Review Articles

Metagenomic studies are beginning to clarify the huge phylogenetic and functional diversity of plant viruses and their importance for ecosystem stability. In this Review, Varsani and colleagues discuss evolutionary relationships between plant viruses, their vectors and host plants.

Coral reefs are threatened by climate change; one avenue to address this threat is to understand and manipulate the microbial partners of corals. In this Review, van Oppen and Blackall discuss the bacteria found in the coral microbiome and their roles.

Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). In this Review, Xavier and colleagues highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.

In this Review, Andersson and colleagues outline factors to consider when studying and defining heteroresistance, and they explore the different genetic mechanisms underlying heterogeneity in antibiotic resistance phenotypes, the impact of such mechanisms on the efficacy of treatment and the methods and difficulties in diagnosing heteroresistance in clinical bacterial isolates.

Whole genome sequencing (WGS) offers new opportunities in the clinical management and surveillance of Mycobacterium tuberculosis. In this Review, Meehan and colleagues explore the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

In this Review, Reyes-Lamothe and Sherratt describe the contributions of chromosome structure and nucleoid folding to cell cycle regulation, detail the cellular processes involved in the initiation of DNA replication and DNA segregation and explore how those processes are linked to cell growth and cell division.

In this Review, Mitchell and Silhavy explore the cellular envelope stress response pathways and discuss what occurs when these pathways are aberrantly activated. They also discuss how recent insights into stress response activation have highlighted the extreme toxicity of unfolded outer membrane proteins.

Lipopolysaccharide is a key component of the Gram-negative cell envelope and functions, for example, as a permeability barrier or determinant of host immune responses. In this Review, Simpson and Trent guide us through lipopolysaccharide biogenesis and modifications and their functional and therapeutic implications.

Type IV pili (T4P) are dynamic filaments on the surface of many bacteria with essential roles in colonization and pathogenesis. In this Review, Craig, Forest and Maier examine the T4P architecture, present molecular models for T4P dynamics and highlight recent insights into T4P retraction.

Vertebrate genomes typically contain thousands of loci composed of ancient retroviral sequences, known as endogenous retroviruses (ERVs). In this Review, Johnson describes ERV origins, their diversity and their relationships to retroviruses and discusses the potential for ERVs to reveal virus–host interactions on evolutionary timescales. He also describes examples of cellular functions, including protein-coding genes and regulatory elements that have evolved from ERVs.

Most bacteria live in fluctuating environments that can have complex topographies and multiple species present. In this Review, Mukherjee and Bassler discuss how factors such as flow, geometry, biofilms and the presence of the host microbiota influence bacterial quorum sensing.

Many symbioses depend on the acquisition of microbial symbionts from the environment. In this Review, Raina and colleagues argue that chemotaxis and motility are widespread but overlooked mechanisms that enable symbionts to find and/or colonize their hosts.

Hydrothermal vents are unique habitats for chemosynthetic bacteria and archaea and the animals that live in symbiosis with them. In this Review, Dick explores the challenges and opportunities that vent ecosystems provide for microbial life and their relationship to biogeography.

In this Review, Grossart and colleagues conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. They focus on currently unexplored aquatic fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

Electroactive microorganisms can transfer electrons to or take them up from electrodes, and they are used in applications such as microbial fuel cells. In this Review, Logan and colleagues discuss the diversity of exoelectrogenic and electrotrophic microorganisms and their functions.

In this Review, Bush and Bradford describe medically relevant β-lactamase families and various combinations of a β-lactam with a β-lactamase inhibitor that have been developed, or that are being developed, to counteract these enzymes.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen both within hospitals and in the community. In this Review, Fowler and colleagues provide an overview of basic and clinical MRSA research and explore the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease in young children and elderly people. In this Review, Battles and McLellan summarize our current understanding of RSV entry, describe progress on the development of new interventions and conclude with a perspective on gaps in our knowledge that require further investigation.

Combinations of antibiotics and of antibiotics with non-antibiotic activity-enhancing compounds offer a productive strategy to address the widespread emergence of antibiotic-resistant strains. In this Review, Tyers and Wright outline a theoretical and practical framework for the development of effective drug combinations.

Methane metabolism has a central role in the global carbon cycle. In the Review, Tyson and colleagues discuss the enzymatic pathways responsible for archaeal methane metabolism and highlight the evolutionary relationships of key enzymes with recently discovered alkane-oxidizing archaea.