Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

Abstract Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assessed viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes were found to be habitat dependent. Caudovirales species were ubiquitous on surface habitats in the BEs, and some of them were distinct from those present in other environments. Antimicrobial resistance genes were identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants’ skin. Diverse CRISPR-Cas immunity systems and anti-CRISPR proteins were found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus–host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner was identified through a unique gene insertion. This work illustrates that virus–host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.