Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.

Phage defense systems in bacteria exhibit high degrees of modularity, with sensing, signal transmission, and effector enzymes frequently being exchanged among phage defense gene clusters. In this study, we capitalized on this modularity to discover phage defense systems by searching for defense-associated modules in new gene contexts. This approach revealed a large and interconnected network of modular components distributed across diverse gene clusters. From over 500 candidate defense systems, we selected nine for experimental testing and validated three: Dionysus, a TerB-encoding system that disrupts early phage infection vesicle formation by Jumbo phages; Ophion, a Radical SAM-containing system that prevents the formation of the Jumbo phage nucleus; and Ambrosia, a tightly regulated RM-like system. Collectively, we demonstrate that leveraging the modular architecture of phage defense systems is an effective approach to their discovery. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, 101003229 Netherlands Organisation for Scientific Research, VI.C.192.027, OCENW.XS23.1.006 Koningin Wilhelmina Fonds, 15602

Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...

Inducible gene expression and CRISPR interference-mediated depletion in the predatory bacterium Bdellovibrio bacteriovorus.

Viruses encode ribosomal proteins (RPs), but their genomes usually harbor a single RP-coding gene. Here, we reannotate the genome of the jumbo cyanophage PhiMa05 and show that it encodes six RPs, an RP acetyltransferase, and a ribosome biogenesis protein. Evolutionary analyses suggest that these viral RP-coding genes may have been horizontally transferred to certain members of the Vampirovibrionia , a non-photosynthetic basal lineage of Cyanobacteriota , via integration of the viral genome. ### Competing Interest Statement The authors have declared no competing interest. Secretaría de Ciencia, Humanidades, Tecnología e Innovación, Becas de Posgrado para Maestrías y Doctorados en Ciencias y Humanidades en el Extranjero Natural Sciences and Engineering Research Council of Canada, 2022-03350, 2022-00329 Phycological Society of America, Norma J. Lang Early Career Researcher Fellowship

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...