Phagenomic

Phagenomic is the study of bacteriophage genomes, focusing on sequencing, annotation, and comparative analysis to understand phage biology, evolution, and ecological roles. The field covers genomes from isolated phages as well as viral communities in environmental samples, and it intersects with viral taxonomy, host interactions, and phage-mediated horizontal gene transfer.

Methods in phagenomics combine laboratory approaches for phage isolation or direct viral DNA extraction with high-throughput sequencing. Genome assembly for phages can be challenging due to mosaic architectures, terminal repeats, and circular packaging. Phage-specific gene prediction and functional annotation are often required, as many phage genes have no known homologs. Quality assessment tools estimate genome completeness and contamination, and environmental datasets are curated to distinguish complete genomes from fragments. Public databases such as GenBank, RefSeq, and IMG/VR host phage sequences, while ICTV provides taxonomy and classification frameworks. Computational pipelines like PHASTER and VirSorter assist in identifying prophages and characterizing novel phage genomes, supporting large-scale comparative studies.

Applications of phagenomics include discovery of new phages with potential therapeutic or biocontrol uses, elucidation of phage-host interactions, and insights into phage roles in microbiomes and biogeochemical cycles. The field also informs phage therapy development, diagnostics, and the design of phage-derived biotechnologies. Challenges remain, including the high genetic diversity and mosaicism of phage genomes, incomplete reference databases, difficulty linking genomes to hosts, and the need for standardized metadata and taxonomy.

Looking ahead, phagenomics is expanding with advances in metagenomics, long-read sequencing, and integrated databases, aiming to improve genome quality, functional annotation, and our understanding of phage ecology and evolution.