Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages

Background: Viruses that infect prokaryotes (phages) constitute the most
abundant group of biological agents, playing pivotal roles in microbial
systems. They are known to impact microbial community dynamics, microbial
ecology, and evolution. Efforts to document the diversity, host range,
infection dynamics, and effects of bacteriophage infection on host cell
metabolism are still at the surface level. Among phages, some adopt the
lysogenic mode of infection, where the genome integrates into the host
cell genome, forming a prophage. Prophages enable viral genome replication
without host cell lysis and often contribute novel and beneficial traits
to the host genome. Despite their importance, research on prophages is
limited. Current phage research predominantly focuses on lytic phages,
leaving a significant gap in knowledge regarding prophages, including
their biology, diversity, and ecological roles. Results: To bridge this
gap, the creation of Prophage-DB, a prophage database, aims to address the
limited knowledge of these crucial biological entities. To create the
database, we identified lysogenic viruses from genomes in three publicly
available databases. We applied several state-of-the-art tools in our
pipeline to annotate these viruses, cluster them, taxonomically classify
them, and detect their respective AMGs. With our approach, we identified
over 350,000 prophages and 35,000 auxiliary metabolic genes. Conclusion:
By summarizing the collected information we have created a database with
extensive metadata regarding phage and host taxonomy, host information,
and auxiliary metabolic genes. We identified numerous phages, from a wide
variety of archaeal and bacterial hosts, which show a wide environmental
distribution. In addition, the identified auxiliary metabolic genes will
improve our understanding of them given the context of our study. We
estimate this comprehensive prophage database will be a valuable resource
for advancing prophage research, offering insights into viral taxonomy,
host relationships, auxiliary metabolic genes, and environmental
distribution. Its use promises to contribute towards understanding
microbial ecosystems and unlocking the mysteries of microbial dark matter.