Review Articles in 2022

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.