Review Articles in 2016

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.

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 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.

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.

In this Review, Kahne and colleagues discuss how lipopolysaccharide (LPS) is transported across the cellular envelope and inserted into the outer membrane of Gram-negative bacteria. They propose a new model, which explains how energy from the cytoplasm is used to power LPS transport to the cell surface.

In this article, James Liaoet al. review how microorganisms can be explored for the production of next-generation biofuels. They discuss the different substrates that are available for biofuel production and how these substrates can be directed to various biosynthetic pathways, and they highlight examples of microbial engineering aimed at optimizing biofuel production.

Biofilms dominate microbial life in streams and rivers. In this Review, Battin and colleagues describe the interactions between the microbiome of stream biofilms and ecosystem processes, and they consider the effects of global ecosystem change and climate change on these biofilms.

In this Review, Turnbaugh and colleagues discuss several mechanisms by which the human gut microbiome affects the metabolism of xenobiotics, including drugs and dietary compounds, and explore how this knowledge can be applied to improve the treatment of human disease.

The metabolism of pathogens and hosts are intertwined — they compete for resources, sense metabolites produced by each other and target metabolic processes to mediate virulence and immunity. In this Review, Olive and Sassetti discuss the emerging roles of metabolism in host–pathogen interactions.

Shigellaspp. harbour an arsenal of virulence factors that enable host invasion. Here, Baker and colleagues review how these bacteria have evolved fromEscherichia colion several occasions into highly specialized, human-restricted pathogens that have spread globally.

In this Review, Oikonomou and Jensen discuss how electron cryotomography has provided structural and mechanistic insights into the physiology of bacteria and archaea, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions.

In the genomics era,Yersiniahas proven to be a model genus for studying the emergence of pathogenesis. Focusing on this model, McNally and colleagues highlight the events in genome evolution that underlie pathogenesis and argue for an 'eco–evo' perspective of pathogen evolution.