Temperate Bacteriophages Manipulate Bacterial Populations

背景：噬菌体是感染细菌的病毒。它们无处不在，数量丰富(数量超过它们的宿主细菌，10：1)，估计每天杀死所有细菌的20%-40%(3)！以类似于捕食者的方式，它们在塑造微生物群落方面发挥着关键作用(5)。类似于一种更常见的捕食者的生态影响，黄石国家公园自从重新引入狼以来，是一个更健康、更稳定的生态系统。噬菌体还对细菌施加了另一种非常不同的控制形式。一些被称为温带噬菌体的噬菌体在宿主体内进入休眠状态，直到条件有利于它们的觉醒(诱导)。这些休眠噬菌体极大地改变了它们感染的细菌的生理，赋予了对其他噬菌体(32)的免疫力，编码了新的功能(34)，并为受感染的细胞(36)提供了一些健康益处。*由于易于发现以及它们的治疗潜力，人们一直偏向于对毒性(非温带)噬菌体的研究。温带噬菌体的研究还很少，但要普遍得多，包括更稳定的微生物群落中的大多数噬菌体，如人类肠道的噬菌体(7)。它们既能杀死宿主，又能直接让宿主受益，这让这些噬菌体变得特别有趣。愿景：确定温带噬菌体在塑造稳定微生物种群中的作用。*方法：*·寻找新的噬菌体。我可以接触到大量以前无法培养的肠道微生物分离物。这将作为分离新噬菌体和识别能够从肠道细菌中诱导(唤醒)噬菌体的新信号的目标。*·评估它们对东道主的影响。假设：携带噬菌体的细胞通常比无噬菌体的细胞更适合。通过竞争感染和未感染的细菌并观察它们的表型，我将确定每个新的温带噬菌体是如何影响其细菌宿主的生理的。*·探测含噬菌体的细菌群落。假设：具有温带噬菌体的细菌群落更稳定。我将创建包括噬菌体在内的微生物模型种群。这将允许我操纵环境和噬菌体，以便观察这些扰动对整个社区的影响。影响：噬菌体是细菌的主要操纵者。分离新的噬菌体必然会发现噬菌体衍生的操纵细菌的工具，就像它过去所做的那样(例如，抗CRISPR、T4DNA连接酶)。此外，温带噬菌体本身可以作为一种非转基因手段来改善生物修复、生物受精和细菌发酵等过程中使用的细菌的适应性。最后，了解噬菌体在塑造微生物群落中的作用以及确定可能触发其噬菌体驱动的扰动/稳定的因素将有助于我们为生物技术应用创造稳定的复杂细菌混合物。

Background: Bacteriophages (phages) are viruses that infect bacteria. They are ubiquitous, abundant, (outnumbering their hosts, bacteria, 10:1), and are estimated to kill 20-40% of all bacteria every day (3)! In a manner akin to predators, they play a critical role in shaping microbial communities (5). By analogy to a more familiar predator's ecological impact, Yellowstone National Park is a healthier and more stable ecosystem since the re-introduction of wolves (6). Phages also exert another very different form of control over bacteria. Some, known as temperate phages, enter a dormant state within the host until conditions favour their awakening (induction). These dormant phages drastically alter the physiology of the bacteria they infect, conferring immunity to other phages (32), encoding new functions (34), and providing some fitness benefits to infected cells (36). *** Due to ease of discovery as well as their therapeutic potential, there has been a bias towards the study of virulent (non-temperate) phages. Temperate phages are understudied, but far more common, comprising the majority of phages in more stable microbial communities such as that of the human gut (7). Their ability to both kill and directly benefit their hosts make these phages particularly interesting. ******Vision: Determine the role of temperate phages in shaping stable microbial populations.******Approach: *** • Find new phages. I have access to a large collection of previously unculturable gut microbiome isolates. This will serve as the target for isolation of new phages and identification of new signals capable of inducing (awakening) phages from gut bacteria. *** • Assess their impact on their host. Hypothesis: Phage-carrying cells are generally fitter than their phage-free counterparts. By competing infected and uninfected bacteria and observing their phenotypes, I will identify how each new temperate phage is affecting its bacterial host's physiology. *** • Probe phage-containing bacterial communities. Hypothesis: Bacterial communities with temperate phages are more stable. I will create model microbial populations which include phages. This will then allow me to manipulate the environment and the phages in order to observe the effects of those perturbations on the community as a whole. ******Impact: Phages are master manipulators of bacteria. Isolating new phages is bound to uncover phage-derived tools to manipulate bacteria, much as it has in the past (e.g. anti-CRISPRs, T4 DNA ligase). Furthermore, temperate phages themselves can serve as a non-GMO means to improve the fitness of bacteria used in processes such as bioremediation, biofertilization and bacterial fermentations. Lastly, understanding the role of phages in shaping microbial communities as well as identifying factors that can trigger their phage-driven perturbation/stabilization will aid us in creating stable complex bacterial mixes for biotechnological applications.