Nature Reviews Microbiology

Proteorhodopsins: an array of physiological roles?

Publication Date: 2008 May 13 PMID: 18475306
Authors: Fuhrman, J. A. - Schwalbach, M. S. - Stingl, U.
Journal: Nat Rev Microbiol

Metagenomic analyses have revealed widespread and diverse retinal-binding rhodopsin proteins (named proteorhodopsins) among numerous marine bacteria and archaea, which has challenged the notion that solar energy can only enter marine ecosystems by chlorophyll-based photosynthesis. Most marine proteorhodopsins share structural and functional similarities with archaeal bacteriorhodopsins, which generate proton motive force via light-activated proton pumping, thereby ultimately powering ATP production. This suggests an energetic role for proteorhodopsins. However, results from a growing number of investigations do not readily fit this model, which indicates that proteorhodopsins could have a range of physiological functions.

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Microbiology in the post-genomic era.

Publication Date: 2008 May 13 PMID: 18475305
Authors: Medini, D. - Serruto, D. - Parkhill, J. - Relman, D. A. - Donati, C. - Moxon, R. - Falkow, S. - Rappuoli, R.
Journal: Nat Rev Microbiol

Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology.

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Microbial diversity and the genetic nature of microbial species.

Publication Date: 2008 May 7 PMID: 18461076
Authors: Achtman, M. - Wagner, M.
Journal: Nat Rev Microbiol

The earth contains a huge number of largely uncharacterized Bacteria and Archaea. Microbiologists are struggling to summarize their genetic diversity and classify them, which has resulted in heated debates on methods for defining species, mechanisms that lead to speciation and whether microbial species even exist. This Review proposes that decisions on the existence of species and methods to define them should be guided by a method-free species concept that is based on cohesive evolutionary forces. It summarizes current approaches to defining species and the problems of these approaches, and presents selected examples of the population genetic patterns at and below the species level.

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The ecology and biotechnology of sulphate-reducing bacteria.

Publication Date: 2008 May 7 PMID: 18461075
Authors: Muyzer, G. - Stams, A. J.
Journal: Nat Rev Microbiol

Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that use sulphate as a terminal electron acceptor in, for example, the degradation of organic compounds. They are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. SRB can cause a serious problem for industries, such as the offshore oil industry, because of the production of sulphide, which is highly reactive, corrosive and toxic. However, these organisms can also be beneficial by removing sulphate and heavy metals from waste streams. Although SRB have been studied for more than a century, it is only with the recent emergence of new molecular biological and genomic techniques that we have begun to obtain detailed information on their way of life.

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The surprisingly diverse ways that prokaryotes move.

Publication Date: 2008 May 7 PMID: 18461074
Authors: Jarrell, K. F. - McBride, M. J.
Journal: Nat Rev Microbiol

Prokaryotic cells move through liquids or over moist surfaces by swimming, swarming, gliding, twitching or floating. An impressive diversity of motility mechanisms has evolved in prokaryotes. Movement can involve surface appendages, such as flagella that spin, pili that pull and Mycoplasma 'legs' that walk. Internal structures, such as the cytoskeleton and gas vesicles, are involved in some types of motility, whereas the mechanisms of some other types of movement remain mysterious. Regardless of the type of motility machinery that is employed, most motile microorganisms use complex sensory systems to control their movements in response to stimuli, which allows them to migrate to optimal environments.

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Making a difference: 30 years of TDR.

Publication Date: 2008 May PMID: 18414503
Authors: Ridley, R. G. - Fletcher, E. R.
Journal: Nat Rev Microbiol

When the UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR) was established in the mid-1970s, it represented an innovative institutional formula in terms of its structure and the manner in which scientists were convened from both developed and developing countries to address some of the world's most neglected parasitic diseases. A review of TDR's historical record sheds light not only on some important milestones in tropical-disease research, but also on how future challenges could be approached and hopefully surmounted.

MeSH Categories: Anti-Infective Agents/history/therapeutic use, Artemisinins/history/therapeutic use, Biomedical Research/history/trends, Developed Countries/history, Developing Countries/history, Eflornithine/history/therapeutic use, History, 20th Century, History, 21st Century, Humans, International Cooperation/history, Ivermectin/history/therapeutic use, Parasitic Diseases/history/therapy, Program Evaluation, Tropical Medicine/education/*history/trends, United Nations/history

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Emerging and re-emerging rickettsioses: endothelial cell infection and early disease events.

Publication Date: 2008 May PMID: 18414502
Authors: Walker, D. H. - Ismail, N.
Journal: Nat Rev Microbiol

Rickettsiae cause some of the most severe human infections, including epidemic typhus and Rocky Mountain spotted fever. Substantial progress has been made in research into the genomics, vector relationships, pathogenesis and immunity of these obligate, intracellular, arthropod-transmitted bacteria. This Review summarizes our understanding of the early and late events in pathogenesis and immunity, modulation of the host response to rickettsial infection by the vector, host defence, virulence mechanisms and rickettsial manipulation of host cells.

MeSH Categories: Endothelial Cells/*microbiology, Host-Pathogen Interactions/*immunology, Humans, Rickettsia/genetics/*pathogenicity, Rickettsia Infections/*immunology/*microbiology, Virulence

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Modification of intracellular membrane structures for virus replication.

Publication Date: 2008 May PMID: 18414501
Authors: Miller, S. - Krijnse-Locker, J.
Journal: Nat Rev Microbiol

Viruses are intracellular parasites that use the host cell they infect to produce new infectious progeny. Distinct steps of the virus life cycle occur in association with the cytoskeleton or cytoplasmic membranes, which are often modified during infection. Plus-stranded RNA viruses induce membrane proliferations that support the replication of their genomes. Similarly, cytoplasmic replication of some DNA viruses occurs in association with modified cellular membranes. We describe how viruses modify intracellular membranes, highlight similarities between the structures that are induced by viruses of different families and discuss how these structures could be formed.

MeSH Categories: Animals, Autophagy, Humans, Intracellular Membranes/*ultrastructure/*virology, Mice, *Virus Replication

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Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques.

Publication Date: 2008 May PMID: 18414500
Authors: Amann, R. - Fuchs, B. M.
Journal: Nat Rev Microbiol

The ribosomal-RNA (rRNA) approach to microbial evolution and ecology has become an integral part of environmental microbiology. Based on the patchy conservation of rRNA, oligonucleotide probes can be designed with specificities that range from the species level to the level of phyla or even domains. When these probes are labelled with fluorescent dyes or the enzyme horseradish peroxidase, they can be used to identify single microbial cells directly by fluorescence in situ hybridization. In this Review, we provide an update on the recent methodological improvements that have allowed more reliable quantification of microbial populations in situ in complex environmental samples, with a particular focus on the usefulness of group-specific probes in this era of ever-growing rRNA databases.

MeSH Categories: Archaea/classification/genetics/*isolation & purification, Bacteria/classification/genetics/*isolation & purification, In Situ Hybridization, Fluorescence/*methods, Oligonucleotide Probes/chemistry, Phylogeny, RNA Probes/chemistry, RNA, Ribosomal/*analysis/genetics, Ribotyping/*methods, Sensitivity and Specificity

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Diatoms in a future ocean--stirring it up.

Publication Date: 2008 May PMID: 18392034
Authors: Peters, F.
Journal: Nat Rev Microbiol

MeSH Categories: *Biodiversity, *Diatoms, Oceans and Seas, *Seawater

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Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention.

Publication Date: 2008 May PMID: 18392032
Authors: Ahmed, N. - Dobrindt, U. - Hacker, J. - Hasnain, S. E.
Journal: Nat Rev Microbiol

The increasing availability of DNA-sequence information for multiple pathogenic and non-pathogenic variants of individual bacterial species has indicated that both DNA acquisition and genome reduction have important roles in genome evolution. Such genomic fluidity, which is found in human pathogens such as Escherichia coli, Helicobacter pylori and Mycobacterium tuberculosis, has important consequences for the clinical management of the diseases that are caused by these pathogens and for the development of diagnostics and new molecular epidemiological methods.

MeSH Categories: Animals, Bacteria/*genetics/isolation & purification/*pathogenicity, *Bacterial Infections/diagnosis/epidemiology/therapy, *Evolution, Molecular, *Genome, Bacterial, Humans

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Searching for the cause of Kawasaki disease--cytoplasmic inclusion bodies provide new insight.

Publication Date: 2008 May PMID: 18364728
Authors: Rowley, A. H. - Baker, S. C. - Orenstein, J. M. - Shulman, S. T.
Journal: Nat Rev Microbiol

Kawasaki disease (KD) has emerged as the most common cause of acquired heart disease in children in the developed world. The cause of KD remains unknown, although an as-yet unidentified infectious agent might be responsible. By determining the causative agent, we can improve diagnosis, therapy and prevention of KD. Recently, identification of an antigen-driven IgA response that was directed at cytoplasmic inclusion bodies in KD tissues has provided new insights that could unlock the mysteries of KD.

MeSH Categories: Adult, Antigens/analysis/immunology, Child, Coronary Aneurysm/immunology/pathology, Cytoplasm/immunology, Humans, Immunoglobulin A/analysis/*immunology, Inclusion Bodies/*immunology, Mucocutaneous Lymph Node Syndrome/complications/*immunology/pathology, Plasma Cells/immunology

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Mucosal delivery of therapeutic and prophylactic molecules using lactic acid bacteria.

Publication Date: 2008 May PMID: 18345021
Authors: Wells, J. M. - Mercenier, A.
Journal: Nat Rev Microbiol

Studies of lactic acid bacteria (LAB) as delivery vehicles have focused mainly on the development of mucosal vaccines, with much effort being devoted to the generation of genetic tools for antigen expression in different bacterial locations. Subsequently, interleukins have been co-expressed with antigens in LAB to enhance the immune response that is raised against the antigen. LAB have also been used as a delivery system for a range of molecules that have different applications, including anti-infectives, therapies for allergic diseases and therapies for gastrointestinal diseases. Now that the first human trial with a Lactococcus strain that expresses recombinant interleukin-10 has been completed, we discuss what we have learnt, what we do not yet understand and what the future holds for therapy and prophylaxis with LAB.

MeSH Categories: Animals, Drug Delivery Systems/*methods, Humans, Immunity, Mucosal, Lactic Acid/biosynthesis, Lactobacillus/genetics/*immunology, Mice, Mucous Membrane/microbiology, Recombinant Proteins/genetics/immunology/*therapeutic use, Streptococcaceae/genetics/*immunology, Vaccines, DNA/genetics/immunology/*therapeutic use

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