The Hna (Helicase-nuclease Abi) phage defence system consists of a single protein and provides defence through abortive infection. We show that Hna's abortive infection response can be recreated in a...

Bacteria evolved a variety of phage defence strategies to combat the constant onslaught of viral threats. DarTG toxin-antitoxin systems provide phage defence by ADP-ribosylation of bases in single-stranded DNA which interferes with viral replication and aborts phage infection. Here, we describe DarHTG, a system widespread among bacteria, that combines DarTG with a non-processive superfamily I helicase functioning as co-toxin for DarT and thereby enabling the ADP-ribosylation of double-stranded DNA. We identified two such DarHTG subclasses which catalyse the ADP-ribosylation of adenosine and guanosine bases, respectively, and reverse these modifications with structurally unique ARH superfamily antitoxins. Thus, DarHTG antitoxins expand the known macromolecular target spectrum of the ARH enzyme class to nucleic acids. These DarHTG systems confer resistance to a broad range of bacteriophages and can be triggered by the highly charged tails of viral single-stranded DNA-binding proteins, which occlude the active site of the ARH antitoxin. ### Competing Interest Statement The authors have declared no competing interest. Lise Meitner Fellowship by Max Planck Society

Nature Microbiology, Published online: 29 October 2026; doi:10.1038/s41564-026-02480-7Screening millions of CRISPR spacers across globally distributed metagenomes reveals unexpected dynamics of phage–host interactions, including many cases where phage genomes seem to repeatedly enter non-host cells.

PhD Project - Molecular recognition of biofilm polysaccharides by phage enzymes at University of York, listed on FindAPhD.com

PhD Project - Sex-Specific Phage Therapy for Conflict Wound Healing at University of Southampton, listed on FindAPhD.com

In this Review, the authors summarize structural, biochemical and genetic insights into bacterial immunity, focusing on steps that link infection sensing to activation and effector function.

HIDEN-SEQ (hidden Acr-enabled transposon-insertion sequencing) is a transposon-insertion sequencing method for phages that systematically links their genes to selectable phenotypes.

Lomeli-Ortega et al. review how peptide-mediated arbitrium signaling enables communication both within and between bacteriophage populations, highlighting how viral crosstalk may influence phage competition, cooperation, and microbial community dynamics while creating opportunities for phage-based technologies.

Synergistic peptide-antibiotic-phage cocktails eradicate multidrug-resistant Serratia marcescens biofilms.

Screening millions of CRISPR spacers across globally distributed metagenomes reveals unexpected dynamics of phage–host interactions, including many cases where phage genomes seem to repeatedly enter n...

Filamentous phages play important roles in molecular biology and bacterial pathogenesis. There is therefore great interest in the genomes of the phages, including M13 and Pf, which infect Escherichia coli and Pseudomonas aeruginosa , respectively. However, efficient methods for purifying single-stranded DNA (ssDNA) from filamentous phages are scarce and rely mainly on repurposed commercial kits developed for dsDNA. These kits yield variable amounts of ssDNA, varying considerably from one phage to another, their solutions are proprietary and troubleshooting, and customizing the protocol to improve purification is not possible. Here, we developed and optimized two protocols based on ssDNA binding to silica columns in the presence of guanidine hydrochloride and potassium iodide chaotropic salts, for filamentous phages M13KO7 and Pf4. The protocols achieved 60 to 100% recovery, equal to or higher than the Monarch Spin gDNA Extraction and DNeasy Blood and Tissue kits, with similar A260/280 and A260/230 ratios, intact DNA in agarose gels, and no detectable host genomic DNA by PCR. Recovery depended critically on the chaotropic salts and on ethanol, and did not increase at lower pH, consistent with a water-exclusion model in which hydrophobic interactions and hydrogen bonding dominate over electrostatic repulsion. Phage-specific differences in recovery indicate that optimization may be needed for some phages, which the fully customizable nature of these protocols facilitates. Comparing the virion ssDNA with the double-stranded replicative form (RF) revealed genome variants in both phages, including a shorter M13KO7 form lacking the kanamycin resistance-p15A insert, and illustrates the value of analyzing both RF and ssDNA forms to study filamentous phage biology. Implementing these protocols in routine filamentous phage workflows should facilitate their characterization and engineering. ### Competing Interest Statement The authors have declared no competing interest. Stanford Maternal and Child Health Research Institute, Postdoctoral Fellowship Cystic Fibrosis Research Institute (CFRI), Elizabeth Nash Memorial Fellowship National Institutes of Health, K08 AI190313, R01 HL148184-01, R01 AI12492093, R01 DC019965, K24 AI166718, P01AI1960471 Cystic Fibrosis Foundation, https://ror.org/00ax59295

Antimicrobial resistance poses a critical global health threat, and renewed interest in bacteriophage (phage) therapy highlights its potential as a targeted alternative to antibiotic monotherapy. However, phage resistance in bacteria remains a key limiting factor in phage therapy, driven by evolutionary adaptations to phage exposure. Antibacterial modalities (antibiotics, adjuvants, antimicrobial peptides, and RNA-based therapeutics) could help overcome these barriers and represent untapped potential for synergistic, precision antimicrobial interventions when combined with phage therapy. Importantly, bacterial physiology and environmental context could strongly influence treatment outcomes, underscoring the need for clinically relevant models for testing combinations. Integration of multi-omics and artificial intelligence-driven approaches could help predict patterns for the development of precision therapies and support the development of novel antimicrobial interventions.

The primary physiological role of toxin/antitoxin (TA) systems is phage defense; they are also used to stabilize mobile genetic elements. In the initial publication in 1996, plasmid-encoded Hok/Sok, a type I TA system (protein toxin, RNA antitoxin that inhibits toxin mRNA), was shown to inhibit T4 phage infection in Escherichia coli by reducing its efficiency of plating and burst size and by increasing the time for mature phage to form (latent period). This publication also identified that the mechanism of Hok/Sok inhibiting T4 was host transcription shutoff, arguably the most-general phage inhibition system since most phages impair host transcription. However, recently, the role of Hok/Sok in phage inhibition has been challenged. Therefore, here we investigated the role of four E. coli chromosomally-expressed, hok+/sok+ loci and the one orphan hok+ locus and found that the Hok proteins inhibit the infection of E. coli by BASEL phage 48, a Vequintavirus with myovirus morphology. Of the five Hok proteins, the greatest phage inhibition was by HokB, and infection by BASEL phages 34 and 39 were also inhibited by HokB. We also find BASEL phage 48 requires the WecB-generated receptor NGR for infection. Therefore, chromosomally-derived orphan Hok proteins, produced at physiological levels, are relevant for phage inhibition. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, https://ror.org/021nxhr62, 2515448