Bacteriophages and microbial interactions

Temperate phages limit their own propagation under spatial constraint in biofilms on chitin

This study shows temperate phages in V. cholerae biofilms can displace non-lysogenized bacteria but face spatial and immunity constraints that limit their competitive advantage.

Piercing mechanism in the minimal contractile tail of bacteriophage P2.

This study uses cryo-EM and tomography to reveal the structural changes in bacteriophage P2 during tail contraction and host infection, identifying new architectural features and mechanisms of genome translocation.

Harnessing Alpine Lake Bacteria for the Development of Synthetic Communities with Broad-Spectrum Antiviral Activity

The paper investigates antiviral activity in alpine lake bacteria, develops synthetic communities with broad-spectrum antiviral properties, and links bacteriophage resistance to viral inactivation.

Persistent co-infection mediates inter-virus and host-virus gene exchange in marine protists

The paper identifies a new viral order, Skiavirales, in marine protists through long-read sequencing and shows gene exchange between viruses and host genomes.

H-NS silences antiviral immunity through 3D chromatin compaction

This study shows H-NS silences bacterial antiviral immunity by compacting chromatin, and its deletion enhances phage defense in E. coli.

Mapping Structural Constraints and Adaptive Potential in a Capsule-Degrading Phage Tailspike Protein

This study uses deep mutational scanning to analyze a phage tailspike protein, revealing structural constraints and adaptive flexibility that influence its function and host range.

Antibacterial activity of a newly identified phage-derived endolysin and its parental bacteriophage against clinical uropathogenic Escherichia coli

This study characterizes a bacteriophage and its endolysin against antibiotic-resistant uropathogenic E. coli, showing lytic activity and potential as antimicrobial tools.

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7

The study identifies surface glycan layers as primary or optional recognition substrates for phage infection in E. coli O157:H7, revealing their role in receptor access and infection outcomes.

Capsular Polysaccharide Safeguards a Prophage-Bacterium Symbiosis by Preventing Collateral Attack and Promoting Viral Transmission

The paper identifies capsular polysaccharides as a mechanism that stabilizes prophage-bacterium symbiosis by preventing collateral viral attack and enhancing transmission.

Sequential assembly in vivo of the bacteriophage P22 genome translocation channel

The paper determines the in vivo structures of P22 infection intermediates and explains how gp10 templates the sequential assembly of three proteins into a trans-envelope channel for genome translocation.

Mobile genetic elements are active and responsive to community context in model microbial consortium

The paper examines GI activity in a microbial consortium under stress, finding increased excision and expression compared to monocultures, and highlights the importance of community context in GI dynamics.

Machine learning prediction of eukaryotic hosts for giant viruses

This study develops GVHoP, a machine learning tool that predicts eukaryotic hosts for giant viruses using genomic data, achieving high accuracy and revealing novel host associations across environments.

Structure of NO16, a marine non-tailed vibriophage with a global distribution

This study characterizes the structure of the non-tailed vibriophage NO16, revealing its capsid organization and potential host interaction mechanisms.

A widespread NADase domain links bacterial immunity with human TEP1

The paper identifies a conserved NADase domain, NIR, in bacterial immunity and eukaryotic proteins like human TEP1, linking bacterial defense mechanisms to eukaryotic functions.

Shuttling, swapping and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites

The paper identifies and characterizes defence hotspots in P2-like phages and P4-like satellites, revealing rapid modular evolution of antiviral systems through gene swapping and recombination.

Discovery of novel enzybiotic candidates targeting human bacterial pathogens through large-scale viral-host profiling

The paper identifies novel enzybiotic candidates targeting human bacterial pathogens by analyzing viral-host associations in a large viral genome database.

Structural and functional insights into QueC-family protein in QatABCD anti-phage system

The paper investigates the structural and functional role of QueC-family protein QatC in the QatABCD anti-phage system, showing its role in protein modification similar to type IV CBASS.

Phage proofing Pseudomonas putida uncovers novel broad-spectrum phage resistance protein Psh

The paper identifies a novel phage resistance mechanism in Pseudomonas putida through experimental evolution, revealing a secreted protein Psh that confers broad-spectrum phage resistance without fitness costs.

Repurposing anti-phage defenses to differentially arrest the viral lifecycle reveals the regulatory logic of a parasitic satellite

The paper uses anti-phage defense systems to block viral lifecycle stages and reveals that PLE activation depends on progressive transcriptional cues from the phage's developmental program.

Multiobjective learning and design of bacteriophage specificity

This paper uses deep learning to design bacteriophage receptor binding proteins with multiobjective specificity, showing high tunability and success rates in targeting diverse strains.

PhageTAILor leverages machine learning for phage tail-like elements detection and classification in plant-associated bacteria

PhageTAILor uses LightGBM on 74 detector features to flag prophages and bacterial phage tail-like elements (tailocins, T6SS, eCIS), recovering 12 of 13 validated tailocins under leave-one-genus-out.

Structural characterization the LlaI anti-phage defense system reveals insights into the evolution of nucleotide specificity and the organization of DNA binding in McrBC restriction complexes

The paper reports crystal structures of LlaI components, revealing nucleotide specificity evolution and DNA binding mechanisms in McrBC restriction complexes.

Cryo-electron microscopy structure of Jabs, a bacteriophage infecting the multidrug-resistant pathogen Mycobacterium abscessus

The paper determines the cryo-EM structure of Jabs, a bacteriophage infecting Mycobacterium abscessus, revealing unique capsid assembly and adhesion features.

RNA virus infection reshapes carbon and nitrogen partitioning in a marine diatom.

This study shows that RNA virus infection alters carbon and nitrogen metabolism in marine diatoms, reducing population-level nutrient assimilation.

Small serine recombinases are markers for antiphage defense system discovery

The paper develops a bioinformatic pipeline using small serine recombinases to identify antiphage defense systems in bacterial genomes and metagenomes, finding they are genetically linked to these systems.

Loss of replication and transcription systems accompanying transition to nucleus-dependent replication in Ariadnavirales, a proposed new order in nucleocytoviricot class Megaviricetes

The paper identifies a new viral order, Ariadnavirales, based on genomic analysis of SmDNAV, which lacks key replication and transcription genes, indicating host-dependent replication.

PhageTransformer - scalable and accurate host assignments for bacteriophages

PhageTransformer predicts phage hosts with high accuracy and speed, outperforming existing tools on benchmark datasets.

Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics

The paper reassesses viral decay assumptions in 17 datasets, finding biphasic decay is common and shows aggregation mechanisms can explain high virion abundances and low infection prevalence.

Genetic dissection of Mycobacteriophage D29 host lysis reveals two lysis regulators and a novel lipoprotein that regulate the lysis event and are localized to distinct regions of the genome

This study identifies two lysis regulators and a novel lipoprotein in Mycobacteriophage D29 that regulate lysis, showing distinct genetic and functional roles in the lysis process.

Five Rotational Registers Define Modular Portal-Capsid Assembly in Cyanophage P-SSP7

The paper determines the near-atomic structure of the P-SSP7 virion and identifies five rotational registers defining modular portal-capsid assembly.