Bacteriophages and microbial interactions

The paper shows that HHQ enables Gephyrocapsa huxleyi to evade viral lysis by remodeling host processes, not by inhibiting viral transcription.

The paper identifies three new families of archaeal extrachromosomal elements and shows their relatedness is due to horizontal gene transfer, not common ancestry.

The paper investigates phage activity during vegetable fermentation and shows phages influence bacterial succession without disrupting fermentation stability.

The paper tracks gene flow in the gut microbiome, showing diet and community ecology influence phage activation and horizontal gene transfer.

The paper investigates how prophage costs and competitive benefits shape bacterial evolution in polymicrobial environments, finding environment-dependent adaptive strategies and trade-offs.

This study identifies Rhc as a multifunctional protein essential for DNA replication and transcription in nucleus-forming phages, revealing its role in resolving R-loops and coordinating gene expression.

This study identifies a unique DNA replication mechanism in the chimallivirus PhiKZ, where a sliding clamp-derived protein enhances polymerase activity through a transient interaction.

This study identifies Tiamat as an ATPase and DNase in bacteria and shows its homologs are widespread across eukaryotes, with some acquiring non-defense roles.

The paper identifies a novel virus lineage, IME1, found in Dehalococcoides-containing cultures, characterized by features similar to filamentous bacterial viruses.

The paper isolates and characterizes a new jumbo Klebsiella phage, BMCPR_005026, identifying it as a new species within the Alcyoneusvirus genus with limited host range.

The paper shows that RecBCD clears self-DNA ends during bacterial replication termination to prevent autoimmunity, similar to TREX1 and DBR1 in eukaryotes.

Two polinton-like viruses, Larry and Curly, replicated in C. parva cultures only with the Algavirales phycodnavirus CpV-BQ1, not with the Imitervirales virus CpV-BQ3, and they reduced BQ1 replication.

The paper identifies capsule types in carbapenem-resistant Klebsiella pneumoniae from Pakistan that lack corresponding phages, highlighting regional disparities in phage coverage.

The paper reconstructs the MS2 phage genome using cDNA and shows that the current NCBI reference genome does not produce infectious phage, highlighting the need to verify reference genome infectivity.

The paper investigates how viral anti-defense systems vary with genomic traits, host immunity, and environmental stress across microbial ecosystems.

The paper examines the association between phage and antibiotic resistance in Pseudomonas aeruginosa clinical isolates and finds a positive correlation between the two resistance phenotypes.

This study identifies a bacterial protease that influences phage susceptibility and links it to host epithelial responses in ulcerative colitis.

This study investigates how giant virus and virophage co-infection alter the host lipidome, finding distinct lipid remodeling patterns associated with each infection type.

CheckAMG identifies auxiliary viral genes by combining annotation-based prediction with a genome-language model, improving accuracy and uncovering novel genes with no sequence similarity to references.

This study investigates how Burkholderia thailandensis responds to antibiotics and phages in spatial refuges, revealing distinct subpopulation behaviors and interactions.

This study shows that loss of type I restriction-modification methyltransferases in Pseudomonas aeruginosa increases fluoroquinolone persistence through enhanced SOS response and slower growth.

This study shows bloom-forming bacteria, like GSB-TRL01, invest heavily in anti-phage defense systems, which reduces lysis and allows blooms to persist.

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.

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.

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.

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

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.

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.

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.

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.