Biomedical subjects
Publications and source records attributed to Zachary N Flamholz.
We report the genome of Vanta, a lytic bacteriophage isolated from wastewater using Pseudomonas aeruginosa PA14. Phage Vanta is a Yuavirus with a circularly permuted, 61,663-bp, 64.5% guanine-cytosine, dsDNA genome. Head width is 56 ± 2 nm, and tail length is 133 ± 5 nm. Vanta plaques on two drug-resistant clinical P. aeruginosa isolates.
We report the genome of Luminis, a lytic bacteriophage isolated from wastewater using Pseudomonas aeruginosa mPAO1Δpf4Δpf6. Phage Luminis is a Yuavirus with 61,617 bp of circularly permuted dsDNA and 64.4% GC content. In addition to reference strains, Luminis plaques on two drug-resistant clinical isolates of P. aeruginosa.
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.