Reviews & Analysis

In this Review, Brennan and Garrett discuss the multifaceted associations of Fusobacterium nucleatum with its human host that range from symbiotic in oral biofilms to potential infectious pathogen at several sites and cancer-promoting member of the microbiota in the gut.

In this Review, Nancy P. Keller describes the classification and genetics of secondary metabolites and biosynthetic gene clusters, cluster regulation and the ecological roles of secondary metabolites, and she explores avenues for the discovery of new fungal metabolites and current challenges in their identification.

Coronaviruses have a broad host range and distribution, and some highly pathogenic lineages have spilled over to humans and animals. Here, Cui, Li and Shi explore the viral factors that enabled the emergence of diseases such as severe acute respiratory syndrome and Middle East respiratory syndrome.

Studies of ancient DNA and endogenous viral elements have revealed extraordinary conservation of virus genome sequences over thousands or millions of years. In this Opinion article, Simmonds, Aiewsakun and Katzourakis describe a niche-filling model that describes how viruses can rapidly evolve to adapt to new host environments while their longer-term evolution is increasingly driven by their hosts.

Eukaryotic viruses have evolved a variety of ways to manipulate the cellular translation apparatus. In this Review, Jaafar and Kieft present important examples of viral RNA-based strategies to exploit the cellular translation machinery.

Influenza A viruses cause pandemics when they cross between species. In this Review, Barclay and colleagues examine the host barriers that influenza A viruses must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host.

Fungi are enormously diverse, not the least in potential genetic markers that can be used for high-throughput sequencing studies of the mycobiome. In this Review, Nilsson and colleagues provide advice for leveraging next-generation technologies to explore mycobiome diversity in different habitats.

Cyanobacteria have evolved a number of photoreceptor-controlled mechanisms that enable them to sense and respond to environmental light conditions. In this Review, Kehoe and Wiltbank examine physiological responses that are controlled by members of the phytochrome photoreceptor superfamily and discuss the signal transduction pathways through which these photoreceptors operate.

Bacterial membrane vesicles can transfer material between cells and function as decoys for antibiotics and phages. This Review provides an overview of different vesicle types, including classic outer-membrane vesicles and newly identified types that are induced by phage-derived autolysins.

Light controls important physiological and morphological responses in fungi. In this Review, Yu and Fischer review the structural basis for light sensing in filamentous fungi and explore the light signalling mechanisms for blue-light photoreceptors, green-light photoreceptors and red-light photoreceptors.

Most infections with enterococci involve the formation of biofilms, which further increases the antibiotic tolerance and resistance of these priority pathogens. In this Review, Kline and colleagues summarize how enterococci form biofilms, including polymicrobial biofilms, and highlight new treatment options.

This Consensus Statement presents the barriers that currently prevent the timely development and implementation of novel and rapid antimicrobial susceptibility testing platforms, including the costs involved, uptake of new tools, legal and regulatory aspects, difficulties conducting clinical trials and quality control, and presents possible solutions.

The dynamic and polymicrobial oral microbiota is a direct precursor of diseases such as dental caries and periodontitis. In this Review, Lamont, Koo and Hajishengallis discuss the mechanisms by which oral microbial communities develop and become functionally specialized. They also examine the progression of polymicrobial communities towards pathogenicity.

Marine oxygen minimum zones are expanding globally as a result of rising temperatures. In this Progress article, Bertagnolli and Stewart describe the ecological and functional diversity of the microbial communities that inhabit these zones and their contribution to biogeochemical cycles.

In this Review, Rokas, Wisecaver and Lind discuss the diversity in the structure and content of fungal metabolic gene clusters, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations.

In this Progress article, McGinn and Marraffini review recent studies that have advanced our understanding of the molecular mechanisms of spacer integration, protospacer capture and primed spacer acquisition, and discuss the future of the field.

Viral infection is a major contributor to the global cancer burden. In this Review, Krump and You explore the molecular mechanisms of viral oncogenesis in humans. They highlight how viral manipulation of host cellular signalling, DNA damage responses, immunity and microRNA targets promotes the initiation and development of cancer.

In this Review, Gilbert and Stephens outline the history of the field of microbiology of the built environment and discuss insights into microbial ecology, adaptation and evolution. They consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.

Many phages use tails to attach to and penetrate the cell envelope of their bacterial hosts. In this Review, Brouns and colleagues explore recent structural and mechanistic insights into the interaction of phage tails with receptors on the bacterial surface.

Archaea have been found in biofilms in a variety of habitats. In this Review, Albers and colleagues explore the different stages of archaeal biofilm development and highlight the similarities and differences between archaea and bacteria. They also consider their role in different industrial processes.