Data from: CRISPR-induced distributed immunity in microbial populations

In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show how the CRISPR-mediated adaptive immune response of hosts to invading viruses facilitates the emergence of an evolutionary mode we call distributed immunity - the coexistence of multiple, equally-fit immune alleles among individuals in a microbial population. We use an eco-evolutionary modeling framework to quantify distributed immunity and demonstrate how it emerges and fluctuates in multi-strain communities of hosts and viruses as a consequence of CRISPR-induced coevolution under conditions of low viral mutation and high relative numbers of viral protospacers. We demonstrate that distributed immunity promotes sustained diversity and stability in host communities and decreased viral population density that can lead to viral extinction. We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities.在细菌与古菌（Archaea）中，病毒是主要的感染因子，作为烈性且通常致命的病原体发挥作用。一类被称为CRISPR-Cas的适应性免疫防御系统，可使微生物细胞通过识别病毒基因组中编码的特定序列，获得对病毒病原体的免疫能力。该系统独特的生物学特性，使得宿主与病毒多样性的进化动力学无法完全通过传统的微生物-病毒共进化动力学描述模型得到解释。本研究阐明了宿主针对入侵病毒的CRISPR介导适应性免疫应答，如何促成一种我们称之为分布式免疫（distributed immunity）的进化模式的出现——即微生物种群内的个体间可共存多种适配度相当的免疫等位基因。我们采用生态进化建模框架对分布式免疫进行量化，并证实：在低病毒突变率、相对较多的病毒前间隔序列（protospacers）的条件下，CRISPR介导的共进化会使宿主与病毒的多菌株群落中出现分布式免疫并使其发生动态波动。研究表明，分布式免疫可促进宿主群落维持持久的多样性与稳定性，并降低病毒种群密度，甚至可引发病毒灭绝。我们对活跃表达CRISPR-Cas系统的嗜热链球菌（Streptococcus thermophilus）与其病毒的共进化实验种群的序列多样性进行分析，发现宿主种群中快速出现了分布式免疫现象，这证明了该新兴现象在进化微生物群落中的重要性。