Bacteriophages and microbial interactions

Towards a unifying phylogenomic framework for tailed phages

This paper presents a phylogenomic framework for tailed phages using gene presence/absence data to reconstruct evolutionary relationships and quantify gene exchange events.

Involvement of Pf-like phages in resistance to phage infection in clinical isolates of P. aeruginosa from cystic fibrosis patients

The paper identifies 12 new Pf-like phages in P. aeruginosa clinical isolates and links their presence to resistance against phage infection through novel anti-phage defence systems.

Uncovering the hidden RNA virus diversity in Lake Nam Co: evolutionary insights from an extreme high-altitude environment

This study identifies 742 RNA virus species in Lake Nam Co, revealing novel viral groups and evolutionary adaptations in an extreme high-altitude environment.

Multi-strain phage induced clearance of bacterial infections

This study uses computational models to show that phage cocktails targeting different bacterial receptors improve treatment outcomes in immunocompromised hosts and reduce resistance evolution.

Mobile genetic elements exhibit increased sequence diversity with increasing host range within the gut microbiome of the Western Honey bee

The paper shows that mobile genetic elements in honey bee gut microbiomes show increased sequence diversity with broader host range.

TIR signaling activates caspase-like immunity in bacteria

This study identifies a bacterial immune system where TIR-domain proteins activate caspase-like proteases to induce cell death and block phage replication.

Metabolic remodeling of microorganisms by obligate intracellular parasites alters mutualistic community composition

This study investigates how obligate intracellular parasites alter microbial community composition through metabolic remodeling in an in vitro system.

Phage defense and genome editing using novel retrons sourced from isolated environmental bacteria

The paper isolates and characterizes novel retrons from environmental bacteria, tests their phage defense mechanisms, and engineers them for genome editing in E. coli.

Using cryogenic electron microscopy methods to gain insight into structure and initial host attachment of the flagellotropic bacteriophage 7-7-1

The paper uses cryo-EM to determine the structure of bacteriophage 7-7-1 and shows it uses capsid fibers for initial host attachment.

Enhanced Suppression of Stenotrophomonas maltophilia by a Three-Phage Cocktail: Genomic Insights and Kinetic Profiling

This paper identifies and characterizes three phages that form a cocktail effective against Stenotrophomonas maltophilia, showing enhanced bacterial suppression compared to individual phages.

A LexA-like repressor and global H-NS-like regulators enable the fine-tuning of R-tailocin expression in environmental Pseudomonas

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.

A VersaTile approach to reprogram the specificity of the R2-type tailocin towards different serotypes of Escherichia coli and Klebsiella pneumoniae

This paper introduces a VersaTile platform to engineer R2 tailocins with broad specificity against multiple E. coli and Klebsiella pneumoniae serotypes, achieving high efficacy and cross-species activity.

Optimization of an improved, time-saving, and scalable, protocol for the extraction of DNA from diverse viromes

The paper compares a commercial DNA extraction kit with the phenol-chloroform method for viromes, finding no significant differences in virome diversity but noting the kit's advantages and limitations.

Discovery and analysis of an 841 kbp phage genome: the largest known to date

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

Pseudomonas superinfection drives Pf phage transmission within airway infections in patients with cystic fibrosis

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.

Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages

The paper introduces Prophage-DB, a database of over 350,000 prophages and 35,000 auxiliary metabolic genes, providing insights into prophage diversity, distribution, and ecological roles.

Combinatorial phenotypic landscape enables bacterial resistance to phage infection

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.

Asesino: a nucleus-forming phage that lacks PhuZ

The paper studies a phage lacking PhuZ, showing it replicates efficiently without this protein, highlighting variation in nucleus-based replication pathways.

Coexistence of Virome-Encoded Human Probiotic Genes and Pathogenic Genes in Global Habitats

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

Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks

The paper isolates and characterizes novel bacteriophages targeting wheat phyllosphere bacteria, identifies DNA modifications and single-strand breaks, and finds widespread distribution of similar phages in public metagenomes.

Protein and genomic language models chart a vast landscape of antiphage defenses

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.

A Class 1 OLD family nuclease encoded by Vibrio cholerae is countered by a vibriophage-encoded direct inhibitor

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.

Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium

The paper identifies a mechanism of phage resistance in Synechococcus involving tRNA gene expression loss, showing that reduced LeuTAA tRNA levels prevent phage gene translation.

Actinobacteriophage Inteins: Host Diversity, Local Dissemination, and Non-Canonical Architecture

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

Soil viral and prokaryotic communities shifted significantly after wildfire in chaparral and woodland habitats

This study examines how wildfire affects soil viral and prokaryotic communities in chaparral and woodland habitats, finding significant shifts in community composition and viral particle abundances.

Episomal virus maintenance enables bacterial population recovery from infection and virus-bacterial coexistence

This study shows that episomal virus maintenance in Salinibacter ruber allows population recovery from infection and supports virus-bacterial coexistence under high MOI.

Provirus deletion from Haloferax volcanii affects motility, stress resistance and CRISPR RNA expression

The paper deletes four proviruses in Haloferax volcanii and finds increased motility, stress resistance, and altered CRISPR RNA expression.

Eco-evolutionary dynamics of temperate phages in periodic environments

This study examines eco-evolutionary dynamics of temperate phages in periodic environments, showing how temperate strategies can outperform lytic or lysogenic strategies under varying host availability and viral mortality.

Phage-phage competition and biofilms reduce the efficacy of a combination of two virulent bacteriophages against Pseudomonas aeruginosa

This study investigates how phage-phage competition and biofilm formation affect the efficacy of a two-phage combination against Pseudomonas aeruginosa in vitro.

Generalists in a Specialist World: Vibrio-Phages with Broad Host Range

This study examines broad-host-range Vibrio phages, identifying genetic features and ecological trade-offs that influence their host range and environmental distribution.