Phagenomes

A phagenome is the complete genetic content encoded by bacteriophages, the viruses that infect bacteria. In a strict sense it can refer to the genome of a single phage particle, but in environmental microbiology the term phagenome (or phageome) denotes the collection of phage genomes recovered from a sample such as seawater, soil, or the human gut. Phagenomes are studied to understand phage biology, evolution, and interactions with bacterial hosts.

Phage genomes vary widely. Most bacteriophages have double-stranded DNA genomes, though RNA phages and single-stranded DNA phages exist. Genome sizes range from about 5 kilobases in some small phages to over 500 kilobases in jumbo phages, with many in the 40–170 kilobase range. Phage genomes are compact and mosaic, often organized into modules for replication, transcription, structural proteins, and lysis. The frequent recombination among phages produces mosaic architectures and modular shuffling of gene blocks.

Life cycles and genes: Temperate phages can integrate into host genomes as prophages during lysogeny, carrying regulatory genes such as integrases and repressors. Lytic phages replicate and assemble virions, then kill the host with lysis mechanisms involving holins and endolysins. Structural gene modules encode capsid and tail proteins; replication modules include DNA polymerases and helicases. Many phages also carry auxiliary metabolic or host-derived genes that may influence host physiology or phage fitness.

Ecology and methods: Phagenomes influence microbial community dynamics and horizontal gene transfer, contributing to nutrient cycling through bacterial lysis. Viral metagenomics and genome-resolved analyses aim to reconstruct individual phage genomes from complex datasets, though high mosaicism and limited universal markers complicate annotation. Advances in sequencing and bioinformatics have expanded knowledge of phagenomes and their roles in ecosystems and biotechnological applications such as phage therapy and biocontrol.