Reviews & Analysis

Richards and Talbot propose that in osmotrophic eukaryotic microorganisms, horizontal gene transfer has had a major role in reconfiguring osmotrophic functions, which involve the production and acquisition of public goods.

Hepatitis C virus (HCV) is a positive-strand RNA virus that causes significant pathology in humans. Here, Lindenbach and Rice discuss recent insights into the unique properties of HCV particles and then review HCV entry and assembly, with a focus on the viral and host factors involved.

Assessing the genetic variation of bacteria has become ever more complex as more sequencing data has become available. Here, Maiden and colleagues propose a gene-by-gene approach of analysing whole-genome data; this approach is based on their experience with multilocus sequence typing (MLST) and reflects the functional and evolutionary relationships among bacteria.

Recent studies have revealed that bacteriophages have a remarkable capacity to defend against the antiviral systems of their bacterial hosts. Here, Moineau and colleagues discuss the diverse mechanisms that phages use to evade adsorption inhibition, restriction–modification systems, CRISPR–Cas systems and abortive infection.

In budding yeast, growth at the neck region connecting the mother and daughter cell is prevented by a septin ring inside the cell membrane and a chitin ring in the cell wall. Cabib and Arroyo describe recent work supporting the hypothesis that the attachment of the chitin ring to β-1,3-glucan is crucial for the control of morphogenesis at the neck.

Recent studies have provided mechanistic insight into the cell cycle of coccoid bacteria. In this Review, Pinho, Kjos and Veening discuss our current understanding of the molecular mechanisms orchestrating peptidoglycan synthesis, cell division and chromosome segregation inStaphylococcus aureus and Streptococcus pneumoniae.

Although the gut microbiota has been linked to a wide range of diseases in humans, including type 2 diabetes and obesity, moving from correlation to causation is notoriously difficult. In this Opinion article, Liping Zhao discusses some of the correlations that have been made between the microbiota and obesity to date, and how to move towards causation using the conceptual framework of Koch's postulates.

Achieving intestinal homeostasis is a balancing act of attacking pathogens while tolerating the gut microbiota, and repairing damaged tissue following infection. Here, Lemaitre and colleagues discuss insights obtained from the study of host–microorganism interactions in theDrosophila melanogastergut.

Bernander and Lindås provide an overview of recent studies that have enhanced our understanding of the archaeal cell cycle. They discuss the multiple-origin mode of DNA replication, the archaeal replisome, the identification of a genome segregation machinery, the first cytoskeletal structure and the discovery of a novel cell division system.

Bacterial persistence poses a major obstacle for current efforts to tackle the global rise of antibiotic resistance. Here, Balaban, Gerdes, Lewis and McKinney discuss the physiological features of persister cells and the factors leading to their emergence, as well as the implications of persistence for antibiotic treatment regimens and bacterial heterogeneity.

Vaheri and colleagues discuss the molecular and cell biology of hantavirus infection and provide an overview of the virus-induced and immune-mediated pathology caused by this virus family in humans.

Raoult and colleagues review recent developments in clinical microbiology, including the development of mass spectrometry-based diagnostics and point-of-care tests, which might change clinical practice.

Clathrin-mediated endocytosis is exploited by bacterial and viral pathogens during internalization. Humphries and Way review recent studies which highlight the fact that, in addition to a structural role, clathrin can function as a signalling platform during pathogen entry, and other studies revealing that, in conjunction with actin, clathrin is involved in pathogen cell–cell spread and release.

Many mobile genetic elements, such as transposons, plasmids and viruses, must cleave their own DNA to effect transposition, replication or conjugation. Here, Chandler and colleagues describe the HUH endonucleases, which use a unique mechanism to cleave and rejoin single-stranded DNA in order to mobilize and disseminate such elements.

Cyclic di-AMP is one of the latest cyclic nucleotide second messengers to be discovered in bacteria. Here, Corrigan and Gründling provide an overview of the enzymes involved in its synthesis and degradation, the currently known receptor proteins and the cellular pathways that are known to be directly or indirectly controlled by this newly identified second messenger.

The obligate intracellular bacteriumCoxiella burnetii causes both acute and chronic zoonotic infections. Here, Samuel and colleagues discuss the recent technological advances that have facilitated a deeper understanding of the molecular mechanisms of C. burnetiipathogenesis, including host cell invasion and modulation by virulence factors exported through the type IV Dot/Icm secretion system.

Lipid A is the bioactive component of the Gram-negative outer membrane and is extensively remodelled to enable the bacterium to subvert the immune system of the host. Here, Needham and Trent describe the regulation of lipid A-modifying enzymes, the host defences that target lipid A and the strategies that bacterial pathogens use to avoid immune detection.

Hepatitis C virus infection is a major cause of liver cirrhosis and cancer, and current therapies are often ineffective or have severe side effects. Here, Bartenschlager and colleagues review how structural and functional insights into the viral life cycle have allowed the development of novel direct-acting antiviral agents.

Katze and colleagues provide an overview of the evolution of systems virology and the insights obtained from using such methodologies to study virus–host interactions. Combining systems, mathematical and computational approaches with traditional virology research will offer a better understanding of how viruses cause disease and will help in the development of therapeutics.

The combination of transposon mutagenesis with next-generation sequencing has emerged as a useful tool for identifying putative gene function in a high-throughput manner. Here, van Opijnen and Camilli describe the four main techniques that are used for this purpose, with a focus on their application for uncovering bacterial gene function.