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.

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.

A study looking at the Tibetan Plateau finds that microbial shifts might contribute to irreversible soil degradation.

This study used engineered bacteria to record the transcriptional responses of transiting bacteria in the gut environment.

A study in mice shows that antibiotic treatment predisposes to invasive fungal infection through gut dysbiosis and barrier dysfunction.

This Genome Watch highlights recently reported methods that enable genome editing of microorganisms within phylogenetically diverse communities.

This Genome Watch highlights how metagenomics can fill the knowledge gap of the wild avian gut microbiome and enable the early detection of antibiotic-resistant bacteria with implications for public health policy and conservation management.

A recent study shows that chemotaxis shapes the microscale organization of the ocean’s microbiome.