Reviews & Analysis

Numerous metabolic functions, social interactions and survival mechanisms are specific to, or more pronounced in, biofilms than in planktonic cells. In this Review, Flemming and colleagues highlight the central role of the self-produced matrix in establishing these 'emergent properties' of biofilms.

The dominant lifestyle of most bacteria involves little or no growth. In this Review, Newman and colleagues discuss the physiology of these little-studied growth states, including changes to metabolism, transcription and translation, and the maintenance of genome replication and integrity.

In this Review, Browning and Busby describe the advances that have been made in recent years in understanding the molecular details of how transcription initiation is regulated to fine tune gene expression, highlighting factors that relate both to the RNA polymerase and to the promoter.

Microbial biofilms exhibit vast complexity in terms of both resident species composition and phenotypic diversity. Here, Foster and colleagues discuss theoretical and experimental work that reveals how the spatial arrangement of genotypes within microbial communities influences the cooperative and competitive cell–cell interactions that define biofilm form and function.

In this Review, te Velthuis and Fodor detail the recently obtained high-resolution structures of the influenza virus RNA polymerase and the insights that have been gained into the mechanisms of viral transcription and replication. They also discuss how these structural data could help to identify novel antiviral targets.

Metagenome-wide association studies (MWAS) are designed to detect associations between the human microbiome and disease. In this Review, Jia and Wang describe the principal findings of MWAS of human diseases, and consider how these findings might be integrated into medical research and practice.

Plasmodiumparasites alter the physiology and morphology of erythrocytes by exporting hundreds of proteins into the host cell. In this Review, de Koning-Wardet al. discuss how these parasites use distinct protein trafficking motifs, protease-mediated polypeptide processing, a novel translocon and membranous structures to induce host cell remodelling and promote their own survival.

Insights into coronavirus emergence, replication and pathogenesis gained from the SARS and MERS outbreaks have guided the development of preventive and therapeutic measures. In this Review, Munster and colleagues highlight recent achievements and areas that need to be addressed to combat novel coronaviruses.

The evolution of monoderm and diderm cell envelopes, and thus of Gram-positive and Gram-negative bacteria, is a long-standing question. In this Opinion article, Tocheva, Ortega and Jensen propose, based on recent electron cryotomography data, a new model that places sporulation at the heart of bacterial evolution.

Molecular-based studies of fungal biodiversity have revealed fundamental differences from the biodiversity of bacteria, plants and animals. In this Review, Peay and colleagues consider the roles of ecology and fungal biology in determining fungal biodiversity at different spatial scales.

Many host structures are vital for viral infection and the endoplasmic reticulum (ER), in particular, is essential. In this Review, Tsai and colleagues highlight examples of subversion of the ER by diverse viruses to promote all stages of their life cycle, from entry to egress.

In this Opinion article, Kreft and colleagues discuss how the combination of individual-based observations with individual-based models (IBMs) can lead to the new approach of microbial individual-based ecology (μIBE). They illustrate this point by describing how IBMs help to explore competitive and cooperative microbial interactions, which include the emergence of spatial patterns in biofilms and bacteria–phage dynamics.

In this Review, McDonaldet al. describe the mechanisms and outcomes of reassortment for three well-studied viral families — Cystoviridae, Orthomyxoviridae and Reoviridae— and discuss how these findings provide new perspectives on the replication and evolution of segmented RNA viruses.

In the modern world, several factors have increased the global health challenge posed by noroviruses. In this Review, Koopmans and colleagues describe advances in the study of norovirus transmission, pathogenesis and evolution, and consider future prospects for therapeutics.

Pattern recognition receptors (PRRs) detect conserved molecular features of viral pathogens and initiate signalling that results in the expression of antiviral genes. In this Review, Chan and Gack highlight the major classes of intracellular viral RNA and DNA sensors and discuss the viral strategies that are used to escape immune surveillance by those sensors.

The initial sensing of an infection is mediated by innate pattern recognition receptors, which detect pathogens, such as bacteria and viruses. In this Review, Stewart and Cookson discuss the molecular mechanisms by which microorganisms evade or inhibit intracellular detection that is coupled to pro-inflammatory caspase-dependent protective responses, thus delaying protective host responses.

The gut of honey bees is inhabited by a small group of highly host-adapted bacteria. In this Review, Kwong and Moran detail the composition and functions of the microbiota of honey bees and highlight similarities and differences to the human microbiota.

Chlamydiaspp. are intracellular bacteria that depend on the host for their metabolic requirements, while hiding from host immune defences. In this Review, Elwell, Mirrashidi and Engel detail the molecular mechanisms that enable these pathogens to shape and thrive in their niche in host cells.

The failure of antibiotics can arise by different bacterial survival strategies, each with implications for treatment. In this Opinion article, Balaban and colleagues propose a new experimental framework for distinguishing between several forms of resistance, tolerance and persistence to antibiotic treatment.

Bacterial cell division occurs under tight temporal and spatial regulation by the divisome. In this Review, Haeusser and Margolin review the structure and function of the divisome, highlighting insights into the assembly of this multicomponent machinery that were provided by recent technical advances.