Microorganisms in the ruminant gastrointestinal tract play key roles in lignocellulose degradation and energy conversion. Prokaryote-infecting viruses play a pivotal role in shaping host abundance and metabolism. Despite their importance, host–virus prediction in this environment remains limited, partly due to the lack of specialized clustered regularly interspaced short palindromic repeat spacer datasets. Here, RuSpacer, a database of 181,023 clustered regularly interspaced short palindromic repeat spacers extracted primarily from publicly available rumen-associated prokaryotic genomes, was established. Each spacer is annotated with the taxonomic identity of the genome from which it was derived. RuSpacer enables host–virus prediction via spacer–protospacer matching, particularly in the rumen ecosystem. It can also be integrated with existing publicly available spacer datasets and used for host–virus prediction in environments other than the rumen. Overall, this resource supports research on host–virus interactions, microbial ecology, and virus-based biocontrol strategies in livestock and other complex microbiomes.
Yoshiaki Sato (Sat,) studied this question.