Single-Cell Analysis of Virus-Host Interactions

描述（由申请人提供）：动物是数百种微生物细胞的家园，其数量远远超过构成生物体本身的细胞。然而，我们仍然在很大程度上对居住在这种环境中的病毒的多样性及其宿主的身份一无所知。此外，这些病毒的生态作用甚至更不清楚。因此，病毒在很多方面都是微生物宇宙的暗物质。我们认为，环境微生物学的核心挑战之一是绘制出哪些病毒与哪些宿主相关，并了解遗传信息在这个复杂的相互作用网络中的流动。在这里提出的工作中，我们建立在我们早期的工作基础上，利用白蚁后肠样本的数字PCR将病毒与宿主共定位。特别是，我们将使用数字PCR来探索病毒与宿主在其他环境（如哺乳动物肠道）中的相互作用。此外，我们的计划是在这些早期努力的基础上，对白蚁和哺乳动物的肠道样本进行单细胞测序，从而提供数十个病毒（噬菌体）的全基因组以及它们感染的细菌的基因组。有了这种前所未有的基因分辨率，我们希望重新定义当前对病毒如何与宿主在野外相互作用的理解，潜在地揭示相互作用的新的基本机制。

DESCRIPTION (provided by applicant): Animals are home to cells of hundreds of microbial species, far outnumbering the cells comprising the organism itself. However, we still remain largely ignorant of the diversity of the viruses that inhabit such environments and the identity of their hosts. Further, the ecological role of these viruses is even more unclear. As such, viruses in many ways are the dark matter of the microbial universe. We argue that one of the central challenges in environmental microbiology is to map out which viruses are associated with which hosts and understand the flow of genetic information in this complex web of interactions. In the work proposed here, we build on our earlier efforts using digital PCR on termite hindgut samples to colocalize viruses with their hosts. In particular, we will use digital PCR to explore virus-host interactions in other environments such as mammalian guts. In addition, our plan is to build upon these earlier efforts by performing single-cell sequencing on termite and mammalian gut samples thus providing access to tens of full genomes of the viruses (prophages) as well as the genomes of the bacteria they infect. With such unprecedented genetic resolution we hope to redefine the current understanding of how viruses interact with their hosts in the wild, potentially uncovering new fundamental mechanisms of interaction. PUBLIC HEALTH RELEVANCE: In recent years it has become increasingly clear that human health is directly tied to the microbial communities we harbor within us. The work proposed here begins to explore the way in which viruses can impact these microbial communities. We expect that just as different humans have different microbial community structures with corresponding implications for their health, the structure of the viral communities will add another dimension to our growing understanding of the health consequences of our partnerships with the microbes that populate us.