Reviews & Analysis

Fungi communicate with one another using chemical languages that consist of extracellular signals and sophisticated cellular responses. Glass and colleagues review the languages that are used by the largest phylum of fungi, the Ascomycota, during developmental processes such as germination, formation of mycelial networks through cell fusion, coordination of colony development, and both sexual and asexual reproduction.

Planctomycetes are bacteria that lack peptidoglycan in their cell walls and possess membrane-bound intracellular compartments, some of which may be analogous to the nucleus and the mitochondria of eukaryotes. Here, Fuerst and Sagulenko summarize recent progress in planctomycete cell biology and its implications for our understanding of the origin of eukaryotes.

Sulphate-reducing microorganisms have key roles in the biogeochemical cycling of sulphur, carbon, nitrogen and metals, as well as great biotechnological potential. Here, Zhou and colleagues describe recent applications of 'omics' tools to study the stress responses of these organisms, particularlyDesulfovibriospp., at the cell, population, community and ecosystem levels.

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems are immunity systems that are present in many bacteria and archaea. Here, Koonin and colleagues present a new classification of these systems and introduce a new nomenclature of the genes in the CRISPR–casloci that better reflects the relationships between the proteins.

Manipulation of the host cell actin cytoskeleton is a common feature for many viruses. In this Review, Taylor, Koyuncu and Enquist describe how the interaction of viral proteins with the actin cytoskeleton alters the structure and function of this cytoskeleton, allowing viral infections to initiate, persist and spread.

Egress of herpesviruses requires that viral capsids containing the viral DNA travel from the nucleus to the cell surface, traversing nuclear and cytoplasmic membranes. Johnson and Baines describe how viral proteins remodel cellular membranes in order to escape host cells.

Entry of enveloped viruses into the host cell is an intricate process. Here, Connolly and colleagues describe the different proteins of herpes simplex viruses and Epstein–Barr virus that are involved in tethering the viruses to host cells and promoting fusion of the viruses with these host cells.

Termination is an important way of regulating transcription and requires stringent control. Here, Santangelo and Artsimovitch discuss the different mechanisms of antitermination in bacteria and phages.

Xanthomonasspp. cause disease in nearly 400 plant hosts, including many economically important crops. Dow and colleagues discuss the insights that functional and comparative genomic studies are providing into the adaptation of these bacteria to exploit an extraordinary diversity of plant hosts and different host tissues.

In this Review, Krulwich, Sachs and Padan describe how the evolution of diverse mechanisms for pH sensing and homeostasis has enabled bacteria to survive sudden changes in external pH and to grow in environments with external pH values that would otherwise be toxic.

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.