Data from: Coevolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection

Microbes that protect their hosts from pathogenic infection are widespread components of the microbiota of both plants and animals. It has been found that interactions between ‘defensive’ microbes and pathogens can be genotype-specific and even underlie the variation in host resistance to pathogenic infection. These observations suggest a dynamic coevolutionary association between pathogens and defensive microbes, but direct evidence of coevolution is lacking. We tested the hypothesis that defensive microbes and pathogens could coevolve within host populations by co-passaging a microbe with host-defensive properties (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within Caenorhabditis elegans nematodes. Using both phenotypic and genomic analyses across evolutionary time, we found patterns of pathogen local adaptation and defensive microbe-pathogen coevolution via fluctuating selection dynamics. Moreover, coevolution with defensive microbes resulted in more rapid and divergent pathogen evolution compared to pathogens evolved independently in host populations. Taken together, our results indicate the potential for defensive microbes and pathogens to coevolve, driving interaction specificity and pathogen evolutionary divergence in the absence of host evolution.能够保护宿主免受致病性感染的微生物，是动植物微生物群中广泛分布的组成部分。已有研究表明，“防御性”微生物与病原菌之间的相互作用具有基因型特异性，甚至是宿主对致病性感染抗性差异的潜在驱动因素。上述观测结果提示，病原菌与防御性微生物之间存在动态的协同进化关联，但目前仍缺乏协同进化的直接实证证据。我们通过在秀丽隐杆线虫（Caenorhabditis elegans）体内共传代具有宿主防御特性的粪肠球菌（Enterococcus faecalis）与病原菌金黄色葡萄球菌（Staphylococcus aureus），检验了“防御性微生物与病原菌可在宿主种群内发生协同进化”这一假说。通过对进化历程中的表型与基因组进行分析，我们发现了病原菌的局部适应模式，以及防御性微生物与病原菌通过波动选择动态实现的协同进化现象。此外，相较于在宿主种群中独立演化的病原菌，与防御性微生物发生协同进化的病原菌展现出更快的进化速度与更显著的分化程度。综上，本研究结果表明，在宿主未发生演化的前提下，防御性微生物与病原菌具备协同进化的潜力，可推动宿主-病原菌互作特异性的形成以及病原菌的进化分化。