Bacteriophages and microbial interactions

A hierarchical orthology framework reveals viral carbohydrate-active genes across the global virosphere

The paper identifies viral carbohydrate-active genes across diverse viral lineages using a hierarchical orthology framework and reveals their evolutionary and functional diversity.

Mathematical Modelling of Bacterial DNA Inversion Dynamics Uncovers an Organized Multi-Locus Response to Phage Predation in Bacteroides fragilis

The paper models bacterial DNA inversion dynamics in Bacteroides fragilis under phage predation, revealing a structured, multi-locus response with persistent and transient phase-variable contributions.

Genome-resolved biogeography reveals multidimensional structuring of freshwater giant viruses across global deep lakes

This study identifies biogeographic patterns of freshwater giant viruses using MAGs from deep lakes, revealing cosmopolitan and restricted species, and factors influencing their distribution.

Exploration of Bacteriophages Against Vancomycin-Resistant Enterococcus faecium: A Report from India

This study isolates and characterizes two bacteriophages active against vancomycin-resistant Enterococcus faecium (VREfm) and multidrug-resistant E. faecium from India, showing different lysis efficiencies and host ranges.

R-pyocin-mediated selection restores aminoglycoside sensitivity in a pan-drug resistant Pseudomonas aeruginosa isolate

This paper shows that R-pyocin selective pressure can induce chromosomal deletions in Pseudomonas aeruginosa, leading to loss of multidrug resistance and restoration of aminoglycoside sensitivity.

Trained phages constrain evolutionary routes to antibiotic resistance in Escherichia coli

This paper shows that trained phages can limit bacterial evolution to costly antibiotic resistance pathways by eliminating cost-free resistance routes.

Pathogen-Phage Geomapping to Overcome Resistance

This paper develops a method to discover virulent phages against antibiotic-resistant pathogens by combining environmental sampling, 16S rRNA sequencing, and a portable device for phage enrichment.

Deep learning-guided identification of bacteriophage receptor-binding protein candidates for foodborne pathogen detection

The paper develops a computational pipeline to identify high-confidence bacteriophage receptor-binding protein candidates for foodborne pathogen detection using deep learning and structural analysis.

Defining the ESKAPE pathogen prophage repertoire with PHORAGER

The paper introduces PHORAGER, a pipeline for identifying prophages in bacterial genomes, and reports the discovery of 23,132 putative prophages in ESKAPE pathogens.

Second-order kinetics describe systemic clearance of therapeutic bacteriophages

This study shows that therapeutic bacteriophages clear from the body following second-order kinetics, challenging first-order assumptions and informing dose design.

The structure of the Salmonella phage epsilon15 tailspike reveals multiple O-antigen binding sites and a protruding esterase domain

This paper determines the structure of the Salmonella phage epsilon15 tailspike, identifies multiple O-antigen binding sites, and reveals its dual enzymatic role in de-acetylation and cleavage.

Phage terminase recognition by the bacterial immune sensors Avs2 and Upx

This study determines the structural basis of phage terminase recognition by Avs2 and Upx, revealing distinct binding mechanisms despite structural differences.

Multiple origins of endogenous virophage and polinton-like virus in the halophilic protist Halocafeteria seosinensis

The paper identifies 41 endogenous polinton-like viruses and 36 virophage sequences in the genome of Halocafeteria seosinensis, revealing genetic exchange and co-occurrence of these viral elements.

Viruses help rewire carbon metabolism in a methane-suppressed peat microcosm

The paper investigates how viral dynamics influence carbon metabolism in peat microcosms amended with catechin, showing that viral lysis redistributes intermediates to sustain methane suppression.

Formation and role of the portal of Staphylococcus aureus bacteriophage 80α

The paper investigates the structure and function of the portal protein in Staphylococcus aureus bacteriophage 80α, showing temperature-dependent ring formation and domain-specific roles in assembly and DNA packaging.

Diverse bacterial pattern recognition receptors sense the core phage proteome

The paper identifies 90 structurally distinct STAND NTPase families in bacteria and archaea that recognize phage proteins, revealing their role in antiviral defense.

A broad-spectrum phage-encoded mechanism to disarm bacterial type IV filaments

This paper identifies Aqs1, a phage-encoded protein that inhibits type IV pilus function in multiple Gram-negative bacteria by targeting the PilB ATPase.

Phage VP882 possesses quorum-sensing-driven lytic induction and stress-mediated host growth suppression mechanisms

This paper identifies two pathways in phage VP882: quorum-sensing-driven lysis and stress-mediated host growth suppression, with QtiQ inactivating a complex that causes growth arrest.

Preclinical safety assessment of Koomba kaat 1 and Biyabeda mokiny 1 phages for respiratory application against Staphylococcus aureus

This study evaluates the respiratory safety of two Staphylococcus aureus bacteriophages in human and mouse models, finding no adverse effects on epithelial integrity or inflammation.

Evaluation of phage activity against diverse Enterococcus faecalis from infective endocarditis

This study evaluates phage activity against E. faecalis isolates from infective endocarditis, finding that 83% of isolates were susceptible to at least one phage, and phage cocktails or combinations with antibiotics improved bacterial killing and survival in a model organism.

Evolutionarily Optimal Phage Life-History Traits: Burst Size vs. Lysis Time

The paper models phage life-history traits, showing optimal balance between lysis time and burst size, and predicts how interventions and environmental conditions affect these traits.

Fluoroquinolone-Triggered Prophage Induction in Streptococcus anginosus Reveals Lytic Cycle, CRISPR-Prophage Interplay, and the potential for Cross-Species Horizontal Gene Transfer

This study shows fluoroquinolone antibiotics induce prophage lytic cycles in Streptococcus anginosus, revealing CRISPR-prophage interactions and cross-species horizontal gene transfer potential.

Counting to two: how phages decide between lysis and lysogeny

The paper introduces a minimal model to explain how temperate phages make lysis-lysogeny decisions based on multiplicity of infection and host factors, showing how asymmetry can arise from simple coupling to host machinery.

Convergent Cysteine Enrichment in Diverse Gut Phage Capsids Suggests Gut-Associated Structural Adaptation

The paper identifies convergent cysteine enrichment in gut phage MCPs, suggesting structural adaptations for capsid stability in the gut environment.

Community diversity favors coexistence between bacteria and parasitic bacteriophages

The paper shows that diverse microbial communities promote phage-bacteria coexistence by limiting resistance evolution in bacteria, increasing phage persistence.

Virome-mediated ecological firewalls govern pathogen eradication in the gut microbiome

The paper introduces a dynamical model to study how gut virome influences microbiome recovery after antibiotic-induced dysbiosis, identifying ecological thresholds and a firewall mechanism for pathogen suppression.

Host Physiology Dependent Lysis Timing Shapes Bacteriophage Competition Under Nutrient Fluctuations

The paper models how phage lysis timing in response to host physiology affects competition under fluctuating nutrient conditions, showing delayed lysis is advantageous in feast-famine environments.

Influence of heterotrophs on phage infection of marine picocyanobacteria

This study investigates how heterotrophic bacteria affect phage infection of Prochlorococcus and Synechococcus, finding that heterotrophs enable host recovery and confer resistance through non-genetic metabolic changes.

Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens

This study identifies 42 bacterial genes involved in Klebsiella phage infection using RB-TnSeq, revealing cross-family resistance and genus-specific gene dependencies.

The mechanism of biofilm degradation by a detachable tailspike of gene transfer agents

This study identifies TspA, a biofilm-degrading enzyme from Rhodobacter capsulatus GTA, which enhances gene transfer by clearing biofilms and navigating the extracellular matrix.