phagenome

Phagenome is a term used to refer either to the genome of an individual bacteriophage (phage) or, less commonly, to the collective genomes of phages present in a particular environment. As individual entities, phage genomes encode the information needed for infection, replication, assembly and release from bacterial hosts. Genome sizes and architectures vary widely, from a few thousand to several hundred thousand base pairs, and may consist of single- or double-stranded DNA or RNA. Many phage genomes are organized in functional modules and display mosaicism caused by frequent genetic exchange.

When used to describe the collective phage genetic content of a sample, the term emphasizes diversity and ecological roles. Environmental phagenomes, explored through viral metagenomics and single-virus genomics, reveal immense sequence diversity and a high proportion of genes with unknown functions. Phage genomes often carry auxiliary metabolic genes that can influence host metabolism and biogeochemical cycles, and they are major agents of horizontal gene transfer among bacteria.

Study of phagenomes employs plaque isolation, high-throughput sequencing, electron microscopy, and bioinformatics for assembly and annotation. Challenges include incomplete reference databases, rapid phage evolution, and limited functional characterization of novel genes. Applications of phage genomic knowledge include development of phage therapy, tools for bacterial detection and typing, biocontrol in agriculture, and synthetic biology. Ongoing advances in sequencing and computational annotation are expanding understanding of phage diversity, evolution, and ecological impact.