Bacteriophages and microbial interactions

Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms

This paper demonstrates that prophages can be used to synthesize functional extracellular DNA superstructures via rolling circle replication in bacterial biofilms.

Systematic discovery of TIR-based immune signaling systems in bacteria

The paper systematically identifies TIR-based immune signaling systems in bacteria, finding they exist in 8% of bacterial genomes and use signaling molecules similar to those in plant and human immunity.

Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle

The paper identifies a phage-encoded small RNA that regulates E. coli genes by hijacking host replication machinery during the phage lytic cycle.

Identifying Phage Host Receptors Using TraDIS

This study identifies genes involved in phage infection and resistance using TraDIS in E. coli, revealing two proteins critical for phage recognition and infection.

Structural diversity and conservation among CRESS-DNA bacilladnaviruses revealed through cryo-EM and computational modelling

This study determines the capsid structure of ClorDNAV using cryo-EM and analyzes AlphaFold3 predictions to reveal structural conservation and divergence in Bacilladnaviridae.

An unprecedented DNA recognition-mimicry switch governs induction in arbitrium phages

The paper reveals a DNA recognition-mimicry switch mechanism in SPBeta-like phages where an antirepressor inactivates a repressor via DNA mimicry, enabling lytic induction under SOS conditions and in the absence of neighboring prophages.

Unraveling the archaeal virosphere: diversity, functional and virus-host interactions

This study identifies 9,697 novel archaeal proviruses across 19 phyla, revealing broad host infectivity, antiviral systems, and auxiliary metabolic genes that impact biogeochemical cycles.

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

The paper analyzes Borg archaeal extrachromosomal elements using in silico methods, revealing features similar to giant eukaryotic viruses, suggesting convergent evolution.

Small siphophage binding to an open state of the LptDE outer membrane lipopolysaccharide translocon

This paper identifies a novel open state of the LptDE translocon bound by a phage RBP, revealing potential for peptidomimetic inhibition and insights into phage resistance mechanisms.

Structure of bacteriophage P1 head provides insight into capsid polymorphism

The paper investigates the structural differences between two capsid sizes in bacteriophage P1, revealing the role of protein appendages in DNA packaging and capsid morphogenesis.

DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics

The paper compares DNA extraction and virome processing methods to show how they affect the characterization of human gut viral communities, finding that MDA significantly biases results.

Four Decades of Genomic Stability and Adaptive Divergence in Xanthomonas arboricola pv. pruni-Infecting Phages: Defining Duraznoxanthovirus arenicola and Its Evolutionary Framework

The paper characterizes 15 phages infecting Xanthomonas arboricola pv. pruni, identifying a new genus and species and proposing taxonomic changes within the Anamaviridae family.

Characterisation of novel bacteriophages against the cattle pathogen Moraxella bovis

The paper isolates and characterizes four novel bacteriophages against Moraxella bovis, finding high genomic similarity among three and distinct properties in MB43.

Structural insights into scaffold-guided assembly of the Pseudomonas phage D3 capsid

This study investigates the structural mechanisms of capsid assembly in phage D3, revealing the role of the scaffold domain in determining capsid size and maintaining structure during maturation.

Protein Set Transformer: A protein-based genome language model to power high diversity viromics

The paper introduces PST, a protein-based genome language model that outperforms existing methods in relating viral genomes through shared protein content and demonstrates structural and functional awareness.

Quantitative Dual Predation by a Wild-type Bdellovibrio-like Organism and Lytic Bacteriophage Reveals Host-Specific Synergy

The paper quantifies dual predation by a wild-type BALO and lytic phage on two bacterial hosts, showing host-specific synergy in prey clearance.

Integrated host phage RNA seq analysis of Mycobacteriophage D29 infection reveals dual arm balanced phage genome expression and inhibited expression of host transporter and VapC target genes.

This study uses transcriptomic analysis of Mycobacteriophage D29 infection to show balanced expression of phage genome arms and inhibited host transporter and VapC target gene expression.

Cytokine and Immunoglobulin Dynamics in Phage Therapy: Insights from Clinical Cases

This study examines cytokine and immunoglobulin responses in nine patients undergoing intravenous phage therapy, finding heterogeneous cytokine patterns and IgM responses that vary with immune status and pathogen.

Temperate bacteriophage induced in Pseudomonas aeruginosa biofilms can modulate bacteriophage and antibiotic resistance

The paper examines Pseudomonas aeruginosa isolates from cystic fibrosis patients to assess prophage presence and their impact on phage and antibiotic resistance.

Pera virus mimics bacteria to infect Pedopumella sp. a freshwater heterotrophic Chrysophyceae

The paper describes Pera virus, a giant virus infecting Pedospumella sp., and reports its morphological features and ecological dynamics in freshwater lakes.

Experimental Phage Evolution Results in Expanded Host Ranges Against MDR and XDR Klebsiella pneumoniae Isolates

The paper demonstrates that experimental phage evolution can expand the host range of phages to kill multidrug-resistant and extensively-drug-resistant Klebsiella pneumoniae isolates.

Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery

This study reveals the structural basis and evolutionary origin of the Lamassu bacterial immune system, showing its adaptation from DNA repair machinery to detect and respond to viral replication.

Optimizing phage-antibiotic combinations: impact of administration order against daptomycin non-susceptible (DNS) MRSA clinical isolates

This study evaluates phage-antibiotic combinations against DNS-MRSA strains, finding that simultaneous administration outperforms sequential regimens in ex-vivo models.

Cultivation and genomic characterization of human gut-associated Bdellovibrio reveals natural predatory bacteria with specialized prey interactions

This paper isolates and characterizes viable Bdellovibrio from human fecal samples, revealing genomic conservation and prey specialization in the human gut microbiome.

Surface-by-temperature interactions shape the relationship between viral free-living survival and reproduction

This study examines how temperature and surface chemistry interact to affect viral survival and reproduction, finding non-additive effects that decouple stability from replication.

Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes

This paper develops a machine learning framework to predict strain-level phage-host interactions from genomes, achieving high accuracy without phylogenetic constraints.

Proteolytic activation of diverse antiviral defense modules in prokaryotes

The paper identifies proteolytic activation mechanisms in prokaryotic antiviral defense modules and shows their functional diversity and convergence with stress responses.

Surviving phage attack primes bacterial immunity to defeat counterdefenses

The paper shows that restricted phage infection primes bacterial immunity to defeat counterdefenses by increasing defense protein abundance and altering host-phage stoichiometry.

KlebPhaCol: A community-driven resource for Klebsiella research identified a novel gut phage order associated with the human gut

The paper introduces KlebPhaCol, a resource containing 53 phages and 74 Klebsiella isolates, including a novel gut phage order, to advance understanding of Klebsiella-phage interactions.

Bridging in vitro and in vivo insights: A PKPD model for effective phage therapy against multidrug-resistant Pseudomonas aeruginosa

This study develops a PKPD model integrating in vitro and in vivo data to optimize phage therapy against multidrug-resistant Pseudomonas aeruginosa, showing that phage combinations delay resistance but may lead to immune clearance of resistant mutants.