Review Articles in 2019

The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. In this Review, Koonin and colleagues provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on major developments, and outline a complete scenario for the origins and evolution of CRISPR–Cas systems.

In the outer membrane, trimeric porins control the cellular uptake of small molecules, including nutrients and antibacterial agents. In this Review, Pagès and colleagues discuss advances in our understanding of the roles of general porins in small-molecule translocation in Enterobacteriaceae and consider the crucial contribution of porins in antibiotic resistance.

Secreted siderophores help bacteria to take up iron from the environment. In this Review, Kramer, Özkaya and Kümmerli discuss the functions and implications that siderophores have for social interactions between bacterial cells and the resulting consequences for communities and hosts.

With rising rates of antibiotic resistance, it is essential that new antibiotics are developed. In this Review, Theuretzbacher et al. take stock of the preclinical antibiotic pipeline and discuss challenges and opportunities for the discovery and development of novel antibacterial therapies.

Mycobacterium tuberculosis has a distinctive cell envelope that contributes to its resistance against the human immune system and antibiotic therapy. In this Review, Dulberger, Rubin and Boutte discuss mycobacterial cell envelope dynamics and their relevance for infection and drug treatment.

DNA methylation affects DNA–protein interactions and has important cellular roles, including the control of reversible switching (phase variation) of gene expression. In this Review, Sánchez-Romero and Casadesús review epigenetic signalling by DNA methylation, focusing on its contribution to phenotypic heterogeneity in bacterial populations.

Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. In this Review, Caugant and Brynildsrud discuss how high-throughput sequencing approaches have advanced our understanding of the diversity and evolution of Neisseria meningitidis and the pathogenesis of N. meningitidis infection and how they are helping to explain the epidemiology of meningococcal disease.

In this Review, Coleman and colleagues discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during viral infection alters the flow of energy and nutrients in aquatic ecosystems.

In this Review, Jansson and Hofmockel explore the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems and the potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.

Going from description of the diversity and disease associations of the human gut microbiota towards functional understanding and applications is challenging. In this Review, Raes and colleagues present synthetic ecology approaches that reduce the complexity and advance translation of human gut microbiota research.

Microbiome engineering has many potential applications, ranging from agriculture to medicine. In this Review, Lawson, McMahon and colleagues guide us through the design–build–test–learn cycle that has been successful in many disciplines and explain how it applies to microbiome engineering.

Citrobacter rodentium, an extracellular mouse-specific enteric pathogen, provides a robust model for the study of physiological host–pathogen–microbiota interactions. In this Review, Frankel and colleagues highlight how the C. rodentium model has advanced our understanding of enteric infections and inflammatory bowel disease, in particular changes to host metabolism and inflammation.

In this Review, Kolodziejczyk, Zheng and Elinav describe the latest advances in understanding diet–microbiota interactions, the individuality of gut microbiota composition and how this knowledge could be harnessed for personalized nutrition strategies to improve human health.

Microorganisms are known for their vigorous growth and enormous capacity to reproduce. Nevertheless, several microorganisms exhibit ageing, for example through asymmetrical cell division and persistence. In this Review, Moger-Reischer and Lennon consider the mechanisms and implications of microbial ageing.

Post-translational modifications of bacterial proteins have a role in various cellular processes such as protein synthesis and turnover, metabolism, the cell cycle, morphogenesis and virulence. In this Review, Macek and colleagues introduce the major types of protein post-translational modifications in bacteria and discuss their roles in various aspects of bacterial cell biology.

Microorganisms have a central place in the marine sulfur cycle through the production and consumption of organic matter. In this Review, Moran and Durham examine sulfur metabolites that are synthesized and catabolized by marine microorganisms in the pelagic ocean and explore how these metabolites function as ecological links between microorganisms.

Epstein–Barr virus (EBV) establishes latent and persistent infections in humans, and is associated with several cancers. In this Review, Münz discusses the evidence for EBV persistence without B cell transformation and the role of early abortive lytic replication as well as non-coding RNAs in EBV-driven tumorigenesis.

Protozoa use various mechanisms to establish persistent infections. In this Review, Barrett and colleagues describe protozoan parasite ‘persister-like cells’, and they explore their possible role in persistent infections and drug treatment failure, and outline possible treatment options.

Simple animal models are emerging as valuable tools for microbiome research. In this Review, Douglas discusses the opportunity for microbiome research on the traditional biomedical models Drosophila melanogaster, Caenorhabditis elegans and zebrafish. Other systems, for example, hydra, squid and the honeybee, are valuable alternative models to address specific questions.

Invasive alien plants and animals are known to cause disease and disrupt communities. In this Review, Thakur and colleagues discuss examples and impacts of microorganisms that have been introduced in new regions by human activities.