Bacteriophages and microbial interactions

This paper introduces RPST, a ramanome-based platform for rapid and quantitative phage susceptibility testing, achieving 96% concordance with plaque assays and enabling dynamic assessment of infection dynamics.

The paper identifies novel viruses in wastewater treatment plants and shows their central role in microbial community structure and evolution through a multilayered network analysis.

This paper introduces a label-free method to monitor bacteriophage dynamics and interactions using caustics in conventional microscopy, demonstrating feasibility with three phage strains.

This study identifies structural modularity in Klebsiella pneumoniae phage RBPs, showing how modular exchange drives host-range diversification across multiple scales.

The paper develops a genome-based framework to predict bacteriophage infectivity against diverse Pseudomonas aeruginosa strains using machine learning and experimental data.

This study investigates how Vibrio parahaemolyticus quorum sensing regulates phage VP882 transmission by controlling receptor accessibility and enabling superinfection.

The paper identifies phages infecting E. coli HS, shows their resistance to restriction via modifications, and links phage infection to a Klebsiella-like capsule.

This study examines the role of the mobilome, particularly prophages, in shaping biotic interactions in Pseudomonas syringae by analyzing 590 genomes and identifying defense mechanisms and effectors.

This study investigates virus-host interactions and viral population dynamics in cloud water, revealing active viral predation, genetic adaptations, and rapid population turnover across cloud events.

The paper identifies a phage-encoded factor that activates the Hna anti-phage defense system by overcoming its auto-inhibition.

This study identifies the DruH-DruE two-component system in Mycobacterium smegmatis as a type III Druantia defense mechanism that prevents phage DNA cyclization and replication.

This paper presents an optimized ddPCR assay to quantify phage vector titer and purity, showing improved accuracy and precision compared to biological activity assays.

This study identifies a phage resistance mechanism in Mycobacterium smegmatis involving XylR-mediated cell-envelope remodeling that impedes phage DNA injection.

The paper identifies chemical inhibitors of SpbK, an antiphage defense system in Bacillus subtilis, showing they promote phage dissemination and reveal mechanisms of inhibiting TIR-domain enzymes.

This paper introduces VIP2B, a method to extract viral features from bulk metagenomes, showing that viral data improves disease diagnosis and reveals distinct gut virome community states.

This study identifies c-di-AMP, ppGpp, and H2O2 as regulators of prophage induction in Listeria monocytogenes, showing how these factors influence phage production and bacterial competition.

This study uses phage-based manipulation to reveal ecological interactions in gut microbiomes by targeting Escherichia fergusonii and analyzing its role in community dynamics.

This study shows that bacteriophage T4 uses two glucosyltransferases to modify its DNA, helping it evade bacterial defense systems, with redundancy providing an evolutionary advantage.

The paper analyzes retron diversity in the SPIRE metagenome, identifying novel type XI-like lineages and their ecological distribution.

The paper shows a secreted bacterial protease reduces phage infectivity by degrading phage DNA, with phages escaping by mutating a tail-associated protein.

This study examines the biogeography of giant viruses across hydrothermal vents and the pelagic ocean, finding that horizontal transport via hydrothermal plumes drives their global distribution while environmental selection shapes their presence in vent habitats.

The paper develops ACTIVE to profile prophage activity in gut bacteria, revealing 5.4% of prophages are active under standard culture and identifying distinct viral lineages.

This study investigates the molecular mechanism of the Druantia anti-phage defense system, showing that DruH-E provides robust immunity and revealing its DNA unwinding and regulation by ATP.

This paper designs phage-antibiotic cocktails to suppress resistance by exploiting evolutionary tradeoffs, showing that LPS-targeting phages enhance sensitivity to lipophilic antibiotics.

This study investigates how Druantia III and Zorya II antiphage defence systems in bacteria synergize through shared DNA intermediates, showing their coordinated response during phage infection.

The paper reports the structural and functional characterization of QatB and QatC proteins in the QatABCD anti-phage defense system, revealing their complex formation and potential regulatory roles.

This study isolates and characterizes two lytic bacteriophages from Romanian river water that target multidrug-resistant E. coli, showing potential for phage therapy.

This paper introduces a closed-loop control system to stabilize phage-bacteria coevolution, preventing extinction or dominance by one species.

LysinFusion improves phage lysin prediction using a hybrid CNN-Transformer model, achieving higher accuracy and fewer false positives than existing methods.

This study evaluates a three-phage combination's activity against Mycobacterium tuberculosis under hypoxic, acidic, and stationary-phase conditions, finding that phages require replicating bacteria for lytic activity.