Bacteriophages and microbial interactions

The paper uses deep mutational scanning to map the functional landscape of the T7 bacteriophage receptor binding domain, identifying host-specific functional residues and tradeoffs between activity and host range.

This paper uses Grad-seq to identify RNA-protein complexes in Pseudomonas aeruginosa under standard and bacteriophage infection conditions, revealing new insights into RNA regulation and phage-host interactions.

The paper identifies 780 phage-plasmids across diverse bacterial phyla, groups them into 8 families based on gene repertoire similarity, and highlights their conserved phage genes and variable plasmid-like genes.

This paper introduces PHP, a Gaussian model for predicting hosts of prokaryotic viruses in metagenomics, achieving higher accuracy than existing methods.

The paper introduces a machine learning method for detecting prophages in bacterial genomes, finding more phages than existing tools while being faster.

The paper reports the genome sequence of bacteriophage L, compares it to related phages, and identifies features related to restriction-modification systems in Salmonella.

The paper analyzes prophage distribution in A. baumannii genomes, finding two common families, variable prophage numbers, and AMR gene carriage in prophages.

The paper characterizes the structure and function of a novel DNA-dependent RNA polymerase from a crAss-like phage, showing its role in phage gene transcription and structural similarity to eukaryotic RNA interference polymerases.

PhANNs classifies phage ORFs into structural protein classes or 'other' with high accuracy using an artificial neural network ensemble trained on curated phage sequences.

This study shows that removing gene overlaps in a bacteriophage genome reduces viral replication efficiency, highlighting the importance of gene overlap for viral function.

The paper characterizes the complete genome of the Staphylococcus bacteriophage Metroid and compares it to other cluster C1 phages, highlighting similarities in the lysis cassette.

VIBRANT improves virus recovery and virome function analysis from metagenomes, outperforming existing tools in accuracy and completeness.

The paper investigates DNA methylation in giant viruses, finding widespread methylation, bacterial-origin MTases, and potential roles in virus-virus interactions.

This study provides a high-resolution transcriptome map of bacteriophage ΦX174 by sequencing RNA from infected E. coli, confirming existing models and revealing new transcriptional features.

This study profiles the human gut virome using Oxford Nanopore Technology, revealing high individuality, novel sequences, and epigenetic modifications on phages.

The paper analyzes APSE phage genomes from Hamiltonella symbionts in aphids, revealing recombination events and variable toxin regions.

Phigaro annotates prophage regions in genome and metagenome assemblies, producing prophage genome maps and taxonomic annotations.

The paper identifies a conserved positively charged arginine-rich domain in icosahedral viruses that correlates with capsid assembly and genome packaging strategies.

This study analyzes Pseudomonas aeruginosa virus PA5oct using hybrid sequencing and proteomics to reveal its genomic structure, transcription dynamics, and interactions with host bacteria.

This study compares CRISPR and marker-based methods for engineering phage T7, finding marker-based selection most efficient and type II CRISPR-Cas easier to use than type I.

The paper uses engineered bacteriophage to reduce shigatoxin production in an enteric mouse model by targeting virulent bacteria without significantly affecting bacterial concentrations.

This study compares dsDNA bacteriophage diversity in stabled and feral horses, finding higher richness and even distribution compared to human viromes, with no over-represented phage genotypes.

The paper describes a protocol for generating saturation mutagenesis libraries of the {Phi}X174 bacteriophage using unamplified oligo pools and golden gate assembly, enabling comprehensive mutation analysis of viral proteins.

The paper identifies widespread prophages and satellite prophages in Streptococcus species, showing their association with pneumococcal virulence in a mouse model.

This study shows that phages and plasmids increase prokaryotic genome size, while CRISPR reduces it, with CRISPR targeting phages more than plasmids.

The paper shows phage can have indirect effects on microbial communities, with outcomes depending on metabolic and evolutionary factors.

ProphET identifies prophages in bacterial genomes with higher precision than existing tools and includes a self-updating reference database.

This paper develops a method to engineer phage tail fibers to alter host range and suppress bacterial resistance, showing effectiveness in vitro and in vivo.

The paper uses a machine-learning classifier to distinguish gene transfer agents from viral homologs in alphaproteobacterial genomes, finding that many prophage predictions are likely GTAs.

PhaMers identifies 103 novel phage sequences from Yellowstone hot spring metagenomes using tetranucleotide frequency analysis and compares results with VirSorter.