Review Articles

The gut microbiota and the host immune system are in a careful balance. The Paneth cells in the endothelium of the small intestine produce a large array of antimicrobial proteins that help set this balance and protect the host from pathogens.

Human skin is colonized by a diverse range of microorganisms. In this Review, Grice and Segre describe how molecular techniques are improving our understanding of our skin microbiota, the factors that affect its composition and its relationship with skin disorders.

Many diseases may be caused by the combination of a specific host genetic background and a viral infection. Here, Foxman and Iwasaki describe how viral infections may be involved in type 1 diabetes, asthma and inflammatory bowel disease.

In recent years, the composition of the gut microbiome has become the subject of intensive study. In this Review, Spor, Koren and Ley describe how host genetics and the environment shape the gut microbiome, both in health and in chronic disease.

The mucus barrier provides a crucial defence against commensal microorganisms and enteric pathogens. In this Review, McGuckin and colleagues describe the structure of the mucus barrier and discuss how the composition of the mucus layer is regulated under normal conditions and in response to infection.

The transcription factor nuclear factor-κB (NF-κB) plays a central part in the immune response to bacteria and viruses. To influence the host's immune response, many bacteria and viruses have devised ways of modulating the activity of NF-κB.

The use of antibiotics is making lasting alterations to the long-term relationship between a host and its microbiota. Willing, Russell and Finlay describe how these changes can result in the disruption of immune homeostasis and in increased susceptibility to disease.

An accurate test for diagnosing active tuberculosis at the point of care is greatly needed, as it would substantially decrease associated death rates and could reduce disease transmission. In this Review, McNerney and Daley outline the status of research into such diagnostic tests and discuss barriers to their further development.

Sortases are enzymes that produce transpeptide bonds which can either link proteins to the cell wall or introduce intermolecular bonds in pili. Schneewind and colleagues describe how these enzymes function on a molecular level and provide an overview of the pili on which they function.

Cryptococcus neoformansis generally considered to be an opportunistic pathogen of immunocompromised individuals. However, as discussed here, this view has been challenged by recent evidence of specialized host–pathogen interactions, and by the emergence of the related speciesCryptococcus gattiias a primary pathogen of immunocompetent populations.

Despite the fact that fungi are biochemically and ecologically suited to the degradation of a range of hazardous environmental chemicals, they have rarely been exploited for bioremediation. Here, Harms and colleagues describe the features that make fungi suitable for bioremediation and discuss their potential applications in this field.

In this Review, Armitage and colleagues describe how some bacterial species, as typified byRhodobacter sphaeroides, have evolved to contain complex chemotaxis signalling networks that integrate sensory information from the environment with metabolic information from within the cell to produce a balanced response at the flagellar motor.

RNA polymerase is an ancient enzyme that is present in all cellular life. Werner and Grohmann provide an evolutionary view of this enzyme by describing the differences and similarities in the three domains of life, and propose a hypothesis for the evolution of transcriptional regulation.

Dormancy is a bet-hedging strategy used by microorganisms to generate a seed bank that helps bacteria survive adverse conditions. Lennon and Jones describe some of the mechanisms of dormancy and explain how dormancy affects the stability of ecosystems.

Viruses have traditionally been thought of as pathogens, but many confer a benefit to their hosts and some are essential for the host life cycle. In this Review, Marilyn Roossinck describes beneficial viruses that are found in a range of hosts, including bacteria, insects, plants and animals.

The formation ofCandida albicans biofilms on implanted medical devices is a major source of infection. Here, Finkel and Mitchell review the latest insights into the mechanisms and regulatory pathways that govern C. albicansbiofilm formation and biofilm-based drug resistance.

Non-coding DNA motifs play a central part in the bacterial cell cycle. El Karoui and colleagues review the roles of such motifs in replication, DNA segregation, DNA repair, cell division and DNA uptake, and explain how their distribution can be analysed quantitatively.

Infections involving slow-growing and persistent bacteria, includingMycobacterium tuberculosisand biofilms, are difficult to treat. Here, Hurdle and colleagues argue that developing antibiotics to target the bacterial membrane and membrane functions is a promising approach for the treatment for these difficult-to-treat infections.

In this Review, Mahadevan, Palsson and Lovley describe how genome-scale metabolic modelling ofGeobacterspp. has improved our understanding of the metabolism and physiology of these environmentally important bacteria and discuss the implications for applications such as bioremediation.

The Archaea evolved over 3 billion years ago but were only formally proposed as a domain 20 years ago. Today, many of the unique features and many of those that are shared with either the Bacteria or the Eukarya are well understood. Here, Ricardo Cavicchioli describes some of the important events in our appreciation of this fascinating group of organisms.