- 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...
- CRISPR provides acquired resistance against viruses in prokaryotes
Danisco USA Inc, 3329 Agriculture Drive, Madison, WI 53716, USA
Science 315:1709-12. 2007
..Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity...
- A Toll-like receptor recognizes bacterial DNA
Department of Host Defense, Research Institute for Microbial Diseases, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Suita
Nature 408:740-5. 2000
..effects on mammalian immune cells, which depend on the presence of unmethylated CpG dinucleotides in the bacterial DNA. In contrast, mammalian DNA has a low frequency of CpG dinucleotides, and these are mostly methylated; ..
- WebLogo: a sequence logo generator
Gavin E Crooks
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Genome Res 14:1188-90. 2004
..A command line interface and the complete, open WebLogo source code are available for local installation and customization...
- Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
J Clin Microbiol 44:4498-510. 2006
..This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies...
- 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...
- 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...
- An efficient recombination system for chromosome engineering in Escherichia coli
Gene Regulation and Chromosome Biology Laboratory and Mouse Cancer Genetics Program, National Cancer Institute, Division of Basic Science, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
Proc Natl Acad Sci U S A 97:5978-83. 2000
..This system will be especially useful for the engineering of large bacterial plasmids such as those from bacterial artificial chromosome libraries...
- Review and re-analysis of domain-specific 16S primers
G C Baker
Department of Biotechnology, University of the Western Cape, Bellville 7335, Cape Town, South Africa
J Microbiol Methods 55:541-55. 2003
..These primers are found to amplify sequences from Crenarchaeote and Euryarchaeote type strains and environmental DNA...
- Genome-wide insertional mutagenesis of Arabidopsis thaliana
Jose M Alonso
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
Science 301:653-7. 2003
..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
- CpG motifs in bacterial DNA and their immune effects
Arthur M Krieg
Department of Veterans Affairs Medical Center, Iowa City, Iowa 52246, USA
Annu Rev Immunol 20:709-60. 2002
..CpG ODN also enhance the development of acquired immune responses for prophylactic and therapeutic vaccination...
- GATEWAY vectors for Agrobacterium-mediated plant transformation
Dept of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, K L Ledeganckstraat 35, B 9000, Gent, Belgium
Trends Plant Sci 7:193-5. 2002
..Because these vectors are generally large, cloning can be time-consuming and laborious. Recently, the GATEWAY conversion technology has provided a fast and reliable alternative to the cloning of sequences into large acceptor plasmids...
- Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
C K Stover
PathoGenesis Corporation, Seattle, Washington 98119, USA
Nature 406:959-64. 2000
..We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances...
- A gateway cloning vector set for high-throughput functional analysis of genes in planta
Mark D Curtis
Institute of Plant Biology and Zurich Basel Plant Science Centre, University of Zurich, Zollikerstrasse 107, Ch 8008 Zurich, Switzerland
Plant Physiol 133:462-9. 2003
..All vectors were derived from pCambia T-DNA cloning vectors, with the exception of a chemically inducible vector, for Agrobacterium sp.-mediated transformation of a wide range of plant species...
- 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...
- Pyrosequencing analysis of the oral microflora of healthy adults
B J F Keijser
TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Zeist, The Netherlands
J Dent Res 87:1016-20. 2008
..This work gives a radically new insight into the diversity of human oral microflora, which, with an estimated number of 19,000 phylotypes, is considerably higher than previously reported...
- Opinion: Re-evaluating prokaryotic species
Laboratory of Microbiology and the Bioinformatics and Evolutionary Genomics Research Group, Ghent University VIB, Ghent, Belgium
Nat Rev Microbiol 3:733-9. 2005
..We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters...
- Molecular identification of bacteria associated with bacterial vaginosis
David N Fredricks
Program in Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
N Engl J Med 353:1899-911. 2005
..The cause of bacterial vaginosis remains poorly understood despite numerous studies based on cultures. Bacteria in microbial communities can be identified without cultivation by characterizing their ribosomal DNA (rDNA) sequences...
- A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms
Centre for Biomedical Microbiology, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
Mol Microbiol 59:1114-28. 2006
- 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
- RecBCD enzyme and the repair of double-stranded DNA breaks
Mark S Dillingham
DNA Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
Microbiol Mol Biol Rev 72:642-71, Table of Contents. 2008
..In this review, we discuss the biochemical mechanism of the RecBCD enzyme with particular emphasis on new developments relating to the enzyme's structure and DNA translocation mechanism...
- Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication
Patrick H Viollier
Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 101:9257-62. 2004
- Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota
MRC Microbiology and Gut Biology Group, University of Dundee, Dundee, United Kingdom
Appl Environ Microbiol 70:3575-81. 2004
- DNA gyrase, topoisomerase IV, and the 4-quinolones
Public Health Research Institute, New York, New York 10016, USA
Microbiol Mol Biol Rev 61:377-92. 1997
..both for unlinking replicated daughter chromosomes and for controlling negative superhelical tension in bacterial DNA. However, in 1990 a homolog of gyrase, topoisomerase IV, that had a potent decatenating activity was ..
- Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
Jill E Clarridge
Department of Laboratory Medicine, University of Washington, Seattle, USA
Clin Microbiol Rev 17:840-62, table of contents. 2004
- Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates
Genoscreen, 1, rue du Professeur Calmette, Lille 59019 Cedex, France
J Clin Microbiol 46:2692-9. 2008
..The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far...
- 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...
- Plasma levels of bacterial DNA correlate with immune activation and the magnitude of immune restoration in persons with antiretroviral-treated HIV infection
Case Western Reserve University, Cleveland, Ohio 44106, USA
J Infect Dis 199:1177-85. 2009
..These findings are consistent with the importance of microbial translocation in immunodeficiency and T cell homeostasis in chronic HIV infection...
- Human TLR9 confers responsiveness to bacterial DNA via species-specific CpG motif recognition
Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, 81675 Munich, Germany
Proc Natl Acad Sci U S A 98:9237-42. 2001
..The optimal CpG motif for hTLR9 was GTCGTT, whereas the optimal murine sequence was GACGTT. Overall, these data suggest that hTLR9 conveys CpG-DNA responsiveness to human cells by directly engaging immunostimulating CpG-DNA...
- Methicillin-resistant Staphylococcus aureus (MRSA) strain ST398 is present in midwestern U.S. swine and swine workers
Tara C Smith
Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
PLoS ONE 4:e4258. 2009
..However, no studies to date have investigated carriage of MRSA among swine and swine farmers in the United States (U.S.)...
- Multilocus sequence typing system for Campylobacter jejuni
K E Dingle
Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3FY, United Kingdom
J Clin Microbiol 39:14-23. 2001
..Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism...
- Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spre
Laboratory of Hospital Infection, Central Public Health Laboratory, London NW9 5HT, United Kingdom
J Clin Microbiol 41:1574-85. 2003
..This highlights the need for closer international collaboration to monitor the spread of current epidemic strains as well as the emergence of new ones...
- Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA
Science 271:1247-54. 1996
- The genome of Rhizobium leguminosarum has recognizable core and accessory components
J Peter W Young
Department of Biology, University of York, York, UK
Genome Biol 7:R34. 2006
..We have sequenced the genome of R. leguminosarum biovar viciae strain 3841...
- CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
Luciano A Marraffini
Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
Science 322:1843-5. 2008
..We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria...
- Extracellular DNA required for bacterial biofilm formation
Cynthia B Whitchurch
ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, QLD, Australia
Science 295:1487. 2002
- Natural genetic transformation: prevalence, mechanisms and function
Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
Res Microbiol 158:767-78. 2007
..Here we will review the most recent advances in our understanding of the phenomenon and discuss its possible biological functions...
- 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
- The complete genome sequence of the gram-positive bacterium Bacillus subtilis
Institut Pasteur, Unité de Biochimie Microbienne, Paris, France
Nature 390:249-56. 1997
- Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis
Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 228 8555, Japan
Nat Biotechnol 21:526-31. 2003
..In contrast, the terminal regions were not conserved and preferentially contained nonessential genes...
- Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology
DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
Int J Syst Evol Microbiol 52:1043-7. 2002
..The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists...
- Sequence typing reveals extensive strain diversity of the Lyme borreliosis agents Borrelia burgdorferi in North America and Borrelia afzelii in Europe
Department of Microbiology, B240 Medical Sciences I, University of California Irvine, Irvine, CA 92697 4025, USA
Microbiology 150:1741-55. 2004
..burgdorferi. It is concluded that B. burgdorferi and B. afzelii have greater genetic diversity than had previously been estimated, and that the IGS locus alone is sufficient for strain typing and phylogenetic studies...
- spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation
Public Health Research Institute, International Center for Public Health, Graduate School of Biomedical Sciences and New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
J Clin Microbiol 42:792-9. 2004
..This study showed that genetic analysis of the repeat region of protein A comprehensively characterizes both micro- and macrovariation in the primarily clonal population structure of S. aureus...
- Spatial and temporal organization of replicating Escherichia coli chromosomes
Ivy F Lau
Division of Molecular Genetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
Mol Microbiol 49:731-43. 2003
..This asymmetry could provide a mechanism by which the chromosome segregation protein FtsK, located at the division septum, can act directionally to ensure that the septal region is free of DNA before the completion of cell division...
- Molecular evidence for a uniform microbial community in sponges from different oceans
Institut für Molekulare Infektionsbiologie, Universitat Wurzburg, D 97070 Wurzburg, Germany
Appl Environ Microbiol 68:4431-40. 2002
..A picture emerges where sponges can be viewed as highly concentrated reservoirs of so far uncultured and elusive marine microorganisms...
- Development and application of two multiplex real-time PCR assays for the detection of Mycobacterium ulcerans in clinical and environmental samples
Janet A M Fyfe
Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
Appl Environ Microbiol 73:4733-40. 2007
..This suite of new methods is enabling rapid progress in the understanding of the ecology of this important human pathogen...
- Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts
Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, 44691, USA
J Bacteriol 188:3682-96. 2006
..The AY-WB genome is approximately 154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Furthermore, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M...
- Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis
Unite de Recherche en Genomique Vegetale, Institut National de la Recherche Agronomique Centre National de la Recherche Scientifique Université d Evry Val d Essone, CP 5708, 91057 Evry Cedex, France
Plant Cell 16:2089-103. 2004
..These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms...
- 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...
- Vaginal lactobacillus flora of healthy Swedish women
Laboratory of Food Hygiene, Division of Food Technology, Lund University, Sweden
J Clin Microbiol 40:2746-9. 2002
..L. iners has not previously been reported as one of the predominant Lactobacillus species in the vagina...
- Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing
Scot E Dowd
United States Department of Agriculture ARS Livestock Issues Research Unit, Lubbock, TX, USA
BMC Microbiol 8:43. 2008
- 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...
- Conjugative plasmid transfer in gram-positive bacteria
Microbial Ecology Group, University of Technology Berlin, D 10587 Berlin, Germany
Microbiol Mol Biol Rev 67:277-301, table of contents. 2003
- Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance
M J Daly
Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
Science 306:1025-8. 2004
..In contrast, Shewanella oneidensis and Pseudomonas putida have high iron but low intracellular manganese concentrations and are very sensitive. We propose that Mn(II) accumulation facilitates recovery from radiation injury...
- High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology
, , U447, Institut Pasteur de Lille, rue du Prof. Calmette, F-59019 Lille Cedex, France
Proc Natl Acad Sci U S A 98:1901-6. 2001
..This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis...
- Evaluation of Brucella MLVA typing for human brucellosis
Sascha Al Dahouk
Bundeswehr Institute of Microbiology, Department of Bacteriology, Neuherbergstr 11, D 80937 Munich, Germany
J Microbiol Methods 69:137-45. 2007
..MLVA can significantly contribute to epidemiological trace-back analysis of Brucella infections and may advance surveillance and control of human brucellosis...
- Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'
Janelle R Thompson
Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA
Nucleic Acids Res 30:2083-8. 2002
..This simple modification to the protocol may ensure that sequence richness encountered in clone libraries more closely reflects genetic diversity in the original sample...
- Dynamic organization of chromosomal DNA in Escherichia coli
Unit Process and Combined Circuit, PRESTO, Japan Science and Technology Corporation JST, Kumamoto, 862 0976, Japan
Genes Dev 14:212-23. 2000
..These studies thus suggest that the E. coli chromosome is organized to form a compacted ring structure with the Ori and Ter domains; these domains participate in the cell cycle-dependent localization of the chromosome...
- The complete genome sequence of the gastric pathogen Helicobacter pylori
J F Tomb
Institute for Genomic Research, Rockville, Maryland 20850, USA
Nature 388:539-47. 1997
..pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH...
- 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...
- Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
National Research Council, Segrate, Milan 20090, Italy
Antimicrob Agents Chemother 52:2616-25. 2008
..These findings provide novel insight into the genetic basis of A. baumannii resistance...
- Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited
Thomas D Leser
Department of Microbiology, Danish Veterinary Laboratory, Bulowsvej 27, DK 1790 Copenhagen V, Denmark
Appl Environ Microbiol 68:673-90. 2002
..The results document that the intestinal microbial community is very complex and that the majority of the bacterial species colonizing the gastrointestinal tract in pigs have not been characterized...
- Bacterial DNA repair by non-homologous end joining
Sloan Kettering Institute, 1275 York Avenue, New York, New York 10021, USA
Nat Rev Microbiol 5:852-61. 2007
..Although still a young field, bacterial NHEJ promises to teach us a great deal about the nexus of DNA repair and bacterial pathogenesis...
- Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
David C Grainger
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
Nucleic Acids Res 34:4642-52. 2006
..Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase...
- Microbial population structures in the deep marine biosphere
Julie A Huber
Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
Science 318:97-100. 2007
- spa Typing of Staphylococcus aureus as a frontline tool in epidemiological typing
Robert Koch Institute, Wernigerode Branch, Burgstr 37, D 38855 Wernigerode, Germany
J Clin Microbiol 46:574-81. 2008
..They should be selected by dependence on the clonal lineage indicated by spa typing and subsequent BURP analysis as well as on the basis of the particular question to be addressed...
- Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation
Oxford University Department of Paediatrics, Molecular Infectious Diseases Group, Weatherall Institute of Molecular Medicine Oxford, United Kingdom
Annu Rev Genet 40:307-33. 2006
..These SSRs are located within the reading frame or in the promoter of a subset of genes, often termed contingency loci, whose functions are usually involved in direct interactions with host structures...
- DNA as a nutrient: novel role for bacterial competence gene homologs
S E Finkel
Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 1340, USA
J Bacteriol 183:6288-93. 2001
..Homologs of these E. coli genes are present in many members of the gamma subclass of Proteobacteria, suggesting that the mechanisms for consumption of DNA may have been widely conserved during evolution...
- Instability of repetitive DNA sequences: the role of replication in multiple mechanisms
Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA
Proc Natl Acad Sci U S A 98:8319-25. 2001
..Replication plays a critical role in the two slipped misalignment mechanisms, and difficulties in replication appear to trigger rearrangements via all these mechanisms...
- Phylogeny of Wolbachia in filarial nematodes
Istituto di Patologia Generale Veterinaria, Universita di Milano, Italy
Proc Biol Sci 265:2407-13. 1998
..Thus, there is no evidence for recent Wolbachia transmission between arthropods and nematodes. Endosymbiont 16S ribosomal DNA sequences from a subset of filarial species support these findings...
- Distribution of Mycobacterium ulcerans in buruli ulcer endemic and non-endemic aquatic sites in Ghana
Heather R Williamson
Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
PLoS Negl Trop Dis 2:e205. 2008
..These findings imply that focal demography, along with patterns of human water contact, may play a major role in transmission of Buruli ulcer...
- Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function
Department of Genetics, 425 Henry Mall, University of Wisconsin, Madison, WI 53706, USA
J Bacteriol 187:1135-60. 2005
..We suggest that E. coli MG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized...
- Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Nature 413:848-52. 2001
..typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis...
- Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments
Molecular Ecology Unit, Max Planck Institute for Marine Microbiology, Fahrenheitstrasse 1, D 28359 Bremen, Germany
Arch Microbiol 164:165-72. 1995
..The third 'phylotype' was identified as a Desulfovibrio, indicating that sulfate-reducing bacteria, as sources of sulfide, may complement sulfur- and sulfide-oxidizing bacteria ecologically in these sulfide-producing hydrothermal vents...
- Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
Unité d Ecologie et de Physiologie du Système Digestif, INRA UEPSD, 78350 Jouy en Josas, France
Gut 55:205-11. 2006
..However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches...
- The evolution of class 1 integrons and the rise of antibiotic resistance
Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
J Bacteriol 190:5095-100. 2008
..The strong selection pressure imposed by the human use of antimicrobial compounds then ensured their fixation and global spread into new species...
- Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
Georgios S Vernikos
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK
Bioinformatics 22:2196-203. 2006
..g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes...
- Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase
Graduate School of Information Science, Nara Institute of Science and Technology, 8916 5 Takayama, Ikoma, Nara, Japan
DNA Res 13:141-53. 2006
..coli genome, sheds light on the mechanism underlying the transcriptional regulation by H-NS, and provides new insight into bacterial genome evolution...
- Population snapshot of emergent Streptococcus pneumoniae serotype 19A in the United States, 2005
Matthew R Moore
Respiratory Diseases Branch, Centers for Disease Control and Prevention, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
J Infect Dis 197:1016-27. 2008
..To understand this increase, we characterized serotype 19A isolates recovered during 2005...
- Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network
MRC SAIMR Wits Pneumococcal Diseases Research Unit, Johannesburg, South Africa
J Clin Microbiol 39:2565-71. 2001
..This network can serve as a prototype for the collaboration of scientists in identifying clones of important human pathogens and as a model for the development of other networks...
- Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease
M P Conte
Paediatric Gastroenterology Unit, University of Rome La Sapienza, Viale Regina Elena 324, Rome 00161, Italy
Gut 55:1760-7. 2006
..No paediatric reports are available on intestinal endogenous microflora in IBD...
- Microbial gene identification using interpolated Markov models
S L Salzberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 26:544-8. 1998
..As a result, GLIMMER is more flexible and more powerful than fixed-order Markov methods, which have previously been the primary content-based technique for finding genes in microbial DNA...
- FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G + C content
Department of Bioactive Molecules, National Institute of Infectious Diseases, Tokyo, Japan
FEMS Microbiol Lett 174:251-3. 1999
FramePlot is a web-based tool for predicting protein-coding regions in bacterial DNA with a high G + C content, such as Streptomyces. The graphical output provides for easy distinction of protein-coding regions from non-coding regions...
- Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA
Department of Microbiology, University of Bergen, Norway
Appl Environ Microbiol 63:3367-73. 1997
..Several dominant fragments in the DGGE profiles were excised and sequenced. Among the dominant populations were representatives related to Chlorobium phaeovibrioides, chloroplasts from eukaryotic algae, and unidentified Archaea...
- Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites
The Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108 8642, Japan
Proc Natl Acad Sci U S A 98:12215-20. 2001
..These secondary metabolite clusters are widely located in the genome but half of them are near both ends of the genome. The total length of these clusters occupies about 6.4% of the genome...
- ISCR elements: novel gene-capturing systems of the 21st century?
Mark A Toleman
Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
Microbiol Mol Biol Rev 70:296-316. 2006
..It appears that ISCR elements have now firmly established themselves within that regimen...
- Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion
Moorepark Food Research Centre, Moorepark, Fermoy, Co Cork, Ireland
J Bacteriol 190:727-35. 2008
..helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement...
- Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR
Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Section of Microbiology, P O Box 66, FIN 00014 University of Helsinki, Finland
Am J Gastroenterol 100:373-82. 2005
..The gut microbiota may contribute to the onset and maintenance of irritable bowel syndrome (IBS). In this study, the microbiotas of patients suffering from IBS were compared with a control group devoid of gastrointestinal (GI) symptoms...
- Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
INRA, CR de Jouy en Josas, 78352 Jouy en Josas, France
Gut 52:237-42. 2003
..We investigated potential differences in the faecal microflora between patients with colonic CD in remission (n=9), patients with active colonic CD (n=8), and healthy volunteers (n=16) using culture independent techniques...
- The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects
Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, Finland
Gastroenterology 133:24-33. 2007
..Our objective was to characterize putative differences in gastrointestinal microbiota between patients with IBS and control subjects. These differences could potentially have a causal relationship with the syndrome...
- Unique features of a highly pathogenic Campylobacter jejuni strain
Section of Microbial Pathogenesis, School of Medicine, Yale University, New Haven, Connecticut 06536, USA
Infect Immun 74:4694-707. 2006
..This information should help the understanding of the pathogenesis of C. jejuni and, in particular, the unique features of this highly pathogenic strain...
- Bacterial conjugation: a two-step mechanism for DNA transport
Dipartmento de Biología Molecular, Unidad Asociada al CIB CSIC, Universidad de Cantabria, Santander, Spain
Mol Microbiol 45:1-8. 2002
..It is proposed that this second step is catalysed by the coupling proteins. Our 'shoot and pump' model solves the protein-DNA transport paradox of T4SS...
- The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters
Audra J Pompeani
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Mol Microbiol 70:76-88. 2008
..Together, the in silico and biochemical results enabled us to scan the genome and identify novel targets of LuxR in V. harveyi and thus expand the understanding of the quorum-sensing regulon...
- Inhibition of mutation and combating the evolution of antibiotic resistance
Ryan T Cirz
Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
PLoS Biol 3:e176. 2005
..Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance...
- Bacterial DNA activates cell mediated immune response and nitric oxide overproduction in peritoneal macrophages from patients with cirrhosis and ascites
Department of Immunology, Hospital General Universitario, Pintor Baeza s n, Alicante, Spain
Gut 53:860-4. 2004
..We have recently reported the detection of bacterial DNA in blood and ascitic fluid from patients with advanced cirrhosis, what we consider as molecular evidence of ..
- Efficient electrotransformation of corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1
Zentrum für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
Curr Microbiol 45:362-7. 2002
..diphtheriae. Thus, the ability to apply the standard methods of C. glutamicum recombinant DNA technology will greatly facilitate the functional analysis of the recently completed C. diphtheriae genome sequence...
- An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics
Mario G Rosso
GABI Kat, Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, 50829 Köln, Germany
Plant Mol Biol 53:247-59. 2003
..Finally, the functionality of the GABI-Kat population was demonstrated by exemplary confirmation of several new transparent testa alleles, as well as a number of other mutants, which were identified on the basis of the FST data...
- A comparison of homologous recombination rates in bacteria and archaea
Department of Zoology, University of Oxford, Oxford, UK
ISME J 3:199-208. 2009
..This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate...
- Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
Department of Microbiology, Miyazaki Medical College, Kiyotake, Japan
DNA Res 8:11-22. 2001
..A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection...
- Resistance-nodulation-cell division-type efflux pump involved in aminoglycoside resistance in Acinetobacter baumannii strain BM4454
, Institut Pasteur, 75724 Paris Cedex 15, France
Antimicrob Agents Chemother 45:3375-80. 2001
..The products of two upstream open reading frames encoding a putative two-component regulatory system might be involved in the regulation of expression of the adeABC gene cluster...
- Detection of Streptococcus pneumoniae strain cocolonization in the nasopharynx
Silvio D Brugger
Institute for Infectious Diseases, University of Bern, Friedbuhlstrasse 51, CH 3010 Bern, Switzerland
J Clin Microbiol 47:1750-6. 2009
..025). This new technique allows for the rapid and economical study of pneumococcal cocolonization in nasopharyngeal swabs. It will be valuable for the surveillance of S. pneumoniae epidemiology under vaccine selection pressure...