Bacteriophages and microbial interactions

The paper examines how the timing of anti-CRISPR gene expression in phages affects CRISPR-Cas interactions, finding that spacers map to earlier positions in genomes containing anti-CRISPR systems.

The paper analyzes the evolution of small eukaryotic DNA viruses, finding that mosaicism, including module reassociation and domain swapping, shapes their genomic evolution.

This study develops a stochastic model to analyze how tail fiber configuration affects bacteriophage adsorption efficiency, finding an optimal number of fibers balancing binding stability and mobility.

The paper investigates phage susceptibility in E. faecalis clinical isolates, linking it to host genomic background and Epa-associated phage adsorption patterns.

This study shows that single-site DNA methylation activates Retron-Sen2 by enabling RcaT tetramerisation, leading to retron disassembly and toxicity.

The paper shows that diversity in restriction-modification systems is maintained through trade-offs between defense strength and horizontal transferability, and provides collective protection against phages.

This study identifies host determinants for phage infection in Mycobacterium smegmatis using CRISPR interference, revealing receptor proteins and lipid components involved in phage entry.

The paper identifies active giant-virus infections in protists and shows conserved antiviral defenses and potential viral counter-defense mechanisms.

Brig3, a DNA glycosylase from a soil metagenome, excises 5-hydroxymethylcytosine from T-even phage DNA; the glucose hydrolase BapA extends defense to glucosylated genomes such as wild-type T4.

PhageHost-GNN predicts strain-level Klebsiella-phage interactions using a novelty-aware framework, achieving high AUPRC scores in in silico evaluations and showing advantages in handling novel data.

The paper uses large language models to discover a novel family of reverse transcriptases with tandem repeat arrays from metagenomic data.

The paper investigates how a giant virus maintains latency in a green alga by analyzing its genomic architecture and epigenetic regulation.

The paper identifies a prophage-encoded enzyme that links bacterial metabolism, episymbiosis, and phage fitness by remodeling host structures and promoting symbiotic interactions.

The paper analyzes Gardnerella prophages and their endolysins, finding clustering of prophage sequences by bacterial species within the genus.

This study identifies outer membrane porins as phage-specific determinants of mycobacterial susceptibility through a CRISPRi screen in Mycobacterium smegmatis.

This study characterizes the reverse transcription activity of DRT10 and reveals its unique 2:1 RT:ncRNA assembly and mechanism of cDNA synthesis.

The paper introduces a structured-evidence framework for predicting bacteriophage-host interactions using a large language model, achieving high accuracy and enabling interpretable inference.

The paper analyzes the counter-defensome diversity across 50,595 DNA phage genomes from different environments, revealing variation linked to host range, habitat, and geography.

This study investigates how coevolution between phages and bacteria affects interaction networks by analyzing genetic changes in both hosts and phages.

This study identifies a dUTPase from Mosigvirus AV110 that inhibits E. coli growth by disrupting DNA replication and cell division, revealing functional and evolutionary diversity among phage-encoded dUTP/dCTPases.

This study shows that repeated selection for lytic replication in temperate phages drives rapid genomic adaptation, with mutations accumulating in lysis- and lysogeny-associated genes.

This paper introduces a method to quantify phage killing rates by tracking plaque expansion dynamics on semi-solid media, revealing significant variation in expansion parameters across phages and taxonomic families.

This study shows that the virus {Psi}M2 can enter a non-lytic lifecycle alternative to lysogeny in Methanothermobacter marburgensis under suboptimal conditions, with genetic variability in viral populations.

The paper uses epidemiological models to identify molecular mechanisms of antiviral resistance in phytoplankton from experimental data.

This study identifies Htm, a phage-encoded protein that reprograms the transcriptome of ESBL-E. coli to support phage replication by altering gene expression and metabolic pathways.

The paper analyzes Phycodnaviridae viral homologs of heme oxygenase-1 and Phycocyanobilin:Ferredoxin oxidoreductase to predict their subcellular localization and functional divergence from host enzymes.

The paper identifies a conserved viral protein module that displaces host RNA polymerase sigma factors to control transcription in mycobacteria.

This study identifies novel antiviral defense systems in Streptococcus thermophilus by analyzing genomic islands, revealing previously uncharacterized systems and highlighting their role as reservoirs of bacterial immunity.