Bacteriophages and microbial interactions

This paper identifies LysZ as a phage gene required for lysis of Corynebacterium glutamicum, showing that phages overcome mycomembrane barriers by targeting membrane-anchored glycopolymers.

This study determines the structural basis of QueC-family protein function in the qatABCD anti-phage defense system, showing their role in targeting protein substrates for N-terminal modification.

The paper reports the structure of a novel contractile injection system in Salmonella enterica subsp. salamae and identifies a new CIS cluster.

The paper develops an individual-based model to simulate T-even phage lysis dynamics under varying multiplicity of infection, showing how spatial dynamics and secondary adsorption thresholds influence phage-host interactions.

The paper isolates and characterizes EPIPs, a novel phage satellite class in Mycolicibacterium aichiense, which induce prophage excision through unique gene content and structural features.

This study identifies two holin-like proteins in F1 cluster phages that regulate lysis of Mycobacterium smegmatis, showing their distinct roles and interactions in the lysis process.

This study uses electron cryo tomography to reveal the stepwise assembly of SPP1 phage particles from membrane-associated precursors within a viral DNA compartment in infected bacteria.

Cenote-Taker 3 is a tool for virus discovery and annotation in genomic data, outperforming existing tools in speed and accuracy.

DefensePredictor combines ESM2 protein language model embeddings with genomic context features in a gradient boosting classifier to identify prokaryotic anti-phage defense genes, validating 45 previously unknown Escherichia coli systems.

The paper integrates AMGs and phage assembly into a genome-scale metabolic model to predict their impact on host metabolism and phage production, revealing synergistic and antagonistic effects.

This study shows that bacteriophages use cross-species communication via AimP peptides and AimR receptors to influence lysogeny and prophage induction in mixed microbial cultures.

The paper shows that Arbitrium phages from different species can influence each other's lysis-lysogeny decisions through peptide-based communication, leading to fitness advantages and coevolution.

This paper identifies resistance mutations in Pseudomonas aeruginosa exposed to a T4P-targeting phage, showing some mutations allow recovery of pilus function after phage removal.

This study identifies 34 phage tail-like bacteriocins (PTLBs) in Pseudomonas aeruginosa genomes, with some showing strong antimicrobial activity against bacterial infections.

This paper uses agent-based simulations to show that lysis time variability in bacteriophages can provide a fitness advantage in competition, even when reducing growth rate in isolation.

The paper uses clinical surveillance in Bangladesh to study phage-pathogen coevolution in Vibrio cholerae, identifying a parasitic MGE that drives a selective sweep during a major outbreak.

The paper describes a tripartite interaction between a patescibacterial epibiont, its gammaproteobacterial host, and their phages, revealing host specificity and genetic adaptations.

This paper develops a scalable and high-quality method for producing marine cyanophage P-SSP7, enabling efficient structural studies and reducing cryo-EM data collection time.

This study uses Nanopore DRS to analyze MS2 phage transcriptional dynamics in E. coli, revealing complex transcriptional activity and RNA modifications throughout the life cycle.

The paper identifies viral proteins that manipulate bacterial immune signaling by analyzing structural and biophysical traits, and develops a computational pipeline to predict such proteins in phage genomes.

This study uses AlphaFold 3 to identify and characterize phage proteins that inhibit bacterial transcription, revealing novel mechanisms of action.

This study shows that bacteriophages can reduce uropathogenic E. coli (UPEC) colonization in vitro and in a mouse model, suggesting phage therapy as a potential UTI prevention strategy.

This paper identifies and characterizes a new Caulobacter phage, Circe, showing it uses smooth lipopolysaccharide as a receptor for infection.

This study identifies SNIPE as a bacterial membrane-bound nuclease that directly cleaves phage DNA during genome injection, providing a novel mechanism for distinguishing self from non-self.

The paper develops and refines methods to sample and sequence cyanobacteria, cyanophages, and their environment in the Salish Sea to study host-pathogen dynamics.

This study shows the enteric virome influences carbohydrate digestion and absorption through Th17 cells and immune surveillance, highlighting its role in host metabolism.

This study shows pseudolysogenic phages reduce C. acnes abundance and acne lesions without resistance, by limiting antibiotic resistance and virulence.

This study identifies a bacterial anti-phage defense system, Clover, which uses nucleotide signals to dynamically regulate antiviral immunity while avoiding cellular toxicity.

This study evaluates the synergy between phage vB_Kpn_2-P4 and meropenem against OXA-48-producing K. pneumoniae isolates, showing prevention of resistant mutant emergence.

This study uses a mathematical-computer simulation model to evaluate the effectiveness of combining antibiotics and bacteriophage in treating prosthetic joint infections, finding that bacteriophage may not be an effective addition.