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. ImportancePhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by defence mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of antiviral defence system of a collection of genomes, from the rumen. While defence mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defence mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This aligned with the pan-immune system model, which appears to be common across different environments.