Review Articles

The impacts of fungal infections on human health are of increasing concern, and resistance of pathogenic fungi to all licensed systemic antifungals has been documented. In this Review, Fisher, Verweij and colleagues discuss the research and innovation topics that are needed to understand and minimize the occurrence and impact of antifungal resistance.

The human gut microbiota produces an extensive array of carbohydrate-active enzymes to degrade carbohydrates derived from the diet, host and other microorganisms. Withers and colleagues discuss the vast diversity and activities of these enzymes and their potential applications.

In this Review, Wang and colleagues review the strategies microbial pathogens use to evade plant immunity for successful infection. They highlight how microbial effectors manipulate host cellular processes involved in immune sensing, signal integration and defence execution and how to exploit this knowledge to engineer crop resistance.

Chemotaxis is one of the best studied bacterial behaviours, but the underlying mechanisms are much better understood than the reasons and consequences of chemotaxis. In this Review, Keegstra et al. discuss the costs and benefits both for individual bacteria and whole populations.

Combining several antibiotics, either in mixtures or sequential order, is proposed to increase treatment efficacy and reduce resistance evolution. In this Review, Andersson and colleagues discuss the effects of antibiotic combinations, the directional effects of previous antibiotic treatments and the role of stress-response systems as well as the interactions between drugs and resistance mutations.

Soil microorganisms shape global element cycles in life and death. In this Review, Sokol and colleagues explore how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. They also discuss incorporating microbial life and death into trait-based models that predict soil biogeochemical dynamics.

To maintain genome integrity and ensure cell survival, bacteria have evolved several DNA repair pathways to repair different types of DNA damage and non-canonical bases, including strand breaks, nucleotide modifications, cross-links, mismatches and ribonucleotide incorporations. In this Review, Wozniak and Simmons provide a contemporary discussion of the excision-based mechanisms bacteria use to repair the diverse set of lesions they encounter.

Osteomyelitis is an infection of bone that arises when a pathogen colonizes bone tissue owing to injury or surgery. In this Review, Masters and colleagues explore the microbial pathogenesis, immunity and clinical management of bone infections.

Differential availability of oxygen, nutrients and other resources leads to metabolic and structural heterogeneity in multicellular systems, including in biofilms. In this Review, Jo et al. discuss how chemical and physical gradients can affect the physiology of microbial biofilms.

The distinct spatial patterning of microorganisms during infection can influence infection outcomes. In this Review, Azimi et al. detail the microbiogeography of human infections and discuss approaches to study the processes that influence polymicrobial patterning.

The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle. In this Review, Hutchins and Capone explore the latest developments in our understanding of the role of microorganisms in the marine nitrogen cycle, including new taxa, pathways, methods and concepts. They also discuss opportunities to understand and better predict the effects of humans and global change.

Chronic infections caused by microbial biofilms represent an important clinical challenge owing to the recalcitrance of microbial biofilms to antimicrobials and the immune system, causing persistence and clinical recurrence of these infections. In this Review, Ciofu and colleagues discuss our current understanding of the mechanisms of tolerance of such biofilms to the immune system as well as of tolerance and resistance to antimicrobials.

We take up a multitude of foreign substances, so called xenobiotics, such as medications, food additives and pollutants, which affect the composition and function of the gut microbiota. In this Review, Lindell, Zimmermann-Kogadeeva and Patil discuss these reciprocal interactions and their mechanisms.

Microbiome-based therapeutics hold great promise for reducing disease susceptibility and enhancing disease resistance. In this Review, Sorbara and Pamer explore the major bacterial phyla associated with health benefits and the potential of microbiome-based therapeutics, including faecal microbiota transplantation, bacterial consortia, engineered symbiotic bacteria, diet and prebiotics, and microbiome-derived proteins and metabolites. They also discuss the challenges confronting therapeutic development as well as the regulatory hurdles for clinical trials and manufacturing.

The role of CRISPR–Cas systems in defence against mobile genetic elements is well established, but there is increasing evidence that these systems have alternative functions beyond adaptive immunity. In this Review, Staals, van der Oost and colleagues explore these non-canonical functions of CRISPR–Cas systems with relevant consequences for CRISPR-based genome editing applications.

In this Review, Harvey and Holmes explore our changing understanding of the structure, diversity and evolution of the animal virome. They also outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how these impact assessment of the risk of disease emergence.

Toxin–antitoxin systems are composed of a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In this Review, Van Melderen and colleagues summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin–antitoxin systems.

Clostridioides difficile produces up to three different toxins, which are key to the pathogenesis of C. difficile infection of the colon. In this Review, Kordus, Thomas and Lacy discuss the structure and function of these toxins and how this information informs new therapeutic approaches.

Bats harbour a multitude of coronaviruses and owing to their diversity and wide distribution are prime reservoir hosts of emerging viruses. Ruiz-Aravena, McKee and colleagues analyse the currently available information on bat coronaviruses and discuss their role in recent and potential future spillovers.

Bacterial DNA transfers between cells in numerous ways and becomes integrated into the genome, with diverse consequences for bacterial genomes. In this Review, Arnold, Huang and Hanage discuss the underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation.