Bacteriophages and microbial interactions

The paper identifies 8 Giant Endogenous Viral Elements in Euglena gracilis, suggesting they originated from a common viral lineage and expanded the known host range of Asfuvirales.

The paper presents the first genomic catalogue of viruses and mobile genetic elements associated with Nitrososphaeria, revealing novel viral families and insights into their evolution and adaptation.

This study shows that Paenibacillus larvae can rapidly evolve resistance to bacteriophages, but resistance often leads to growth defects and reduced virulence in bee larvae.

The paper characterizes the human gut virome at single nucleotide resolution using a large Chinese dataset, revealing population-specific genetic variations and their associations with health traits.

PIDE detects prophages in bacterial genomes and metagenomes with high accuracy using a protein language model and gene density clustering.

The paper analyzes defense systems in Acinetobacter baumannii genomes and finds that innate systems influence prophage distribution and genome evolution.

This study shows that temperate phages can enhance antibiotic effectiveness in vivo using C. elegans, demonstrating 'temperate phage antibiotic synergy' (tPAS) by reducing phage dormancy and improving infection outcomes.

The paper investigates how soil pH affects phage communities infecting two closely related Bacillus strains across a pH gradient, finding that phage composition varies with pH but pH alone does not block phage distribution to individual hosts.

The paper describes an amyloid-based signal transduction mechanism in Escherichia coli's antiphage defense system, showing functional interchangeability between Bab and fungal HET-S amyloids.

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

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.

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

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.

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

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

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

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.

This paper develops a CRISPR-Cas9-based platform for engineering Twortvirinae phages to create reporter phages for detecting Staphylococcus aureus in clinical and environmental samples.

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.

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.

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.

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

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.

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.

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.

This study characterizes the crAssphage lifestyle as a phage-plasmid, demonstrating its persistence in the gut microbiome without causing host lysis or chromosomal integration.

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

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.