Table 3.

Recommendations for choosing viromes or metagenomes depending on research context

Context	Recommended method(s)	Rationale
Viral community dynamics, overall virus diversity, assembly of uncultivatable virus genomes	Virome	Viromes generally contained more viral species and greater viral sequence enrichment than metagenomes
Bacterial/archaeal communities, no interest in viruses	Metagenomes	Viromes are unnecessary to the study of just the cellular members of communities
Fast-growing, highly dynamic communities, and/or lytic viruses	Virome	Assuming viral lysis is prevalent due to the present biotic or abiotic conditions, viromes will enrich for lytic viruses
Slow-growing, low-biomass communities, and/or integrated viruses	Metagenomes	Assuming lysogeny is prevalent due to the present biotic or abiotic conditions, detecting viruses integrated in the host genome require metagenomics
Host‒virus interactions	Paired viromes and metagenomes	Metagenomes are necessary to provide any host context. While metagenomes alone can yield some viral genomes, viromes are also recommended to maximize viral genome assembly
Maximization of total virus diversity	Paired viromes and metagenomes	Both viromes and metagenomes resulted in the assembly of viral genomes not detected in the other method. Utilizing both methods can maximize the detection and assembly of as many viral genomes as possible