Bacteriophages and microbial interactions

Synteny and linkage decay in bacteriophage pangenomes

The paper analyzes the evolution of 3425 actinobacteriophage genomes, finding conserved synteny and varying linkage decay patterns due to homologous recombination.

A biofilm-tropic Pseudomonas aeruginosa bacteriophage uses the exopolysaccharide Psl as receptor

The paper identifies a Pseudomonas aeruginosa bacteriophage, Clew-1, that uses Psl as a receptor to disrupt biofilms and reduce bacterial burden in a mouse model.

A prevalent huge phage clade in human and animal gut microbiomes

The paper identifies Jug phages as prevalent in human and animal gut microbiomes, showing high transcription activity and potential ecological significance.

Prophage and SaPI diversity in local clinical Staphylococcus aureus reveal hidden drivers of virulence.

The paper examines prophage and SaPI diversity in Mexican S. aureus isolates, finding that many predicted prophages are actually PICIs with virulence genes and anti-phage defenses.

A novel approach to Caudoviricetes taxonomy utilising whole proteome structure-structure comparison

The paper presents a structure-based classification framework for Caudoviricetes using whole-proteome structural clustering to resolve distant viral relationships.

The ambivalent effect of spatial structure on the spread of cooperative anti-CRISPR phages

This study shows spatial structure can either promote or hinder the spread of cooperative anti-CRISPR phages, depending on host and phage efficacy.

Illuminating the active virosphere with BONCAT and single virus genomic sequencing technologies

This study introduces a method to identify and sequence active marine viruses using BONCAT-FACS, revealing differences in viral turnover among various groups.

Synergy in viral-bacterial coinfection expedites algal bloom demise

The paper identifies bacterial-viral synergy as a key factor in algal bloom termination, showing how bacteria enhance viral infection and influence carbon cycling pathways.

Strengthening Phage Resistance of Streptococcus thermophilus by Leveraging Complementary Defense Systems

This study identifies and validates 21 accessory defense systems in S. thermophilus, showing that some provide stronger phage resistance than CRISPR-Cas, especially when combined or expressed from plasmids.

A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans

The paper identifies a novel group of circular mobile genetic elements in marine environments, resembling viruses but lacking typical viral markers, and suggests they may function as virus-like elements.

Evaluating bacteriophage impact on gut microbiome composition in broad-nosed pipefish (Syngnathus typhle)

This study evaluates how bacteriophages affect the gut microbiome of broad-nosed pipefish, showing that lytic phages reduce Vibrio alginolyticus abundance while filamentous phages increase it.

Human bladder organoids model urinary tract infection and bacteriophage therapy

This study develops human bladder organoids to model UTIs and phage therapy, showing phage reduces bacterial loads and inflammation during infection.

Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

Phynteny combines ESM2 protein embeddings, a BiLSTM, and circular-attention transformer layers to exploit phage gene order, assigning one of nine PHROG functional categories to unannotated genes.

Exploring prophages in Salmonella enterica: an in-silico approach

This study identifies and characterizes prophages in Salmonella enterica genomes from poultry and clinical isolates, revealing their diversity and potential role in adaptation and public health.

A phylogenetic host range index reveals contrasted relationships between phage virulence and specialisation

This study introduces a phylogenetic host range index to classify phages as specialists or generalists and examines the relationship between phage virulence and host range across different epidemiological contexts.

Adaptations of DNA viruses are influenced by host and environment with proliferations constrained by environmental niche

The paper analyzes viral genomic traits across estuarine environments to show how salinity and ecological niches influence viral proliferation and adaptation.

The salivary virome during childhood dental caries

This study compares the salivary virome of children with severe dental caries to those with healthy dentition, identifying novel viral taxa and their associations with caries.

Prevalence of Group II Introns in Phage Genomes

This study identifies group II introns in phage genomes using RNA structure-based homology searches, revealing their prevalence across diverse phage lineages.

Production of P2D1 tailocins by Dickeya dadantii 3937: a temporal relationship between the stressor onset, gene expression, and the concentration of active particles

The paper examines the timing of P2D1 tailocin production in Dickeya dadantii 3937, showing gene expression peaks at 2 hours and tailocin concentration peaks at 6 hours post-induction, correlating with cell lysis.

Plasmids link antibiotic resistance genes and phage defense systems in E. coli

The paper analyzes 2,559 E. coli plasmids to show that antibiotic resistance genes and phage defense systems are physically linked, suggesting potential interactions between antibiotic use and phage therapy.

Bacterial Schlafens mediate anti-phage defense

This study identifies bacterial Schlafen nucleases as antiviral effectors that target phage infection by cleaving tRNA and inducing abortive infection.

Biological and genomic characterization of a new chlorovirus isolate expands the diversity and complexity of giant algal viruses in Brazil

This study isolates and characterizes a new chlorovirus, BR-AMG2, from Brazil, revealing its genomic features and expanding the known diversity of giant algal viruses.

PRISM: A platform for illuminating viral dark matter

PRISM isolates, quantifies, and characterizes bacteriophages without plating, recovering non-plaquing phages and improving titering accuracy.

Complementary killing activities of Pbunavirus LS1 and Bruynoghevirus LUZ24 phages on planktonic and sessile Pseudomonas aeruginosa PAO1 derivatives

This paper identifies complementary phage activities against Pseudomonas aeruginosa strains, showing different receptor usage and biofilm degradation efficiencies.

A Phage Ejectosome Protein Moonlights to Inhibit CBASS Anti-Viral Defense System

The paper identifies Gp15, a phage DNA ejection protein that inhibits the CBASS effector CapV to evade bacterial antiviral defense.

Divergence of an extracellular contractile injection system infectivity elucidated by high resolution structural studies of its tail-baseplate complex

The paper uses cryo-EM to determine the atomic structure of the P1 Tail Baseplate complex, revealing how its unique infection mechanism involves LTFs and baseplate movement.

Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages.

This study examines how antibiotic treatment affects the gut phageome, finding reduced diversity and increased virulent phage blooms, which may help restore bacterial diversity through kill-the-winner dynamics.

Structural and genetic diversity of lysis modules in bacteriophages infecting the genus Streptococcus

This study analyzes lysis modules in Streptococcus phages, identifying structural and functional diversity in endolysins and holins across 185 phage genomes.

A dinoflagellate-infecting giant virus with a micron-length tail

This paper describes a novel giant virus, PelV-1, infecting a dinoflagellate with a record-long tail and unique metabolic genes, expanding our understanding of marine virus diversity.