoid...
- Trends between gene content and genome size in prokaryotic species with larger genomes
Konstantinos T Konstantinidis
Center for Microbial Ecology and Departments of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824 1325, USA
Proc Natl Acad Sci U S A 101:3160-5. 2004
..These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil...
- Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions
Nicolaas C Gey van Pittius
DST NRF Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
BMC Evol Biol 6:95. 2006
- Evolution of symbiotic bacteria in the distal human intestine
Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri, United States of America
PLoS Biol 5:e156. 2007
- Explaining microbial population genomics through phage predation
Departmento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, Spain
Nat Rev Microbiol 7:828-36. 2009
..Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate...
- Determination of the core of a minimal bacterial gene set
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Valencia, Spain
Microbiol Mol Biol Rev 68:518-37, table of contents. 2004
..The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed...
- Genome-wide experimental determination of barriers to horizontal gene transfer
Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Science 318:1449-52. 2007
..coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life...
- VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100176, China
Nucleic Acids Res 36:D539-42. 2008
..VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/...
- Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
J Bacteriol 187:6488-98. 2005
..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...
- Insertion sequences in prokaryotic genomes
Laboratoire de Microbiologie et Génétique Moléculaires UMR5100 CNRS Campus Université Paul Sabatier 118, route de Narbonne, F 31062 Toulouse Cedex, France
Curr Opin Microbiol 9:526-31. 2006
..They can have large and spectacular effects in shaping and reshuffling the bacterial genome. Recent studies have provided dramatic examples of such IS activity, including massive IS expansion during ..
- De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
Josephine A Reinhardt
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
Genome Res 19:294-305. 2009
..syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species...
- DOOR: a database for prokaryotic operons
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 37:D459-63. 2009
..We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB...
- An obesity-associated gut microbiome with increased capacity for energy harvest
Peter J Turnbaugh
Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
Nature 444:1027-31. 2006
..These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity...
- Molecular correlates of host specialization in Staphylococcus aureus
Department of Microbiology, Veterinary Pathobiology and Biomedical Genomics Center, University of Minnesota, Saint Paul, Minnesota, United States of America
PLoS ONE 2:e1120. 2007
..aureus clonal groups associated with human and ruminant infection. However, the molecular basis of host specialization in S. aureus is not understood...
- Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum
Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parco Area delle Scienze 11A, 43100 Parma, Italy
Microbiol Mol Biol Rev 71:495-548. 2007
..This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context...
- Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity
Laboratoire de Génomique des Microorganismes Pathogènes and CNRS URA 2171, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex 15, France
Nat Genet 36:1165-73. 2004
..The genome thus reflects the history and lifestyle of L. pneumophila, a human pathogen of macrophages that coevolved with fresh-water amoebae...
- Functional metagenomic profiling of nine biomes
Elizabeth A Dinsdale
Department of Biology, San Diego State University, San Diego, California 92182, USA
Nature 452:629-32. 2008
- Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv
State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
PLoS ONE 3:e2375. 2008
..These findings have implications not only for improved understanding of pathogenesis of M. tuberculosis but also for development of new vaccines and new therapeutic agents...