Viral-induced DNA damage triggers both eukaryotic and prokaryotic innate immunity. Here, we report that self-DNA ends generated routinely during normal termination of bacterial replication suffice to ...

Nature Reviews Microbiology, Published online: 02 October 2026; doi:10.1038/s41579-026-01376-xBacteria deploy diverse immune systems to counter phage infection, yet how these systems sense invasion remains incompletely understood. This Review categorizes phage-derived triggers and outlines emerging principles that govern immune recognition of phage infection.

Cyclic oligonucleotide–based antiphage signaling systems (CBASS) are bacterial immune pathways evolutionarily related to cGAS-STING (cyclic GMP-AMP synthase–stimulator of interferon genes) in humans. ...

Avoiding a diet rich in simple sugars during treatment with antibiotics may mitigate microbiota disruption.

Indole-producing Escherichia coli worsens ischemic stroke through the activation of aryl hydrocarbon receptor signaling in dendritic cells. Limiting AHR signaling in DCs promotes gut-derived DC migrat...

Gene-editing techniques could soon allow researchers to replace entire genes and engineer complex cellular circuits — if the systems can be delivered safely into cells.

RNA modifications play an important role in biological processes. Mapping the diversity of RNA chemistry and studying the biological function of in...

Phage Tn-seq uses Tn5 transposon mutagenesis with anti-CRISPR-based selection and deep sequencing as a method to generate unbiased, genome-wide mutations across diverse phages

Retrotransposons can infect neighboring cells using a mechanism that relies on a small fusogen-like protein rather than on the envelope protein that is typically required for infection.

Viruses must recognize receptors on host surfaces to initiate infection, but these receptors can evolve rapidly, posing a fundamental challenge to ...

Abstract. Toxin-antitoxin systems (TAs) are widespread in bacterial genomes. Yet, their integration, persistence, and impact in chromosome dynamics remain

The amoeba Incendiamoeba cascadensis demonstrates that eukaryotic life can withstand temperatures beyond what was thought possible and sheds light on molecular strategies for survival in extreme heat.

Abstract. Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we id

Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...

Resource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether...

CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...

Plasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...

Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02484-3An engineered non-pathogenic bacterium produces lytic phages and is protective in mouse models of Salmonella infection.

Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...

Modified nanopore simultaneously identifies diverse biomolecules and their modifications.

Insertion sequences (ISs) are small, self-mobilizing DNA elements widespread across prokaryotic genomes, including chromosomes and plasmids. IS elements frequently co-localize with antimicrobial resis...

Taillefer et al. show that a bacterial type VI secretion system is lost or attenuated during experimental evolution when it provides no competitive advantage but is maintained in the presence of susce...

Pathogens target and degrade the extracellular matrix surrounding plant cells. A central question is how cell wall-derived damage-associated molecular patterns (DAMPs) are recognized and integrated to...

Recent years have witnessed a rapid expansion in bacterial defense mechanisms. Alongside established defenses against molecular parasites, hundreds of novel mechanisms are being described annually, contributing to an ever-expanding ‘bacterial immune system’. Terms like ‘defense’ and ‘immune’ are often used as shorthand for an observed anti-infection phenotype, but can also imply an evolutionary adaptation with a specific anti-infection function. Despite the field’s growth, no agreed-upon framework exists for identifying defense adaptations. When is a defense mechanism an evolved adaptation? Here, we review prior debates in evolutionary biology and propose a four-part framework to evaluate the case for a defense mechanism being an evolved adaptation. Beyond bacterial immunity, these criteria offer a research roadmap to address functional controversies across microbiology.

Gabija acts early during phage infection, preventing phage genome circularization and replication. Phage DNA end-binding proteins prevent RecBCD loading onto linear DNA, and the absence of RecBCD lice...