Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Based Isolation v2

Culture-based isolation of bacteriophages from wastewater relies on a limited set of laboratory‐cultivable host strains, causing it to recover only a small fraction of the true viral diversity present in the influent (Chibani‐Chennoufi et al., 2004). In contrast, metagenomic sequencing bypasses cultivation constraints and uncovers both known and novel phage genomes, providing a more comprehensive snapshot of viral community structure and genetic potential (Paez‐Espino et al., 2016; Roux et al., 2016). By comparing metagenomic profiles with culture‐derived isolates, researchers can validate in silico host predictions, recover functional phages for downstream characterization, and elucidate phage–host interactions that neither method alone can fully resolve (Brum et al., 2016).