Bacteriophages and microbial interactions

Prophage {Phi}ESI promotes competitive dominance in the emergent Salmonella serovar Infantis lineage

This paper identifies {Phi}ESI, a prophage in Salmonella Infantis, as a competitive factor that helps the emergent lineage outcompete non-emergent strains by selectively lysing susceptible competitors.

Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ

This study introduces HIDEN-SEQ, a transposon-insertion sequencing method for phages, to systematically map gene essentiality and uncover previously unknown viral anti-defense factors.

Benchmarking virus identification tools on vaginal metagenomes

This paper benchmarks virus identification tools on vaginal metagenomes, finding geNomad excels in overall classification, VIBRANT minimizes false positives, ViraLM detects short contigs and eukaryotic viruses, and VirSorter2 performs well on VLP-enriched assemblies.

Bacteriophage Sf14 survival under simulated gastrointestinal conditions

This study evaluates the survival of bacteriophage Sf14 under simulated gastrointestinal conditions, showing stability in oral and intestinal phases but sensitivity to low gastric pH.

Genomic and phenotype-based framework for rational design of phage cocktails against Escherichia coli isolates from urinary tract infections

This study develops a framework for designing phage cocktails against E. coli UTIs using genomic and phenotypic data, showing that complementary cocktails outperform redundant ones in time-kill assays.

Robust Inference of Phage Host Infection Dynamics from Sparse Single-Cell Transcriptomic Profiles in Pseudomonas aeruginosa

The paper uses scRNA-seq to study phage-host interactions in Pseudomonas aeruginosa and identifies non-random infection patterns using machine learning.

Integrating bacterial and viral genomic information enhances and extends the machine learning predictions of bacteriophage activity against pathogenic Escherichia coli

This paper develops a machine learning model that integrates bacterial and viral genomic data to predict phage activity against E. coli, improving prediction accuracy by incorporating phage gene content.

Dual ATPase-activated DNA hemimethylation and cleavage by the MANTIS defence system

The paper defines the mechanism of the MANTIS defence system in Pseudomonas aeruginosa, showing how dual ATPases couple self-modification to non-self restriction through adenine hemimethylation and cleavage.

A tripartite mechanism licenses RNA polymerase import into the phage nucleus

This study identifies a tripartite mechanism involving Imp7 and Imp1 that licenses RNA polymerase import into the phage nucleus, showing that nuclear compartment assembly precedes transcriptional and replicative programs.

A phiKMV ligase-dependent DNA repair mechanism that mitigates DNA-targeting nucleases

The paper identifies a DNA repair mechanism in phages that allows them to resist CRISPR-Cas and R-M systems by repairing nuclease-induced breaks via a ligase-dependent process.

Constructing Virtual Viruses in A Spatial Minimal Cell

The paper constructs virtual viruses within a spatial minimal cell to model viral development and host interactions.

Capsid-specialized protein language models reveal higher-order viral architecture from sequence

This paper introduces ESMCapsid, a protein language model that detects viral capsids and infers their architecture from sequences, revealing hidden structural patterns in metagenomic data.

Discovery and Characterization of Four Novel Vibrio coralliilyticus Phages Support the Proposal of Two New Genera

The paper isolates and characterizes four novel Vibrio coralliilyticus phages, proposing two new genera based on genomic and morphological analyses.

Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways

This study identifies host factors critical for ssRNA and ssDNA phage infection in E. coli, revealing conserved dependencies and lineage-specific requirements.

A compact Druantia defense clears phage infections via single-stranded DNA recognition and directional duplex unwinding

This paper describes how the Druantia type III-A defense system in E. coli clears phage infections by recognizing single-stranded DNA and unwinding DNA duplexes directionally.

Trimethoprim suppress phage activity and reduces toxin production in a clinical STEC strain, even in the presence of DNA-damaging antibiotics

CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut

The paper constructs a large-scale resource of bacteria-MGE interactions in the human gut microbiome using CRISPR-Cas cassettes and links them to diet and lifestyle factors.

Municipal Wastewater in Ottawa, Canada contains a reservoir of bacteriophages with clinically relevant Escherichia coli and Klebsiella pneumoniae Hosts

This study identifies and characterizes bacteriophages in Ottawa's municipal wastewater that can infect clinically relevant E. coli and K. pneumoniae strains, showing high similarity to European phages but with genetic divergence.

Dosing and Delivery of Bacteriophage Therapy In a Murine Wound Infection Model

This study evaluates phage therapy dosing and delivery in a mouse wound infection model, finding topical high-dose repeated administration effective and developing a sustained-release hydrogel system.

Engineering the Pseudomonas aeruginosa virus-isolation host viPAO1 reveals how host genetic barriers shape recoverable phage diversity

The paper shows that removing genetic barriers from Pseudomonas aeruginosa hosts increases the diversity of recoverable phages, leading to the isolation of 69 new phages from clinical isolates.

Global, single-cell-resolution of antiviral defenses in marine prokaryoplankton

The paper quantifies antiviral defenses in marine prokaryoplankton using single-amplified genomes to show taxon-specific defense repertoires and lateral transfer of defense systems.

Pharmacokinetics and Physiologically Based Pharmacokinetic Modeling of Mycobacteriophages: Insights into Pulmonary Distribution and Clearance

The paper studies pharmacokinetics of mycobacteriophages in mice and develops a PBPK model to predict their distribution and clearance, showing that inhalation improves lung exposure.

DepoCat: Interactive database of experimentally verified phage depolymerases

DepoCat is a database of experimentally verified phage depolymerases that enables sequence and structure-based classification and specificity prediction.

Genome-wide overexpression screen of Pseudomonas putida phage Emajogi

This study identifies eight cytotoxic genes in a Pseudomonas putida phage through genome-wide overexpression, revealing metabolic remodeling and conserved proteins across diverse phages.

Mycobacteriophage Adephagia gp48 inhibits essential host cell wall biosynthesis enzyme mannose-1-phosphate guanylyltransferase

This paper identifies gp48, a mycobacteriophage protein that inhibits the host enzyme Mpg, essential for cell wall biosynthesis, by disrupting its dimer formation.

Chemical stressors differentially induce prophage replication in Acinetobacter baumannii strains

The paper investigates how different chemical stressors induce prophage replication in Acinetobacter baumannii strains, revealing differential induction patterns across host backgrounds.

The Mosigvirus AV110 Elongasome-Modulating Peptide (Emp) inhibits Escherichia coli growth by targeting Mre-dependent peptidoglycan synthesis

The paper identifies an antibacterial peptide from a phage that inhibits E. coli growth by disrupting Mre-dependent peptidoglycan synthesis.

CRISPR mapping unveils global prevalence of viral predators of Myxobacteria

The paper uses CRISPR spacer analysis to identify 790 myxophages across 3,229 myxobacterial genomes, revealing six new viral lineages and their functional roles in host interactions.

Biofilm compactness and spatial community composition determine bacterial phage-susceptibility

This study shows that multispecies biofilm structure and matrix composition influence phage susceptibility, with V. anguillarum protecting E. coli and K. cryocrescens from lytic phages.

Identification of novel inhibitors of Mycobacterium smegmatis growth through genome-wide overexpression of Cluster P3 mycobacteriophage Xavia genes

The paper screens mycobacteriophage Xavia genes for growth inhibition of Mycobacterium smegmatis and identifies toxic and growth-reducing genes.