- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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.)...
- 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
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- 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...
- 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
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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 complete genome sequence of the gram-positive bacterium Bacillus subtilis
Institut Pasteur, Unité de Biochimie Microbienne, Paris, France
Nature 390:249-56. 1997
- 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...
- 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 ..
- 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...
- 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...
- 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...
- 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...
- Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli
Centre de Génétique Moléculaire du CNRS, Bat 26, 1 Avenue de la Terrasse, F 91198 Gif sur Yvette, France and Centre de Biophysique Moléculaire du CNRS, Avenue Ch Sadron, F 45071 Orléans, France
Mol Microbiol 55:601-10. 2005
..These results correlate the ability of a DNA sequence to be cleaved by DNA gyrase with topological insulator activity. Implications of the asymmetry in supercoil diffusion for the control of DNA topology are discussed...
- 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...
- Macrodomain organization of the Escherichia coli chromosome
Centre de Génétique Moléculaire du CNRS, Avenue de la Terrasse, Gif sur Yvette, France
EMBO J 23:4330-41. 2004
..Also the interactions between sister chromatids are rare, suggesting that chromosome segregation quickly follows replication. These results reveal structural features that may be important for chromosome dynamics during the cell cycle...
- 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...
- 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...
- Biofilm formation by Streptococcus pneumoniae: role of choline, extracellular DNA, and capsular polysaccharide in microbial accretion
Departamento de Microbiologia Molecular, Centro de Investigaciones Biologicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
J Bacteriol 188:7785-95. 2006
..Those results, in turn, may provide insight into strategies to prevent pneumococcal colonization of its human host...
- Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
Scot E Dowd
USDA ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA
BMC Microbiol 8:125. 2008
..We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows...
- The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
Nucleic Acids Res 36:3950-5. 2008
..We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness...
- 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...
- 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
- Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses
Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
BMC Genomics 9:42. 2008
..Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene...
- 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...
- Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM
Graduate Program in Biophysics, Harvard Medical School, Boston, Massachusetts 02115, USA
J Biol Chem 285:1468-78. 2010
MutM, a bacterial DNA glycosylase, protects genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions, thereby initiating base excision DNA repair...
- Long PCR improves Wolbachia DNA amplification: wsp sequences found in 76% of sixty-three arthropod species
Department of Entomology and Nematology, University of Florida, Gainesville, Florida 32611, USA
Insect Mol Biol 9:393-405. 2000
..Hence, superinfection also may be more widespread than the 1.2% incidence previously estimated...
- Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements
D van Soolingen
Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
J Intern Med 249:1-26. 2001
..tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted...
- Evaluation of a two-step approach for large-scale, prospective genotyping of Mycobacterium tuberculosis isolates in the United States
Lauren S Cowan
Division of TB Elimination, National Center for HIV, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
J Clin Microbiol 43:688-95. 2005
..IS6110 fingerprinting can then be used as a secondary typing method to type the clustered isolates when additional discrimination is needed...
- Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum
Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich Wilhelms Universitat Bonn, Meckenheimer Allee 168, D 53115 Bonn, Germany
J Bacteriol 187:1392-404. 2005
- Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system
Andrew P Tomaras
Department of Microbiology, Miami University, 40 Pearson Hall, Oxford, OH 45056, USA
Microbiology 149:3473-84. 2003
- Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
Scot E Dowd
USDA ARS Livestock Issues Research Unit, Lubbock, Texas 79403, USA
Foodborne Pathog Dis 5:459-72. 2008
..Using bTEFAP, we can expect to gain a better understanding of how the microbiome of an animal contributes to its health and well-being...
- Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
Seong Woon Roh
Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
ISME J 4:1-16. 2010
- High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease
Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
Gut 56:669-75. 2007
..One way of determining which bacteria might be likely candidates is to use culture-independent methods to identify microorganisms that are present in diseased tissues but not in controls...
- Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes
Julie C Dunning Hotopp
Institute for Genomic Research, J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 317:1753-6. 2007
..Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions...
- Polymerase chain reaction primers miss half of rRNA microbial diversity
Department of Biology, Northeastern University, Boston, MA, USA
ISME J 3:1365-73. 2009
- Purification and characterization of PCR-inhibitory components in blood cells
W A Al-Soud
Applied Microbiology, Center for Chemistry and Chemical Engineering, Lund Institute of Technology, Lund University, SE-221 00 Lund, Sweden
J Clin Microbiol 39:485-93. 2001
..Including 0.02% (wt/vol) gp32, a single-stranded-DNA binding protein, in the reaction mixture of AmpliTaq Gold was also found to reduce the inhibitory effects of hemoglobin and lactoferrin...
- Cutting edge: Cytosolic bacterial DNA activates the inflammasome via Aim2
Sarah E Warren
Institute for Systems Biology, Seattle, WA 98103, USA
J Immunol 185:818-21. 2010
..We now use biochemical and genetic approaches to demonstrate that the third detector senses bacterial DNA and identify it as Aim2, a receptor that has previously been shown to detect viral DNA.
- Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome--a longitudinal study in IBS and control subjects
VTT Biotechnology, Finland
FEMS Immunol Med Microbiol 43:213-22. 2005
..The present study suggests that instability of intestinal microbiota may be involved in IBS. However, further studies are needed to associate the instability with specific IBS symptoms or with specific bacterial groups and species...
- Wolbachia infection frequencies in insects: evidence of a global equilibrium?
J H Werren
Department of Biology, University of Rochester, NY 14627, USA
Proc Biol Sci 267:1277-85. 2000
..Within each of the three geographic regions surveyed, Hymenoptera are more frequently infected with A group Wolbachia and Lepidoptera more frequently infected with B group Wolbachia...
- Biofilms formed by nontypeable Haemophilus influenzae in vivo contain both double-stranded DNA and type IV pilin protein
Joseph A Jurcisek
Columbus Children s Research Institute, Center for Microbial Pathogenesis, The Ohio State University College of Medicine, 700 Children s Drive, Columbus, OH 43205 2696, USA
J Bacteriol 189:3868-75. 2007
- Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes
J A Carriço
Grupo de Biomatemática, Istituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6 2780 156 Oeiras, Portugal
J Clin Microbiol 44:2524-32. 2006
..803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes...
- Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis
Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam, Germany
Plant J 56:28-39. 2008
- Identification of serotype in culture negative pneumococcal meningitis using sequential multiplex PCR: implication for surveillance and vaccine design
Samir K Saha
Department of Microbiology, Bangladesh Institute of Child Health, Dhaka Shishu Children Hospital, Dhaka, Bangladesh
PLoS ONE 3:e3576. 2008
..Furthermore, PCR has not been used to determine serotype distribution in culture-negative meningitis cases...
- Mucosal flora in inflammatory bowel disease
Innere Klinik, Gastroenterologie, Charité Humboldt Universität, Berlin, Germany
Gastroenterology 122:44-54. 2002
..Microorganisms that directly interact with the intestinal mucosa are obscured by fecal flora and poorly characterized...
- Development of a new PCR-ribotyping method for Clostridium difficile based on ribosomal RNA gene sequencing
Laboratoire de Bacteriologie, Centre Hospitalo Universitaire Saint Antoine, Assistance Publique Hopitaux de Paris, France
FEMS Microbiol Lett 175:261-6. 1999
..This typing method has evidenced major qualities such as easiness, rapidity and reproducibility. However, its discriminatory power has to be evaluated to validate its importance as a typing tool for C. difficile...
- Silencing of episomal transgene expression by plasmid bacterial DNA elements in vivo
Z Y Chen
Departments of Pediatrics and Genetics, Stanford University School of Medicine, 200 Pasteur Drive, Room G305, Stanford, CA 94305 5208, USA
Gene Ther 11:856-64. 2004
We previously demonstrated that sustainable enhanced levels of transgene products could be expressed from a bacterial DNA-free expression cassette either formed from a fragmented plasmid in mouse liver or delivered as a minicircle vector...