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.

To fully harness phage therapy against escalating antimicrobial resistance, it is imperative to elucidate the fundamental mechanisms by which viruses systematically dismantle host physiology. In this ...

Selective DNA delivery to specific members of assembled bacterial communities remains challenging. Bacterial conjugation enables efficient DNA delivery, but transfer to non-target recipients limits its specificity within mixed communities. Here, we repurpose plasmid entry exclusion (Eex) as a recipient-side gate to control conjugative DNA delivery. We demonstrate selective plasmid delivery to Eex-negative recipients within populations containing both Eex-expressing and Eex-negative cells. This recipient selectivity was maintained at increased cell densities and during prolonged mating. By combining RP4-type and F-type conjugation systems with their corresponding exclusion modules, we further directed DNA delivery from distinct donors to defined recipient populations. RP4-derived Eex also functioned in environmental bacteria, including Pseudomonas putida and Sphingobium japonicum, enabling recipient-specific exclusion within a multispecies mixture. Furthermore, repeated cycles of Eex-guided conjugation and selection altered community composition after assembly. These results establish entry exclusion as a recipient-side strategy for selective conjugative DNA delivery and, when combined with selection, for controlling the composition of assembled bacterial communities. ### Competing Interest Statement The authors have declared no competing interest. Japan Society for the Promotion of Science, https://ror.org/00hhkn466, 19K15725, 25K18154, 24KJ0025 Institute for Fermentation, Y-2024-1-007

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

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...

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02471-8In vivo silencing of genes in E. coli strains using CRISPRi reveals specific genetic factors and metabolic adaptations that influence colonization in the mouse gut under variable physiological conditions.

A mechanistic basis for how the hormone salicylic acid promotes transcriptional activation during plant immune responses is described.

Bacterial antiviral immunity systems can be toxic to their hosts and must be tightly regulated. Immunity genes are often encoded by AT-rich mobile genetic elements subjected to silencing by nucleoid b...

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.

Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...

Whole-genome screening reveals strategies to boost CRISPR-associated transposase genome editing efficiency.

While the dynamic changes in genome organization in cellular organisms have been well described, the three-dimensional (3D) folding of phage genomes during the infection of their host is extremely lim...

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...

In this Review, Papenfort discusses established and emerging aspects of bacterial small RNAs (sRNAs), their molecular mechanisms and regulatory principles, and the global impact of sRNAs on cellular g...

The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.

The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...

Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.

Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.

The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome-editing capabilities. However, generating diverse multidomain proteins with robust enzymatic ...

CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...

Shomar, Guillaume, et al. report the genomics-driven discovery of a family of more than 2,000 lanthipeptide biosynthetic gene clusters with anti-phage potential. They experimentally demonstrate anti-p...

EMBL Hamburg / CSSB The European Molecular Biology Laboratory (EMBL) is Europe’s flagship life sciences organization, with more than 110 independent research groups across Heidelberg, Hamburg, Grenobl...

OLD, an abortive immunity protein from prophage P2, consists of an ABC ATPase sensor and a TO-PRIM nuclease effector - a core architecture shared by a large protein family, including components of ant...

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...

Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection. We previously showed that DRT10, a tripartite system comprising an RT, a noncoding RNA (ncRNA), and a SLATT effector protein, catalyzes protein-primed, tandem-repeat DNA synthesis in a mechanism strikingly analogous to eukaryotic telomerase. However, the structural basis by which the RT-ncRNA complex directs repeat addition processivity and controls repeat length remains unknown. Here we present cryo-EM reconstructions of two evolutionarily diverse DRT10 RT-ncRNA systems that reveal an unanticipated 2:1 architecture, wherein two RT monomers bind opposite sides of a single, pseudo-symmetric ncRNA. Biochemical experiments demonstrate that each RT monomer reverse transcribes the template encoded on its respective side of the ncRNA, but only one generates the long repetitive product, with the template sequence defined by the distance between two flanking stem-loop anchors. Together with earlier studies of DRT2, DRT3, and DRT9, our findings identify a conserved mechanistic logic underlying ncRNA-templated tandem-repeat synthesis across Class 2 UG antiviral systems, despite vastly different architectural solutions. ### Competing Interest Statement Columbia University has filed a patent application related to this work. S.H.S. is a co-founder and scientific advisor to Dahlia Biosciences, a scientific advisor to CrisprBits and Prime Medicine, and an equity holder in Dahlia Biosciences and CrisprBits. The remaining authors declare no competing interests.

Genetic manipulation of bacteriophages is essential for interrogating phage biology and advancing antimicrobial therapies. However, current genome editing approaches can be inefficient, require multip...

The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...

Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune ...

Nature - Targeting Cancer-Specific Mutations with RNA-Triggered Chromatin Shredding

Sun et al. show that IS110 transposons utilize two independent RNA-guided transposition pathways: a top-strand copy-out mechanism and a direct top-strand transfer to new targets. These findings redefine IS110 transposition and reconcile prior discrepancies, which provides insight into programmable, RNA-guided genome modification without double-strand DNA breaks.

Nature Microbiology, Published online: 27 May 2026; doi:10.1038/s41564-026-02355-xThe prophage of a clinical Enterobacter isolate uses an RNA-guided transcription factor to alter flagellar composition, leading to enhanced bacterial motility and improved gut colonization in a mouse model.

Noteworthy — A two-gene plasmid is abundant and highly prevalent in human gut microbiomes.

Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...

The anti-CRISPR protein AcrVA2 specifically interrupts Cas12a biogenesis by triggering co-translational mRNA degradation.

Nature Microbiology, Published online: 27 April 2026; doi:10.1038/s41564-026-02312-8A large-scale, comparative cell biology and biochemical screen defines the molecular features controlling antiphage defence systems that encode nuclease effectors and accessory NTPase proteins.