Reviews & Analysis

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.

In this Review, Hoenen, Groseth and Feldmann address strategies that have shown promise in interfering with the filovirus life cycle, including the entry process, viral RNA synthesis and gene expression, as well as morphogenesis and budding.

TRIM5 is a potent restriction factor for HIV-1 and other retroviruses. In this Review, Ganser-Pornillos and Pornillos provide an overview of the current state of knowledge of the molecular mechanism of TRIM5-mediated restriction, highlight recent advances and discuss implications for the development of capsid-targeted antiviral therapeutics.

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.

The microbial majority with which we share Earth often goes unnoticed despite underlying major biogeochemical cycles and food webs, thereby taking a key role in climate change. This Consensus Statement highlights the importance of climate change microbiology and issues a call to action for all microbiologists.

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.

The origin of viruses is an unsolved, controversial question. In this Opinion article, Krupovic, Dolja and Koonin propose a new scenario for the origin of viruses based on primordial, selfish replicators acquiring structural proteins from cells, enabling them to form virions.

In this Viewpoint article, several experts discuss the microbial contributions to climate change and consider the effects of global warming, extreme weather and other consequences of climate change on microbial communities in the ocean and soil, host–microbiota interactions and the global burden of infectious diseases and ecosystem processes, and they explore open questions and research needs.

In this Opinion article, Sonnenburg and Sonnenburg explore whether individuals in the industrialized world may be harbouring a microbial community that is now incompatible with human biology, and they hypothesize that the modern, industrial lifestyle has contributed to alterations in the microbiota that may be linked to the deterioration of human health.

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.

Antibiotic persistence contributes to the survival of bacteria during antibiotic treatment. In this Consensus Statement, scientists working on the response of bacteria to antibiotics define antibiotic persistence and provide practical guidance on how to study bacterial persisters.

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.