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（数量超过宿主细菌，10:1），据估计每天杀死所有细菌的20-40% (3)！以一种类似于捕食者的方式，它们在形成微生物群落方面起着关键作用(5)。通过类比一个更熟悉的捕食者的生态影响，黄石国家公园是一个更健康和稳定的生态系统，因为狼的重新引入(6)。噬菌体还对细菌施加另一种非常不同的控制形式。一些被称为温带噬菌体，在宿主体内进入休眠状态，直到条件有利于它们的唤醒（诱导）。这些休眠的噬菌体极大地改变了它们所感染细菌的生理机能，赋予其他噬菌体免疫力（32），编码新的功能（34），并为被感染的细胞提供一些适应性益处（36）。***由于易于发现以及它们的治疗潜力，人们一直倾向于研究强毒（非温带）噬菌体。温带噬菌体尚未得到充分的研究，但更为常见，包括更稳定的微生物群落（如人类肠道）中的大多数噬菌体(7)。它们既能杀死宿主，又能直接使宿主受益，这使得这些噬菌体特别有趣。******愿景：确定温带噬菌体在形成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菌群分离物。这将作为分离新的噬菌体和鉴定能够从肠道细菌诱导（唤醒）噬菌体的新信号的靶标。***评估他们对东道国的影响。假设：携带噬菌体的细胞通常比不携带噬菌体的细胞更适合生存。通过感染和未感染细菌的竞争和观察它们的表型，我将确定每个新的温带噬菌体如何影响其细菌宿主的生理。***探测含噬菌体的细菌群落。假设：温带噬菌体的细菌群落更稳定。我会创建包括噬菌体在内的微生物种群模型。这将使我能够操纵环境和噬菌体，以观察这些扰动对整个群落的影响。******影响：噬菌体是细菌的操纵者。分离新的噬菌体必然会发现噬菌体衍生的工具来操纵细菌，就像过去一样（例如抗crispr， T4 DNA连接酶）。此外，温带噬菌体本身可以作为一种非转基因手段，用于生物修复、生物施肥和细菌发酵等过程中提高细菌的适应性。最后，了解噬菌体在塑造微生物群落中的作用，以及确定可以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.