Bacteriophages and microbial interactions

Filamentous cheater phages drive bacterial and phage populations to lower fitness

The paper shows that filamentous phages in Pseudomonas aeruginosa can reduce host and phage fitness through hyperactivation and subsequent miniphage invasion.

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail

This study uses cryo-EM to determine the near-atomic structure of the archaeal virus HFTV1, revealing insights into its assembly, infection mechanisms, and host-virus interactions.

Efficacy of a bacteriophage cocktail targeting pathogenic bacteria associated with gastrointestinal dysfunction

This study evaluates a three-phage cocktail's in vitro efficacy against three gastrointestinal pathogens, showing enhanced suppression in mixed cultures but regrowth in single cultures due to resistance.

Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases

This paper models phage depolymerase capsular tropism using graph neural networks and sequence clustering, showing predictive ability and transferability to lytic phages.

Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora

The paper analyzes viral communities in the rhizosphere of Spartina alterniflora, showing that plant compartment and phenotype influence viral composition and identifying novel viruses potentially affecting key microbial functions.

Bacteriophage diversity declines with COPD severity in the respiratory microbiome

The paper examines bacteriophage diversity in COPD patients and finds it declines with disease severity, showing disrupted viral-bacterial relationships in those with frequent exacerbations.

A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins

The paper identifies a novel antiphage system, Panoptes, that uses a minimal CRISPR polymerase to produce cyclic nucleotides and detects phage anti-defense proteins through effector binding and nucleotide depletion.

Discovery of phage defense systems through component modularity networks

The paper identifies phage defense systems by analyzing modular gene clusters, validating three new systems through experimental testing.

A Comprehensive Reference Catalog of Human Skin DNA Virome Reveals Novel Viral Diversity and Microenvironmental Influences

Unlocking the genomic repertoire of a cultivated megaphage

This paper characterizes the genomic and proteomic features of the only cultivated megaphage, phage G, using multiomics and AI, revealing its unique structure, functional genes, and cryptic regions.

Acinetobacter phages use distinct strategies to breach the capsule barrier

This study characterizes three A. baumannii phages that use distinct strategies to breach the bacterial capsule, showing how combining phages with different capsule interactions can reduce phage escape mutants.

Prophage induction states drive structural and synergistic outcomes in marine bacterial biofilms

This study shows that prophage induction states in marine bacteria influence biofilm structure and competitive outcomes, revealing synergistic effects in co-cultures through phage-mediated interactions.

Droplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions

The paper introduces Droplet RB-TnSeq to study phage-host interactions by isolating single mutant cells with defined phage titers, identifying host factors beyond receptor-level interactions.

Understanding the infection mechanism of {Phi}8 using infection method in Pseudomonas syringae pv. Phaseolicola strain: In-situ CryoET analysis

This study uses Cryo-ET to analyze the infection mechanism of {Phi}8 in Pseudomonas syringae pv. phaseolicola, revealing key stages of viral assembly and extracellular virion localization.

Genome-resolved expansion of Nucleocytoviricota and Mirusviricota reveals new diversity, functional potential, and biotechnological applications

The paper expands the database of giant virus genomes, identifies new viral taxa and functions, and highlights potential biotechnological applications.

Central carbon metabolism switching in lytic versus temperate coral reef viral communities

The paper examines viral metabolism in coral reefs, finding that lytic viruses consume central carbon intermediates for virion production, while temperate viruses build them, leading to distinct ecosystem states.

Serine Recombinase PinR Inverts Cryptic Prophage DNA to Block Adsorption of Phages

The paper identifies PinR, a serine recombinase in E. coli, which inverts prophage DNA to block T2 phage infection by creating a protein that prevents phage receptor binding.

Rational Design of Frontline Institutional Phage Cocktail for the Treatment of Nosocomial Enterobacter cloacae Complex Infections

The paper develops a phage cocktail, Entelli-02, effective against multidrug-resistant Enterobacter cloacae complex strains with 99% coverage and 92% efficacy in a hospital strain collection.

The infection cycle of the haloarchaeal virus HFTV1 is tightly regulated and strongly inhibits motility of its host

This paper analyzes the transcriptome of an archaeal virus and its host during infection, revealing tight temporal regulation and a role for anti-sense RNAs in viral gene expression, along with host motility suppression.

Viral infection to the raphidophycean alga Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic community

This study shows that viral infection of the alga Heterosigma akashiwo alters its organic matter composition, promoting growth of specific Vibrio species that may impact marine food webs.

Tracking Microcystis viruses and infection dynamics across distinct phases of a Microcystis-dominated bloom

The paper uses metagenomic analysis and machine learning to study viral diversity and infection dynamics in Microcystis blooms, revealing broad host ranges and environmental adaptations.

Type IV pili increase phage encounter in marine cyanobacteria

This study shows that type IV pili in marine cyanobacteria increase phage encounter, leading to higher viral infection rates and competitive disadvantage in mixed populations.

EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles

The paper introduces EnVhogDB, a database of viral protein families derived from metagenomic data, which improves functional annotation of viral sequences.

Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.

This study isolates and characterizes a novel phage IPK that enhances phenanthrene degradation by its host Paraburkholderia caledonica Bk, showing higher degradation efficiency at higher MOI.

Transitions in human gut viral communities from ancient to modern societies

This study compares gut virome composition across ancient and modern human populations, finding increased similarity and shifts toward temperate lifestyles and bacterial pathogenicity with industrialization.

Latent endogenous viral elements drive active infection and inheritance in a multicellular host

The paper shows that endogenous viral elements in brown algae can reactivate, replicate, and transmit viruses, challenging the view of EVEs as inert.

LicD-Mediated Cell Wall Decoration Governs Phage Sensitivity in Enterococcus faecalis Clinical Isolates

The paper identifies three novel phages targeting vancomycin-resistant E. faecalis and shows that LicD-mediated cell wall decoration influences phage sensitivity and biofilm formation.

A new family of small ArdA proteins reveals an antirestriction activity.

This study identifies a new family of small antirestriction proteins, sArdA, which show structural and functional diversity in interacting with restriction-modification systems.

Generative design of novel bacteriophages with genome language models

Fine-tuned Evo 1 and Evo 2 genome language models designed complete ΦX174-like phage genomes; 16 of 285 assembled designs were viable, and some outperformed ΦX174 in competition.

Large-scale genomic characterisation of phage-plasmids in clinical Enterobacteriaceae isolates

This study characterizes phage-plasmids in clinical Enterobacteriaceae isolates, finding they are common and associated with antimicrobial resistance and disease severity.