Antiviral defence systems in the rumen microbiome

The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanism. However, the diversity and prevalence of antiviral defence systems in complex communities is still unknown. We therefore investigated the diversity and abundance of viral defence systems in 3038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defence systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defence systems in the genomes. However, the number of defence systems, defence system families and systems density varied widely from genome to genome. Additionally, the number of defence system correlated positively with the number of defence systems families and the genome size. Restriction modification, Abi and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defence systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.