Bacteriophages and microbial interactions

The paper identifies helper-embedded satellites (HESs) that integrate into prophage late genes, revealing a new cis-regulatory mechanism and genomic organization.

The paper develops a method combining phage enrichment and long-read sequencing to recover more complete gut phage genomes from fecal samples, identifying a megabase phage and revealing hidden diversity.

The paper analyzes 50 temperate bacteriophages from carbapenemase-producing E. coli isolates, classifying them into viral families and identifying functional features and potential plasmid-like properties.

The paper develops a tool to annotate phage genomes using multiple genetic codes and identifies viral contigs with such features in human gut microbiome data.

This paper develops an ensemble model to predict phage-host interactions for phage therapy, achieving higher accuracy than existing methods across multiple taxonomic levels.

Hecatomb is a bioinformatics platform for viral metagenomics that enables read and contig analysis, integrating reference databases and providing tools for virome discovery.

The paper develops a synthetic communication system using phage M13 to study genetic exchange in E. coli and discovers an extracellular immunity factor that reduces infection rates by 70%.

The paper reports a novel myovirus infecting Oceanospirillaceae, identifies it as a new genus, and describes its genomic and phylogenetic features along with its ecological distribution in polar oceans.

The paper confirms that phages in the human gut microbiome use an alternative genetic code where TAG stop codon is read as glutamine.

The paper identifies prophage regions in Bacillus subtilis 168 and assesses their gene expression through RNA-seq, revealing unexpected high expression of prophage genes.

This study investigates mycobacteriophage D29-induced changes in mycobacterial cells using microscopy, revealing lysis mechanisms and potential programmed cell death features.

The paper analyzes prophage distribution across thousands of prokaryotic genomes to explore their diversity and host relationships.

The paper investigates the association between microbial eukaryote and Imitervirales communities in the Pacific Arctic Ocean, finding strong correlations between eukaryotic and viral communities despite oligotrophic conditions.

The paper uses X-ray footprinting to determine the secondary structures of bacteriophage MS2 RNA in different states, revealing packaging signals and the impact of the Maturation Protein on RNA conformation and capsid structure.

hafeZ identifies active prophages in bacterial genomes using read mapping, demonstrating accuracy on known datasets.

The paper identifies viral quorum sensing systems that manipulate bacterial sporulation timing through density-dependent mechanisms, revealing convergent evolution in bacteriophages.

The paper identifies and characterizes a novel receptor-binding protein from a Clostridium difficile phage, revealing its structure and function, and demonstrates the accuracy of AlphaFold2 predictions for structurome analysis.

The paper develops a platform using proximity-ligation sequencing to reconstruct viral genomes and assign hosts from metagenomic data, showing high accuracy and efficiency.

RaFAH is a machine-learning method for virus-host prediction that outperforms existing methods with an F1-score of 0.97 at the phylum level, discovering new archaeal virus lineages and auxiliary metabolic genes.

PHISDetector detects and integrates diverse in silico phage-host interaction signals to predict phage-host interactions using machine learning.

A linear SVM on Word2Vec 6-mer embeddings of phage nucleotide sequences calls phages virulent or temperate with 98.90% cross-validated accuracy, needing no ORF annotation.

The paper profiles and compares the phageome of oral and gut sites across individuals, finding distinct phage compositions and high diversity in oral sites, particularly on the tongue.

PHERI is a machine learning tool that predicts bacterial hosts for phages and identifies key protein sequences involved in host selection.

CheckV estimates completeness of metagenome-assembled viral contigs against GenBank plus 76,262 metagenome-derived complete genomes and trims host flanks; 86.9% of IMG/VR contigs were low-quality.

The paper characterizes a novel Actinobacteriophage, Giantsbane, and reveals unexpected relationships within phage cluster AU through genomic analysis.

The paper introduces a network-based framework to predict virus-host interactions, achieving higher accuracy than previous methods and expanding known interactions across diverse datasets.

A human gut virome reference catalog compiled from 648 metagenomes identifies 13,203 viral populations across 702 previously uncharacterized genera, boosting viral detection nearly 60-fold over NCBI viral RefSeq.

ClassiPhages 2.0 uses artificial neural networks to classify phages based on sequence data, achieving 84.18% accuracy in cross-validation.

This paper introduces vConTACT 2.0, a network-based tool for prokaryotic virus taxonomy that scales to large datasets and achieves high accuracy in taxonomic assignments.

The paper analyzes the genome, transcriptome, and proteome of Pseudomonas virus PA5oct to uncover its molecular complexity and gene regulation patterns.