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The Ibis T5000 couples nucleic acid amplification to high-performance electrospray mass spectrometry and base-composition analysis and enables the identification and quantification of all known bacteria, all major groups of pathogenic fungi and the major families of viruses that cause disease in humans and animals. Here, Ecker and colleagues describe this new technology.
Using examples from the Cuatro Ciénegas basin in Mexico, Souzaet al. argue that the occurrence of strong ecosystem nutrient limitation, especially by phosphorus, encourages local microbial endemism because it reduces horizontal gene transfer among locally adapting microbial lineages.
Structures of RNA polymerase enzymes have advanced our understanding of transcription initiation in all kingdoms of life. This Review discusses bacterial promoter structure, recent advances in our understanding of the successive promoter–RNA polymerase complexes that contribute to the kinetics of transcription initiation and unconventional regulators that target RNA polymerase, but not DNA, for the control of transcription initiation in bacteria.
The flagellum is a beautiful structure and a fascinating model system for understanding how genes are regulated to ensure the correct assembly of a complex structure. Chevance and Hughes discuss the regulation of flagellar gene transcription and how it is intimately coupled to the assembly of this exquisite bacterial nanomachine.
Thirteen years after the first bacterial genome was sequenced, Rino Rappuoli, Stanley Falkow and colleagues review what has changed in microbiology research as a consequence of genomics and address the implications of the genomic era for the future of microbiology.
The discovery of proteorhodopsin genes during metagenomic analyses of marine bacteria and archaea challenged the notion that all solar energy is captured by microbial chlorophyll molecules in these environments. But have subsequent studies confirmed the energy-transducing roles of microbial proteorhodopsins? Here, the authors suggest that energy transduction might be one of many roles for these fascinating proteins.
The dynamics of infectious diseases are complex, so developing models that can capture key features of the spread of infection is important. Grassly and Fraser provide an introduction to the mathematical analysis and modelling of disease transmission, which, in addition to informing public health disease control measures, is also important for understanding pathogen evolution and ecology.
Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that can use sulphate as a terminal electron acceptor. These organisms are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. Muyzer and Stams provide an overview of the diversity, physiology and distribution of SRB and their applications to environmental biotechnology.
Bacteria and archaea have found many solutions to the problem of how to move in liquids and on solid surfaces. Although the use of a rotary flagellum in bacteria is the best-studied mode of bacterial movement, spirochaetes constrain their flagella in the periplasm, some bacteria move using type IV pili, cyanobacteria use surface spicules and others glide on surfaces without using appendages.
This Review summarizes contemporary approaches for defining species in Bacteria and Archaea and contrasts these approaches with various reports on microbial population genetic patterns. The authors conclude that contemporary method-based approaches lack a theoretical definition and new approaches are needed that should be guided by a method-free species concept that is based on cohesive evolutionary forces.
Many viruses induce the formation of altered membrane structures upon replication in host cells. This Review examines how viruses modify intracellular membranes, highlights similarities between the structures that are induced by viruses from different families and discusses how these structures could be formed.
Although Kawasaki disease (KD) is the most common cause of acquired heart disease in children in the developed world, its aetiology remains unknown. In this Opinion, Anne Rowley and colleagues discuss evidence, including recently identified cytoplasmic inclusion bodies, which suggests that KD is caused by an infectious agent.
Amann and Fuchs provide an update on recent methodological improvements to fluorescencein situhybridization protocols, with a particular focus on whether the original group-specific probes, which were mostly developed more than 10 years ago, are still valid.
The development of lactic acid bacteria as delivery vehicles for therapeutics, anti-infectives and vaccines at mucosa is discussed in this Review. Engineered LAB could be deployed to treat conditions such as allergy and inflammatory bowel disease, and might also be adopted in the fight against pathogens, including HIV-1 infection.
DNA acquisition and loss have important roles in bacterial genome evolution. Jörg Hacker and colleagues look at how this genomic fluidity can be harnessed in the development of new diagnostics and molecular epidemiological methods.
Rickettsiae are obligate parasites that cause sometimes deadly human infections, including epidemic typhus and Rocky Mountain spotted fever. David Walker and Nahed Ismail review the early and late events in pathogenesis and immunity, including virulence mechanisms and rickettsial manipulation of host cells.
Anaerobic ammonium oxidation (anammox) bacteria, which combine ammonium and nitrite or nitrate to form nitrogen gas, were discovered in the early 1990s. Here, Gijs Kuenen recalls the discovery of these bacteria and the subsequent elucidation of their roles in environmental and industrial microbiology.
Streptococcus pneumoniaeis one of the most common bacterial respiratory pathogens. In this article, the authors review the impressive armamentarium of virulence factors the pneumococcus uses to colonize the upper and lower respiratory tracts of the host and cause disease.
Carbohydrate-based polymers are constituents of the cell envelopes of many Gram-positive bacteria. These cell-wall glycopolymers often have highly variable structures and, although their functions are not completely known, recent research has begun to reveal that they have crucial roles in both protecting and maintaining the bacterial cell envelope and in bacteria–host interactions.
