RuSpacer: a CRISPR spacer database derived from ruminant-associated prokaryotes for virome analysis

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.