Bacteriophages and microbial interactions

A base-modifying enzyme extends the range of anti-phage defense provided by DNA glycosylases

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.

Virophage-like viruses replicate with a candidate phycodnavirus of C. parva

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.

PhageTAILor leverages machine learning for phage tail-like elements detection and classification in plant-associated bacteria

PhageTAILor uses LightGBM on 74 detector features to flag prophages and bacterial phage tail-like elements (tailocins, T6SS, eCIS), recovering 12 of 13 validated tailocins under leave-one-genus-out.

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems

DefensePredictor combines ESM2 protein language model embeddings with genomic context features in a gradient boosting classifier to identify prokaryotic anti-phage defense genes, validating 45 previously unknown Escherichia coli systems.

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Phold pairs ProstT5-predicted 3Di tokens with Foldseek searches against 1,363,704 curated phage structures, annotating 49.4% of CDS in 1,419 INPHARED genomes versus 34.7% for Pharokka MMseqs2.

Generative design of novel bacteriophages with genome language models

Fine-tuned Evo 1 and Evo 2 genome language models designed complete ΦX174-like phage genomes; 16 of 285 assembled designs were viable, and some outperformed ΦX174 in competition.

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

Phynteny combines ESM2 protein embeddings, a BiLSTM, and circular-attention transformer layers to exploit phage gene order, assigning one of nine PHROG functional categories to unannotated genes.

PhageAI - Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing

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.

CheckV: assessing the quality of metagenome-assembled viral genomes

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.