Bacteriophages and microbial interactions

This study investigates how temperate phages balance lysogeny and lytic cycles in competitive environments, finding that stable lysogens outcompete others and that dispersal between fluctuating sub-systems reduces their survival against virulent phages.

The paper examines phage interactions with chemosynthetic symbionts of hydrothermal vent snails and mussels, finding species-specific phages influence strain-level diversity and population dynamics.

The paper isolates and characterizes six Pseudomonas aeruginosa bacteriophages, finding they have distinct genomic clusters and morphologies, with some showing lytic activity suitable for phage therapy.

PharaCon uses a conditional BERT framework to improve phage identification in metagenomic data by incorporating label constraints during pre-training.

This study identifies over 1,500 viral histones and histone-fold proteins in dsDNA viruses, revealing their structural and functional diversity beyond nucleocytoplasmic large DNA viruses.

This study elucidates the molecular mechanism of BREX anti-phage immunity by showing how BrxX methyltransferase recognizes DNA and forms an immune complex to protect against phage infection.

The paper isolates and characterizes Jyvaskylavirus, a new giant virus from Finland, revealing its structural features and genomic similarities to other marseilleviruses.

The paper identifies a bacterial anti-phage system that uses nucleobase modification to generate immune messengers, leading to population-level defense through infected cell death.

This study investigates phage-cyanobacteria interactions in Lake Champlain over a decade, finding that phages share environmental niches with bacteria but exhibit distinct dynamics and co-variation patterns.

The paper characterizes new Pseudobdellovibrionaceae strains, revealing genomic features and evolutionary insights into bacterial predation modes.

The paper identifies an orphan antitoxin-like enzyme in phages that neutralizes the bacterial DarTG1 toxin-antitoxin defense system by removing ADP-ribose modifications from phage DNA.

This study analyzes 186 Pseudomonas aeruginosa clinical isolates to assess the association between prophage presence and antibiotic resistance, finding few significant links.

PhageDPO is a machine learning tool that predicts depolymerases in bacteriophage genomes to aid in discovering novel antibacterial agents.

The paper benchmarks Hi-C for virus-host linkage detection using synthetic communities and applies optimized protocols to soil samples, revealing new interactions and establishing performance metrics.

This study examines how colony formation in Microcystis affects viral infection strategies, finding that colonies favor lysogeny while single cells experience more lytic infection.

This study identifies and characterizes 274 auxiliary metabolic genes (AMGs) encoded by RNA viruses from global virome datasets, revealing their functional diversity and potential horizontal gene transfer from non-host organisms.

This study isolates and characterizes a novel virus, vB_PshM_Y4, showing it is not detectable by high-throughput sequencing and belongs to an unknown viral family.

VirMake processes shotgun metagenomic data to identify and characterize viral taxa and functions, showing variability in viral genome richness and taxonomy across environments and protocols.

This paper develops a physiologically based pharmacokinetic model to characterize the whole-body distribution of bacteriophages in mice, finding rapid elimination and the need for multi-dose regimens.

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

The paper identifies conserved phage factors required for protein import into a phage nucleus and characterizes their interactions and roles in selectivity.

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.

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

The paper tracks temperate phages in biofilms, showing lysogens are over-represented in dispersal pools and have advantages in long-term propagation.

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

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

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

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

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

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