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

Area of Science:

• Microbial Ecology
• Virology
• Bioinformatics

Background:

• Rumen microorganisms are crucial for lignocellulose degradation and energy conversion.
• Prokaryote-infecting viruses significantly influence host populations and metabolism in the rumen.
• Limited host-virus prediction in this ecosystem is attributed to a lack of specialized clustered regularly interspaced short palindromic repeat (CRISPR) spacer datasets.

Purpose of the Study:

• To establish RuSpacer, a comprehensive database of CRISPR spacers from rumen-associated prokaryotic genomes.
• To facilitate host-virus prediction within the rumen ecosystem using spacer-protospacer matching.
• To provide a resource for studying virus-host interactions and microbial ecology.

Main Methods:

• Extraction of 181,023 CRISPR spacers from publicly available rumen prokaryotic genomes.
• Annotation of each spacer with the taxonomic identity of its source genome.
• Development of a database (RuSpacer) for host-virus prediction via spacer-protospacer matching.

Main Results:

• Creation of RuSpacer, a specialized database containing 181,023 rumen-derived CRISPR spacers.
• Demonstration of RuSpacer's utility for host-virus prediction in the rumen environment.
• Potential for RuSpacer integration with existing datasets for broader environmental applications.

Conclusions:

• RuSpacer significantly advances host-virus prediction capabilities in the rumen microbiome.
• The database supports research into microbial ecology and virus-based biocontrol strategies.
• RuSpacer is a valuable resource for understanding virus-host dynamics in complex microbiomes beyond the rumen.