Bacteriophages and microbial interactions

The paper identifies regulators that control R-tailocin expression in Pseudomonas protegens CHA0, showing how DNA damage activates these genes through LexA-like and H-NS proteins.

The paper reports the discovery of the largest known phage genome, BF3, and analyzes its protein-coding genes and structural predictions.

The paper investigates Pf phage transmission in Pseudomonas aeruginosa airway infections in cystic fibrosis patients, finding vertical transmission within lineages and new superinfections by Pf+ strains.

The paper profiles single-cell transcriptomes of Bacteroides fragilis infected with a phage, revealing combinatorial phase-variable expression of defense systems that enable super-resistant cells to avoid phage infection without mutations.

The paper identifies probiotic genes in viral genomes across global habitats and shows their coexistence with virulence genes.

The paper uses language models to predict novel antiphage defense proteins in Actinomycetota, discovering six new defense systems and over 45,000 uncharacterized protein families.

This study identifies Vc OLD, a Class 1 OLD family nuclease from Vibrio cholerae, and its inhibitor Oad1 from phage ICP1, revealing their roles in phage defense and the bacterial-viral arms race.

The paper updates a survey of inteins in Actinobacteriophages using a new algorithm, identifies new intein types, and explores their evolution and transfer mechanisms.

The paper shows that an Stx prophage inhibits the induction of co-hosted prophages in Citrobacter rodentium, revealing a novel competition strategy among prophages.

This study shows that spatial structure in bacterial populations affects phage-host coexistence and resistance development in Vibrio anguillarum.

NeoPhAR presents a deep learning model to predict phages for therapeutic use, aiming to simplify and democratize phage therapy for AMR infections.

The paper analyzes viral metabolic functions in soil viromes, finding that most carbohydrate-active enzymes are related to viral lysis rather than auxiliary metabolism.

HieVi uses a protein language model to cluster bacteriophages into a hierarchical taxonomy, aligning with ICTV classifications and capturing evolutionary relationships.

The paper generates genomic resources for bacterial and viral communities in seagrass ecosystems, revealing potential roles for viruses in carbon cycling.

This study shows that chemostat culturing reduces eukaryotic virus load in fecal viromes and delays diarrhea in preterm piglets, but does not prevent NEC and reduces microbiome effects.

This study shows sub-therapeutic antibiotics in Pseudomonas aeruginosa induce prophage activation, leading to reduced virulence through superinfection exclusion and fitness costs.

The paper identifies BrrG as an antiterminator that coordinates the expression of two divergent phage-derived modules in BaGTA, enhancing horizontal gene transfer in Bartonella.

This paper develops an optimized plaque assay to detect chronically infecting haloarchaeal viruses by modifying agar concentration and incubation temperature, successfully identifying two viruses and enabling novel virus discovery.

This study examines how marine biopolymers affect bacteriophage efficiency by measuring plaque-forming units in bacterial cultures.

This paper isolates a novel Pbunavirus phage, {phi}PRS-1, from the Ganges River that effectively reduces multidrug-resistant Pseudomonas aeruginosa in wastewater by downregulating quorum-sensing systems and reducing KPC carbapenemases.

This study analyzes 709 Streptococcus phage genomes to revise taxonomy and identify novel endolysin-derived antimicrobial peptides with therapeutic potential.

This paper develops an E. coli-based system for producing anellovirus vectors for gene therapy, demonstrating successful expression and assembly of capsid proteins.

The paper identifies eight Enterobacter jumbo phages with broad host ranges across pathogenic Gammaproteobacteria, suggesting potential as antibiotic alternatives.

This study evolves a 12-phage cocktail in a diverse Klebsiella environment, revealing strategies for host range modulation through receptor binding proteins and ecological dynamics.

This study examines how phage life history traits affect coinfection dynamics and cocktail efficacy using experimental and modeling approaches.

This study systematically analyzes 132 antiviral defense systems across 212,599 prokaryotic genomes, revealing their diversity and distribution among bacteria, archaea, and viruses.

The paper introduces V-score and VL-score metrics to identify viral signatures in protein families and genomes, finding 38-77% of families are linked to viruses, up to 17x more auxiliary viral genes.

The paper introduces iLund4u, an algorithm to systematically annotate hyper-variability hotspots in phage genomes and plasmids, identifying 13.7K hotspots and 171K diverse protein families across 873K phage and 696K plasmid sequences.

This paper demonstrates a method to directionally immobilize SpyTagged phages on PDMS surfaces for microfluidic phage-based biosensors.

Jaeger is a deep-learning tool that accurately and quickly identifies bacteriophage sequences in metagenomic data, achieving high sensitivity and precision.