Bacteriophages and microbial interactions

This study characterizes the phylogenetic and functional diversity of large and cell-associated viruses in two coastal sites of the Bay of Bengal, revealing high diversity and abundance of large phages and giant viruses.

The paper examines interactions between lytic bacteriophages and Stevia rebaudiana extracts in bacterial environments, finding dynamic conditions alter extract effects based on phage and bacterial species.

The paper develops a method to isolate and analyze protected environmental DNA (peDNA) from marine samples, revealing that extracellular vesicles are a major contributor to non-viral sequence space and play a significant role in horizontal gene transfer.

The paper describes a method for efficiently engineering phage genomes without using selection or CRISPR-Cas systems, achieving mutation rates of 1-14% for single-base substitutions, deletions, and insertions in three phages.

This study investigates the localization dynamics of two phage-encoded RNA polymerases during phiKZ infection, showing vRNAP is injected and excluded from the phage nucleus while nvRNAP is synthesized and localized within the nucleus.

This study shows that mucin promotes phage resistance in K. pneumoniae, but mucolytic agents like NAC reduce this resistance, suggesting their potential use in phage therapy.

The paper investigates how the choice of ultrafilter affects the recovery of bacteriophages from clinical samples, finding that pore size influences recovery strain- and sample-dependently.

geNomad identifies and annotates mobile genetic elements in sequencing data, discovering millions of new viruses and plasmids in public metagenomes.

Phables improves phage genome recovery from fragmented viral metagenome assemblies, recovering more high-quality genomes and resolving variants with high nucleotide identity.

The paper determines the structure of the portal complex from Staphylococcus aureus Pathogenicity Island 1 transducing particles using cryo-electron microscopy, revealing its interaction with the capsid.

The paper characterizes novel recombinant mycobacteriophages generated through homologous recombination between two temperate phages, showing they are homoimmune to Island3 and can overcome antiphage defenses.

This study isolates and characterizes three novel Crassvirales phages infecting Bacteroides cellulosilyticus WH2, revealing they do not co-evolve with their hosts and share a conserved tail spike protein involved in host interaction.

VIRify identifies and classifies viral contigs and prophages from metagenomic data with high accuracy across prokaryotic and eukaryotic viruses.

The paper identifies four new 7-deazaguanine derivatives in phages and characterizes enzymes involved in their biosynthesis and insertion into DNA.

The paper reports the cryo-EM structures of Vibrio phage XM1, revealing its contractile tail and baseplate components, and proposes mechanisms of assembly and infection.

The paper uses protein embeddings to predict phage-host interactions, showing improved performance over handcrafted features with ProtT5 achieving higher F1 scores.

The paper isolates and characterizes four novel bacteriophages from Baltic Sea water that infect bacteria associated with the moon jellyfish Aurelia aurita.

The paper examines HEGs in bacteriophages, finding variable distribution, HEG islands, and domain swapping, suggesting HEGs significantly influence phage evolution.

The paper uses long-read sequencing to show that most gut phages are methylated, with many encoding their own methyltransferases, suggesting methylation helps phages evade host defenses.

ViWrap provides a modular pipeline for analyzing viruses in metagenomes, enabling identification, classification, and host prediction through integration of multiple tools.

Phanta profiles human gut metagenomes to include viruses directly from short reads, identifying more viral species than assembly-based methods and revealing higher interindividual variability in the virome.

The paper presents the first structural data of a cos virus DNA packaging motor from bacteriophage HK97, revealing its termination state and asymmetry mechanisms.

This study shows that Bdellovibrio bacteriovorus uses both binary and non-binary fission depending on prey size, revealing how host size influences bacterial reproduction mechanisms.

The paper identifies two highly conserved core defense hotspots in Pseudomonas aeruginosa containing numerous anti-phage systems, including a newly discovered system called Shango.

The paper finds a loss of crAssphage stability in the human gut virome associated with obesity and metabolic syndrome, suggesting a potential role for these phages in metabolic health.

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

MetaPhage is a pipeline that automates the analysis, annotation, and classification of bacteriophages in metagenomics data, providing a comprehensive report and interactive visualization.

vHULK predicts bacteriophage hosts using genomic features and deep neural networks, achieving high accuracy in genus and species-level classifications.

3CAC improves phage and plasmid classification in metagenomic assemblies by leveraging assembly graph proximity, outperforming existing tools in precision and recall.