What Is Molecular Microbiology?

Molecular microbiology major areas are microbial pathogenesis: analysis of virulence factors, bacterial toxins, lipopolysaccharides, and outer membrane proteins, interactions of pathogens and their products with eukaryotic host cells (cellular microbiology), antigenic variation, contemporary vaccine strategies, bacterial gene regulation (osmoregulation, quorum sensing), bacterial export and secretion, and genetic regulation of bacterial virulence expression; virology: human immunodeficiency virus, cytomegalovirus, hepatitis C virus, resistance to viral infections, viral replication and persistence, viral vaccines, eukaryotic gene regulation, signal transduction pathways, and cellular and molecular mechanisms of human oncogenesis; cellular and molecular immunology: functions of natural killer cells, antigen processing and presentation, functions of T cell subsets, mechanisms of immune cell activation by microbial modulins, immunotoxins, immunoprivileged sites, mechanisms of inflammation, dendritic cells, tumor immunology, and generation of antibody diversity.

Here are some research programmes of molecular microbiology:

Microbial Cell Surfaces, Pathogenicity, and Ecology The attachment of pathogenic microorganisms to host tissues is an important early step in the initiation of infection and involves specific components on the microbial cell surface. Research in this field is focusing on particular cell surface proteins as colonisation determinants of microbes, both eukaryotic (Candida) and prokaryotic (oral streptococci and pneumococci), and as virulence factors (Prevotella intermedia and Porphyromonas gingivalis). The intergeneric coadherence of several of these microorganisms is also under investigation. Characterisation of adhesion interactions in the oral cavity may lead to new ways of preventing oral diseases. In addition, microbial cell surface proteins are considered to be promising candidates for vaccine development. Our research projects aim to develop an understanding of the molecular architecture of oral-pathogen cell surfaces and their interactions.

Examples of molecular microbiology research themes:

The research themes are constantly evolving.

Tuberculosis Epidemiology and evolution of tuberculosis

The introduction of molecular methods for typing Mycobacterium tuberculosis has made epidemiological analysis possible. Now the complete sequence of the genome of this bacterium is available, we can also use this approach to study its evolution. The identification of different strain families will not only enable us to trace the spread of tuberculosis, historically and currently, but will also open up new ways of studying the disease-causing properties of the tubercle bacillus.

Gene expression in mycobacteria

When bacteria are growing inside a host, they express different genes from those seen in laboratory cultures. By understanding how these changes occur, and finding out which genes are affected, we can improve our understanding of how disease is caused, and develop better ways of combating it. Recent advances in molecular biology techniques provide powerful methods for this analysis of gene expression.

Developing TB vaccines

It is now possible to knock out specific genes in the TB bacillus. Studying the properties of these mutants will not only help us to understand the pathogenesis of tuberculosis, but will potentially lead to the development of new vaccines based on these attenuated strains.

Bacterial meningitis

The development of molecular techniques based on PCR for rapid detection of meningococci has considerable potential for improved diagnosis of meningitis and meningococcal septicaemia. We are developing and evaluating procedures for molecular typing of meningococci to enable outbreaks to be identified more quickly.

Metabolomics of the TB bacillus

The long duration of chemotherapy required for treatment of TB; reactivation of TB years after infection and even after successful treatment; detection of live tubercle bacilli in dormant lesions; and persistence of bacilli in infected mice after chemotherapy; all suggest that the bacillus can enter a distinct physiological state where it survives in a very slow growing state. How the pathogen switches to a slow-growing metabolism is completely unknown.

This project will be to utilize the vaccine strain of the tubercle bacillus, M. bovis BCG, which will be inoculated into the chemostat. Cells will be harvested once steady-state growth kinetics has been attained at fast and slow growth rates. Metabolites will be measured and RNA will be isolated from cells and used to screen a M. tuberculosis genome microarray to identify genes whose expression is up or down-regulated by growth rate. Bioinformatic and metabolic flux analysis will be utilized to identify critical genes that are required for maintenance of slow growth rate. Such genes may be new drug targets for TB.

Molecular virology Astrovirus and calicivirus

Astroviruses and caliciviruses are two important pathogens of the enteric tract. These viruses have only recently been characterised at the molecular level and researchers here have pioneered much of this study. Current research investigates the molecular biology of virus replication, regulation of transcription and translation and particularly the survival and dissemination of these agents through the environment through water courses and contamination of food. Work here is developing novel methods for virus detection and quantitation of active particles. Other environmental studies have included honeybee and fish viruses.

Virus Energetics and Apoptosis

Cell suicide is an effective means of containing virus infection in the body. For this reason many viruses have evolved mechanisms to prevent host cell suicide until their replication is complete. Others actually exploit host cell apoptosis for their own ends, eg in deriving proteases required for capsid maturation. Many virus proteins that affect/regulate host cell apoptosis are present in the mitochondrion and this can affect the electron transport chain and thus cell energy supplies. Such disruption becomes especially significant in the context of prolonged persistent or chronic virus infections where it may lead to fatigue or inhibition of cell function. Work in virology at Surrey collaborates with Dr George Kass in the Molecular Toxicology research group to investigate mitochondrial defects induced by virus infection, virus exploitation of caspases for maturational/regulatory cleavages and the mechanisms by which viruses can oppose apoptosis.

Viral translation mechanisms

Virus/host interactions at the translational level, and their role in pathogenesis, are being studied. We are interested in both the effect viral infections have on host cell protein synthesis and their role in cell damage, and the novel mechanisms of translation initiation used by viruses (such as picornaviruses and caliciviruses). We are particularly interested in novel viral internal ribosome entry site (IRES) elements and their exploitation in biotechnology.

Until quite recently acute phase proteins were considered to act as primitive antibodies opsonising a variety of pathogens, activating complement and increasing uptake by phagocytic cells. It is emerging, however, that these markers of inflammation may play important regulatory roles both in innate and acquired immune responses. This may affect a range of cell types through binding to a variety of cell surface receptors. We are investigating several of these roles, particularly for C-reactive protein (CRP), through binding specificities for pathogens and subsequent modulation of immune responses via binding to receptors on host cells such as macrophages and dendritic cells. CRP has also been shown to be a risk factor for cardiovascular disease and research is underway to investigate the role of interactions between CRP and endothelial cells in inflammation and atherosclerosis.

Atherogenesis

It has been recently suggested that the number of microbial infections may critically determine the development and progression of atherosclerotic disease. Several clinical studies have shown that patients with cardiovascular disease have higher titres of anti-bacterial antibodies (e.g. C. pneumoniae) compared with control patients. Also, viruses and/or bacteria have been detected within atherosclerotic lesions, but not in adjacent normal tissue by immunohistochemistry, polymerase chain reaction and electron microscopy and by culturing the organism from lesions. Importantly, studies using rabbit and mouse experimental models of atherosclerosis have shown that these infectious microorganisms can either initiate lesion development or can cause exacerbation of lesions. Although the exact mechanisms remain unknown it has been hypothesised that these microorganisms may have specific tropism for cells of the vascular wall contributing to the vascular injury via direct cytopathic effects or via the induction of focal autoimmune responses. Immunopathological processes such as molecular mimicry, epitope spreading or bystander activation of self-reactive lymphocytes by bacterial or viral antigens could potentially contribute to the chronic inflammatory process in the vascular wall. Our recently created group aims to investigate, among other aspects, the immunophatological mechanisms elicited during atherosclerosis development driven by bacterial/viral infection or by administration of selective microbial antigens.

Host-pathogen interactions in tuberculosis

One of the most striking features of tuberculosis is the ability of Mycobacterium tuberculosis to avoid destruction by the host immune response through the course of an infection that may last decades. We are researching several aspects of the host-pathogen interaction including bacterial control of phagosome biology and host cell recognition of microbial products such as lipoproteins and heat shock proteins.

Molecular based techniques have revolutionized our understanding of environmental microbiology. Over the last decade, the application of these techniques has improved our understanding of the composition, phylogeny, and physiology of microbial communities in the environment. However a thorough understanding of the limitations of these methods is essential to prevent researchers being led astray by their results.

The widespread use of molecular methods has resulted in a dramatic increase in our knowledge of the composition and physiology of microbial communities in the environment. This book is a collection of narrative texts and protocols describing many of these molecular methods and their application to environmental samples. Many of the methods focus on the detection and analysis of DNA, primarily through the use of the polymerase chain reaction (PCR). However, techniques for the analysis of RNA, proteins, and lipids are included, along with the use of DNA analogues such as peptide nucleic acid. The objective of the book is to provide an overview of the various methods and their applications as well as detailed laboratory protocols. Since the analysis of nucleic acids forms the cornerstone of environmental molecular microbiology, a review of the many procedures that have been developed for extracting DNA and RNA is provided. Many of the chapters present an objective description of some of the problems with the methods, including a detailed discussion of PCR biases, artifacts, and contamination. In addition to standard PCR, applications of quantitative PCR, sequence capture, conformation-based analysis, denaturing and thermal gradient gel techniques, gene expression methods, fatty acid profiling, proteomics, and in-situ techniques are all described.

Our knowledge of the types and distribution of microorganisms in the environment is rudimentary. Traditional enrichment techniques and the pure culture approach to microbiology have offered only a narrow portal into the microbial world. Over the last fifteen years, however, a wealth of novel biodiversity has been discovered through the application of molecular methodologies to microbial ecology. In particular, the cloning and sequencing of small subunit (16S/18S) ribosomal RNA genes (SSU rDNA) amplified directly from environmental samples using the polymerase chain reaction (PCR) has revealed significant, and often novel, biodiversity. PCR-cloning strategies have had an enormous impact on our understanding of microbial phylogeny, diversity and ecology.

The mission of the approximately 60,000 water utilities in the U.S. and the water industry worldwide is to provide safe and reliable drinking water. In general, this is accomplished with great success most of the time. A large water utility may produce 1 - 2 billion liters of drinking water every day and while the water that leaves the treatment plant is not sterile, it is free of any pathogens that could otherwise lead to diseases. However, on rare occasions outbreaks of disease within communities are caused by drinking water contaminated with viruses, bacteria, or protozoa.

The extraction, identification, and quantification of phospholipid fatty acids (PLFA) can provide valuable information on the total viable biomass in microbial communities. Information on the overall metabolic or physiological condition of a community can also be obtained. However, nucleic acid-based methods are necessary for fine-scale taxonomic study of microbial communities. Denaturing gradient gel electrophoresis (DGGE) following PCR amplification with primers targeting the small subunit rRNA gene provides a "fingerprint" of microbial communities. Subsequent band identification by DNA sequencing allows fine-scale characterization of specific bacterial members in a community. The combination of lipid analysis with PCR-fingerprinting can enumerate, report on the physiological status, and identify the major components of an actively bioremediating microbial community.

Single-strand conformation polymorphism (SSCP) is a technique to distinguish DNA molecules of the same size but of different nucleotide sequences using electrophoresis in a non-denaturing polyacrylamide gel. The method can be applied for the cultivation-independent analysis of microbial community diversity in environmental samples, based on PCR-amplified small sub-unit (SSU) rRNA gene sequences from directly extracted DNA. For this purpose, PCR is conducted with a phosphorylated and a non-phosphorylated primer both binding to conserved regions in the SSU rRNA genes. The double stranded PCR products are converted to single strands by lambda exonuclease digestion of the phosphorylated strand. By this means, heteroduplex formation during subsequent electrophoresis, which limited early applications of SSCP for microbial community analysis and which cannot be avoided in T/DGGE based methods, is eliminated. With PCR-SSCP, using this single-strand approach, community-patterns can be obtained from a diversity of environmental samples, such rhizosphere, compost or soil. The patterns in the polyacrylamide can be visualized by silver-staining. Single bands of silver-stained profiles can be cut out of the gels, re-amplified by PCR, and sequenced directly or after cloning in Escherichia coli. Due to its methodological simplicity, PCR-SSCP is a powerful tool for the analysis of microbial communities with a large pool of potential applications in microbial ecology and environmental biotechnology.

Denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) are similar techniques that allow PCR products of the same length but of different sequence composition to be separated in gradient gels according to the melting behaviour of the DNA. DGGE involves separation of the double-stranded amplification products in a linearly increasing gradient of formamide and urea while TGGE achieves resolution with a linearly increasing temperature gradient. The techniques are ideal for analysing PCR products amplified from 16S rRNA genes in complex bacterial communities. D/TGGE analysis generates a community fingerprint, but since individual bands can be recovered and analysed following D/TGGE analysis, sequence information can also be obtained. This allows a thorough analysis of microbial communities on several levels ranging from the community structure of dominant populations using conserved sequence primers, to phylogenetic sequence analysis of single bands generated by individual community members.

Molecular microbial ecology is a relatively new field in environmental microbiology, but it is one in which the enormous potential to learn about bacteria at the single cell and community level is enticing to many researchers. The idea that, using nucleic acid-based technology, one could determine bacterial phylogenetics, genetic capabilities, and cellular activity has led to the rapid development of methodologies for such purposes. Even more exciting to the microbial ecologist is the fact that many of these techniques can be carried out on microbial communities in situ. Such investigations provide a far better view of which bacteria are present, what they are doing, and how they interact with one another, than has previously been possible. Such investigations are inherent to any valid ecological study, the observations of life as it occurs and interacts in nature. The following chapter reviews the development of nucleic acid-based in situ methods as they have been applied to studies in environmental microbiology over the last 10 years. We have attempted to follow the progression and refinement of methods in a somewhat chronological manner, beginning with rRNA targeted in situ hybridization, which made it possible to identify bacteria without the need to culture, through to in situ reverse transcriptase PCR technology, whereby the expression of single-copy genes in individual cells can be monitored in natural communities.

To overcome many of the limitations associated with indirect detection methods, new techniques for the sensitive, specific, and direct detection of nucleic acids are required in order to accurately and quantitatively ascribe phenotype/function to uncultivated microorganisms. However, if advanced diagnostic and detection systems are going to be applied in environmental microbiology, future "biodetection" technologies and systems must be developed not from the point of view of the detector, but from the unique aspects of the environmental sample and the entire analytical process.

Current investigations in environmental microbiology concentrate on molecular and biochemical aspects of the biodegradation of organic compounds. Topics include; investigations of the microbial utilisation and mineralization of organoarsenicals and sulphonates; characterisation at the protein and gene level of haloalkane degradation and assimilation into microbial cells and of bacterial carbon-phosphorus bond cleavage with unique regulatory properties; degradation of aromatic compounds by Rhodococcus spp; the elucidation of Rhodococcus genetics in relation to haloalkane degradation; the survival characteristics of environmental bacteria including pathogens; antifungal synergy against Candida albicans using previously untested compounds; and the potential of fungi for use in the removal of dye wastes from effluents; the biochemistry and genetics of polyuphosphate biosynthesis by environmental microorganisms.

Although phosphorus (P) is only the eleventh most common element on earth, for two separate industries it is of paramount importance, albeit for differing reasons. P mining corporations are concerned with its supply as a raw material for chemical manufacturing, while the wastewater treatment sector has responsibility for its disposal, to landfill, as sludge biomass. Both invest considerably in optimisation of these technologies. A more economic and synergistic approach would be the recovery and recycling of the P that is present as polyphosphate in sludges for re-use in industry, instead of its disposal to landfill and ultimate loss from the ecosystem. Recovery, rather than the continuous mining of new resources, would have significant advantages in terms of both sustainable development and the economics of P processing. (Current estimates suggest that rock P reserves may only be sufficient to last the next 45 - 100 years; growth in the world population, necessitating increased food production and elevated P fertiliser application, may lead to even higher consumption rates).

Phosphate (P) removal from wastewaters is important for the control of eutrophication in natural water bodies and is enforced by increasingly stringent legislation. However the activated sludge processes normally used for the treatment of municipal and industrial effluents - whilst they are very effective in eliminating organic pollutants - remove phosphate relatively poorly. Thus P removal is currently achieved largely by chemical precipitation, although a biological process is regarded as preferable. Such a process would necessarily involve the 'luxury' uptake of soluble P by activated sludge microorganisms and its storage in insoluble polymeric form as intracellular polyphosphate.

This group works with viruses, bacteria and fungi and has expertise in molecular genetics, physiology, biochemistry, systematics, computer modelling and population biology. Much of the work is directed towards problems of medical, social or environmental importance. Current research programmes include; the genetic structure and activity of bacteria in natural soil, sediment and water ecosystems; stress responses of bacteria; targeted in situ bacterial activities; effects of UV-B; fungal endophyte-plant host interactions; fungal defences in algae; biotechnology applications of extracellular enzymes; contaminated land remediation; heavy metal and hydrocarbon contaminated environments; microbiological aspects of integrated wastewater treatment technologies; modification of bacterial surface structures in Neisseria and Pseudomonas; pathogenicity and molecular population studies of E.coli 0157 and VTEC phage and VTEC bacteria.

Halophilic Bacteria An existing bacterium has been reclassified into a new genus and a new species of bacterium has been isolated from North Sea water samples. The membrane adaptations of the new species have been studied in depth, the data will contribute to a deeper understanding of how halophiles survive in high concentrations of toxic chemicals. The new genus that has been created has been dubbed Oceanomonas and it has two members: O. baumanni (the new species) and O.doudoroffii (formerly Pseudomonas doudoroffii). Psychrophilic Polysaccharide Utilising Microbes Bacteria, fungi and yeasts have been isolated from the Antarctic Ocean, these microbes have been characterised and identified, currently efforts are under way to clone their psychrophilic carbohydrase enzymes.

Cyanide Degrading Microbes Bacteria, fungi and yeasts have been isolated from a disused Sunderland Coke Works, they have been characterised and identified, currently their nitrile and cyanide hydratase genes are being cloned so that they can be hyperexpressed and used in Bioremediation.

Molecular Phylogenetic Analysis Programs to facilitate the analysis of 16S and 23S rDNA sequences have been produced by Dr Andrew Hunter (School of Computing) and David Humphry, they are written in C++ and can be run under Windows 95/98 and NT. These programs can be downloaded here.

Rhizobia Taxonomy: Rhizobia have been isolated from the root nodules of lentils grown in different countries and these are being biochemically characterised and identified using 16S rDNA analysis and DNA-DNA hybridisation methods. This project hopes to uncover data that will allow the complex range of bacteria nodulating lentils in different countries to be better understood.

Two major aspects are the identification of microbes, both prokaryotic and eukaryotic, utilising molecular technologies and the development of an understanding of the molecular basis of physiology, biochemistry and pathogenicity. Microbes under investigation include sexually transmitted organisms such as Chlamydia trachomatis, Human Papillomavirus, and Trichomonas vaginalis, anaerobes such as Peptostreptococcus magnus and the fungus Ganoderma sp. Clinical studies are underway analysing bacterial interactions and the host response to microbial infections. From a therapeutic standpoint, metabolic products of microbes are being investigated at the molecular and biochemical level. These products include glycosidases from T.vaginalis and Ganoderma sp. DNases and drug pumps of T.vaginalis. Anti-microbial peptides, defensins, from both humans and plants are being analysed with a view to producing recombinant products for clinical trials.

Infectious diseases are among the most critical health problems worldwide. One out of every three people worldwide is infected by Mycobacterium tuberculosis, the causative agent of tuberculosis. Re-emerging infectious agents, as well as new antibiotic-resistant strains, make infectious diseases a major health problem of the new millennium. Between 1973 and 1999, more than 35 newly emerging infectious diseases were identified. Without rapid development of antimicrobials and vaccines, we face an era of drastically increased morbidity and mortality from infectious diseases.

The Center for Molecular Microbiology (CMM) was established in October of 2000 to formally bring together infectious disease researchers and clinicians from the Colleges of Dentistry, Medicine and Veterinary Medicine in order to function as an interdisciplinary group of collaborating scientists to address the issues of infectious diseases. The focus of the center is to conduct research to discover the mechanisms of microbial pathogenesis and invent, develop, and apply novel technologies for the discovery of new antimicrobial targets, vaccines, and diagnostics. In addition, this group of faculty is dedicated to the education and training of future scientists and clinicians who will be leaders in the field of cutting-edge technologies for the diagnosis, treatment, and prevention of infectious diseases. It is also expected that the center will stimulate and act as a resource for the growth of biotechnology companies in Northern Florida.

Standard molecular biological techniques (cloning of genes, expression of recombinant proteins in bacterial and eucaryotic cells, reporter gene assays).

The focus of the Research Centre in Molecular Microbiology is the use of molecular biology to study micro-organisms of importance to human health, agriculture or industry. Organisms under study include thermophilic and soil bacteria, the anaerobic bacterium which causes footrot, and the fungi Aspergillus nidulans, Aspergillus fumigatus, Fusarium and Thielaviopsis basicola. The current academic staff associated with the Centre are Dr Brian Cheetham (leader), Dr David Backhouse, Dr Heather Nonhebel, Dr Margaret Katz and Dr Lily Pereg-Gerk. The projects described below are carried out with technical staff and students in the Centre.

The investigation of antimicrobial chemotherapy and vaccine use in the developing world is of major importance in the fight against infectious disease. There are currently several high quality microbiology facilities operating in developing countries but there is no support network for these laboratories and little access to the research capabilities of a modern molecular facility. More direct links between the Sanger Institute and the regions of the world where the infectious disease burden is greatest would allow greater exploitation of pathogen sequencing data. This could enhance several research programs based around the molecular analysis of host susceptibility as well as pathogen diversity. Collaborations are being established which, it is hoped, will benefit directly research into infectious diseases globally by the exchange of ideas, technology and personnel.

Bacteria are an important cause of human infectious disease. The development of multiresistent pathogens has made it clear that life-threatening infections are still a major threat. Food-borne pathogens represent a major problem for human society. Bacteria have also been linked to "lifestyle diseases" such as stomach ulcers and circulatory diease. Finally, bacteria are also of central importance for the biotechnology industry, in agriculture, and in the environment.

The development of new methods for diagnosis and treatment of bacterial infections, and the application of bacteria in industry, agriculture and the environment, requires basic research on bacterial function at the molecular level and the application of the knowledge obtained. In particular, the existence of total genome sequences is currently providing the basis for a scientific revolution in microbiology. The application of the results of genomic research through "functional genomics" gives unique possibilities for the understanding of bacterial function, the biotechnological application of bacteria, and medical advances including the development of new types of antibacterial compounds ("drug discovery").

The Aeropyrum pernix K1 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was funded by National Institute of Technology and Evaluation, Tokyo, Japan. In addition to a general overview of Aeropyrum pernix, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH).

The Agrobacterium tumefaciens C58 Cereon genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This project was carried out by Cereon Genomics and the University of Richmond, and funded by Cereon Genomics. In addition to a general overview of Agrobacterium tumefaciens, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH.

The Aeropyrum pernix K1 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was funded by National Institute of Technology and Evaluation, Tokyo, Japan. In addition to a general overview of Aeropyrum pernix, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH).

Agrobacterium tumefaciens C58 Cereon The Agrobacterium tumefaciens C58 Cereon genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This project was carried out by Cereon Genomics and the University of Richmond, and funded by Cereon Genomics. In addition to a general overview of Agrobacterium tumefaciens, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH.

Agrobacterium tumefaciens C58 Dupont The Agrobacterium tumefaciens C58 Dupont genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by DuPont, the University of Washington and the University of Campinas, and funded by the US National Science Foundation (NSF) and the US National Institutes of Health (NIH). In addition to a general overview of A. tumefaciens, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Aquifex aeolicus VF5 The Aquifex aeolicus VF5 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was funded by the Diversa Corporation and the US Department of Energy. In addition to a general overview of A. aeolicus, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH). 

 Archaeoglobus fulgidus DSM4304 The Archaeoglobus fulgidus DSM4304 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was funded by The US Department of Energy. In addition to a general overview of A. fulgidus, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH). 

 Bacillus halodurans C-125 The Bacillus halodurans C-125 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. In addition to a general overview of Bacillus halodurans, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Bifidobacterium longum NCC2705 The Bifidobacterium longum NCC2705 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by Nestle and the University of Georgia. In addition to a general overview of Bifidobacterium genus, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Borrelia burgdorferi B31 The Borrelia burgdorferi B31 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was funded by The Mathers Foundation and NIH. Borrelia burgdorferi B31 is the causative agent of Lyme disease. In addition to a general overview of Borrelia burgdorferi B31, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH).

 Brucella melitensis The Brucella melitensis genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This project was carried out by the University of Scranton and Integrated Genomics, and funded by the Defense Advanced Research Projects Agency (DARPA). In addition to a general overview of B. melitensis, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH.

 Brucella suis 1330 The Brucella suis 1330 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. In addition to a general overview of B. suis, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. The sequencing project was funded by the US Defense Advanced Research Projects Agency (DARPA). TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH). 

 Buchnera aphidicola Sg The Buchnera aphidicola Sg genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out at the University of Uppsala, and funded by the US National Science Foundation. This Web site provides information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH). 

 Buchnera sp. APS The Buchnera sp. APS genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. In addition to a general overview of Buchnera, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH). 

 Campylobacter jejuni NCTC 11168 The Campylobacter jejuni NCTC 11168 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. In addition to a general overview of C. jejuni, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by the US National Institutes of Health (NIH).

 Caulobacter crescentus CB15 The Caulobacter crescentus CB15 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by TIGR and funded by The U.S. Department of Energy. Caulobacter crescentus is a Gram- negative bacterium that grows in dilute aquatic enviornments, and differentiates and divides asymmetrically at each cell cycle; as such it is used as a simple and manipulable, single-celled model system to study cellular differentiation, asymmetric division and their coordination with cell cycle progression. In addition to a general overview of Caulobacter crescentus CB15, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Chlamydia pneumoniae AR39 The Chlamydia pneumoniae AR39 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by TIGR and funded by The US National Institutes of Health (NIH) and The National Institute of Allergy and Infectious Diseases (NIAID). In addition to a general overview of C. pneumoniae, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Chlamydia pneumoniae CWL029 The Chlamydia pneumoniae CWL029 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by University of California, Berkeley/Stanford and funded by IncyteGenomics. In addition to a general overview of Chlamydia pneumoniae CWL029, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH.

 Chlamydia pneumoniae J138 The Chlamydia pneumoniae J138 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by TIGR and funded by The US National Institutes of Health (NIH) and The National Institute of Allergy and Infectious Diseases (NIAID). In addition to a general overview of Chlamydia pneumoniae J138, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. l. TIGR is a not-for-profit organisation funded by NIH.

 Chlamydia trachomatis MOPN The Chlamydia trachomatis MOPN genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by TIGR and funded by the US National Institutes of Health (NIH) and The National Institute of Allergy and Infectious Diseases (NIAID). In addition to a general overview of C. trachomatis MOPN, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Chlamydia trachomatis serovar D The Chlamydia trachomatis serovar D genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by the University of California, Berkeley/Stanford and funded by The US National Institutes of Health (NIH) and The National Institute of Allergy and Infectious Diseases (NIAID). In addition to a general overview of C. trachomatis serovar D, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Molecular Sequence Data; Genome, Bacterial; Databases, Genetic; Chlamydia trachomatis / genetics;

 Chlamydomonas reinhardtii EST index The Chlamydomonas reinhardtii EST Index is made available on the Web by the Department of Plant Gene Research at the Kazusa DNA Research Institute, Japan. The Chlamydomonas reinhardtii EST dataset contains almost 38,000 expressed sequence tags that can be searched by similarity or by keyword. EST sequences can be downloaded in Fasta format, and clone request information is provided. Links to publications relevant to this dataset are given. Expressed Sequence Tags; Databases, Genetic; Chlamydomonas reinhardtii / genetics; Base Sequence;

 Chlorobium tepidum The Chlorobium tepidum genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This project was carried out by TIGR, and funded by the US Department of Energy (DOE). In addition to a general overview of C. tepidum, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis; Green Sulfur Bacteria / genetics; Genome, Bacterial; Databases, Genetic; Base Sequence;

 Clostridium acetobutylicum ATCC824 The Clostridium acetobutylicum ATCC824 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This sequencing project was carried out by Genome Therapeutics, and funded by the US Department of Energy. In addition to a general overview of C. acetobutylicum ATCC824, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH.  Clostridium / genetics;

 Clostridium perfringens The Clostridium perfringens genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This sequencing project was carried out by University of Tsukuba, Kyushu University and Kitasato University, and funded by The Japan Society for the Promotion of Science (JSPS). In addition to a general overview of C. perfringens, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis; Genome, Bacterial; Databases, Genetic; Clostridium perfringens / genetics; Base Sequence;

 coliBASE coliBASE is a database for E. coli, Shigella and Salmonella comparative genomics created by Roy Chaudhuri and Mark Pallen of the Bacterial Pathogenesis and Genomics Unit within the Division of Immunity and Infection at the University of Birmingham, as part of a BBSRC funded Exploiting Genomics (ExGen) consortium. The database contains comparative data including whole genome alignments and lists of putative orthologous genes, together with analytical tools and links to existing online resources. coliBASE may be searched by gene name, annotation, and coliBASE number, while BLAST search, genome viewer, and fragment viewer facilities are also available. In addition, a pattern search tool allows the user to search within the genome for short DNA sequence patterns. Shigella / genetics; Salmonella / genetics; Genomics; Genome, Bacterial; Escherichia coli / genetics; Databases, Genetic;

 Corynebacterium glutamicum The Corynebacterium glutamicum ATCC 13032 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This project was carried out by the Kyowa Hakko Kogyo Company. In addition to a general overview of C. glutamicum, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Molecular Sequence Data; Genome, Bacterial; Databases, Genetic; Corynebacterium / genetics;

 CyanoBase : the genome database for cyanobacteria CyanoBase is a genome database for cyanobacteria, giving access to sequence and annotation data for Synechocystis sp. strain PCC6803, Anabaena sp. PCC7120, Thermosynechococcus elongatus BP-1, and Gloeobacter violaceus PCC 7421. Background information is provided on the project and the individual organisms, along with a BLAST similarity search facility, a gene category list, and links to the CyanoMutants and CyanoGenes databases. c, b. Made available on the Web by the Department of Plant Gene Research at the Kazusa DNA Research Institute, Japan. Sequence Analysis, DNA; Genome, Bacterial; Databases, Genetic; Cyanobacteria / genetics; Base Sequence;

 Deinococcus radiodurans R1 The Deinococcus radiodurans R1 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by TIGR and funded by The US Department of Energy. In addition to a general overview of D. radiodurans R1, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. 

 Enterococcus faecalis V583 The Enterococcus faecalis V583 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. In addition to a general overview of Enterococcus faecalis, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis; Molecular Sequence Data; Genome, Bacterial; Enterococcus faecalis / genetics; Databases, Genetic;

 Escherichia coli K12-MG1655 The Escherichia coli K12-MG1655 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by the University of Wisconsin and funded by The National Human Genome Research Institute. In addition to a general overview of E. coli, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis; Molecular Sequence Data; Genome, Bacterial; Escherichia coli / genetics; Databases, Genetic;

 Escherichia coli O157:H7 (EDL933) The Escherichia coli O157:H7 (EDL933) genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. The sequencing project was carried out by the University of Wisconsin and funded by The National Human Genome Research Institute (NHGRI) and The National Institute of Allergy and Infectious Diseases (NIAID). In addition to a general overview of E. coli O157:H7 (EDL933), the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis; Molecular Sequence Data; Genome, Bacterial; Escherichia coli O157 / genetics; Databases, Genetic;

 Fusobacterium nucleatum The Fusobacterium nucleatum ATCC 25586 genome page is provided by TIGR (The Institute of Genome Research) as part of their Comprehensive Microbial Resource, a tool that allows the researcher to access all of the bacterial genome sequences completed to date. This project was carried out by Integrated Genomics and funded by the the US National Institutes of Health. In addition to a general overview of F. nucleatum, the Web site provides more information and analyses on this genome, including protein/gene lists, analyses like GC plots and comparisons, 2D-gels, and recent gene duplications. It is possible to perform a PubMed search or genome searches based on name, locus, position, EC#, TIGRFAM or HMM, and to choose links to external sites related to this genome. TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Molecular Sequence Data; Genome, Bacterial; Fusobacterium nucleatum / genetics; Databases, Genetic;

 Gene pairs for Aeropyrum pernix K1 Gene pairs for Aeropyrum pernix K1 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Archaeal / genetics; Desulfurococcaceae / genetics;

 Gene pairs for Agrobacterium tumefaciens C58 Cereon Gene pairs for Agrobacterium tumefaciens C58 Cereon is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Agrobacterium tumefaciens / genetics;

 Gene pairs for Agrobacterium tumefaciens C58 Dupont Gene pairs for Agrobacterium tumefaciens C58 Dupont is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Agrobacterium tumefaciens / genetics;

 Gene pairs for Aquifex aeolicus Gene pairs for Aquifex aeolicus is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial / genetics;

 Gene pairs for Archaeoglobus fulgidus DSM4304 Gene pairs for Archaeoglobus fulgidus is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Archaeal; Archaeoglobus fulgidus / genetics;

 Gene pairs for Bacillus halodurans C-125 Gene pairs for Bacillus halodurans C-125 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Bacillus / genetics;

 Gene pairs for Bacillus subtilis 168 Gene pairs for Bacillus subtilis is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Bacillus subtilis / genetics;

 Gene pairs for Borrelia burgdorferi B31 Gene pairs for Borrelia burgdorferi B31 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Borrelia burgdorferi / genetics;

 Gene pairs for Brucella melitensis Gene pairs for Brucella melitensis is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Brucella melitensis / genetics;

Many oral bacterial pathogens require haem, and therefore for these bacteria the ability to acquire haem is a virulence factor. We are investigating the mechanisms by which the periodontal bacteria P. gingivalis and P. intermedia i  b, g. acquire haem in the presence of the haem-sequestering proteins haemopexin and haptoglobin which are present in the gingival crevicular fluid.

 Gene pairs for Buchnera sp. APS Gene pairs for Buchnera sp. APS is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial;

 Gene pairs for Campylobacter jejuni NCTC 11168 Gene pairs for Campylobacter jejuni NCTC 11168 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Campylobacter jejuni / genetics;

 Gene pairs for Caulobacter crescentus CB15 Gene pairs for Caulobacter crescentus CB15 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Caulobacter crescentus / genetics;

 Gene pairs for Chlamydia muridarum (strain Nigg) Gene pairs for Chlamydia muridarum (strain Nigg) is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Chlamydia muridarum / genetics;

 Gene pairs for Chlamydia pneumoniae AR39 Gene pairs for Chlamydia pneumoniae AR39 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Chlamydophila pneumoniae / genetics;

 Gene pairs for Chlamydia pneumoniae CWL029 Gene pairs for Chlamydia pneumoniae CWL029 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Chlamydophila pneumoniae / genetics;

 Gene pairs for Chlamydia pneumoniae J138 Gene pairs for Chlamydia pneumoniae J138 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Chlamydophila pneumoniae / genetics;

 Gene pairs for Chlamydia trachomatis serovar D Gene pairs for Chlamydia trachomatis serovar D is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Chlamydia trachomatis / genetics;

 Gene pairs for Clostridium perfringens Gene pairs for Clostridium perfringens is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Clostridium perfringens / genetics;

 Gene pairs for Deinococcus radiodurans R1 Gene pairs for Deinococcus radiodurans R1 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial;

 Gene pairs for Enterococcus faecalis V583 Gene pairs for Enterococcus faecalis V583 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Enterococcus faecalis / genetics;

 Gene pairs for Escherichia coli K-12 MG1655 Gene pairs for Escherichia coli K-12 MG1655 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Escherichia coli / genetics;

 Gene pairs for Escherichia coli O157:H7 (EDL933) Gene pairs for Escherichia coli O157:H7 (EDL933) is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Genes, Bacterial; Escherichia coli O157 / genetics;

 Gene pairs for Haemophilus influenzae KW20 Gene pairs for Haemophilus influenzae KW20 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Haemophilus influenzae / genetics; Genes, Bacterial;

 Gene pairs for Halobacterium sp. NRC-1 Gene pairs for Halobacterium sp. NRC-1 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Halobacterium / genetics; Genes, Archaeal;

 Gene pairs for Helicobacter pylori 26695 Gene pairs for Helicobacter pylori 26695 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Helicobacter pylori / genetics; Genes, Bacterial;

 Gene pairs for Helicobacter pylori J99 Gene pairs for Helicobacter pylori J99 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Helicobacter pylori / genetics; Genes, Bacterial;

 Gene pairs for Lactococcus lactis subsp. lactis IL1403 Gene pairs for Lactococcus lactis subsp. lactis IL1403 is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Lactococcus lactis / genetics; Genes, Bacterial;

 Gene pairs for Listeria innocua Gene pairs for Listeria innocua is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs; the method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probability that the two genes are located in the same operon; n, the number of other evolutionary distant genomes that have the same gene pair; and all homologous gene pairs (in both evolutionary close and distant genomes). TIGR is a not-for-profit organisation funded by NIH. Sequence Analysis, DNA; Operon; Listeria / genetics; Genes, Bacterial;

 Gene pairs for Listeria monocytogenes EGD-e Gene pairs for Listeria monocytogenes EGD-e is provided by The Institute of Genome Research (TIGR) as part of their "Predicting operons in microbial genomes" resource. This resource is based on a method developed at TIGR to detect and analyse conserved gene pairs. The method revealed that a large number of gene clusters are conserved between microbial genomes. This page provides information on: the actual gene; c (confidence), an estimation of the probab