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，我们在很大程度上仍然不知道栖息在这种环境中的病毒的多样性及其宿主的身份。此外，这些病毒的生态作用甚至更不清楚。因此，病毒在许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努力，使用数字PCR对白蚁后肠样本共定位病毒与它们的主机。特别是，我们将使用数字PCR来探索其他环境中的病毒-宿主相互作用，如哺乳动物肠道。此外，我们的计划是通过对白蚁和哺乳动物肠道样本进行单细胞测序，从而获得数十个病毒（原噬菌体）的完整基因组以及它们感染的细菌的基因组，从而建立这些早期的努力。有了这种前所未有的遗传分辨率，我们希望重新定义目前对病毒如何在野外与宿主相互作用的理解，并可能揭示新的相互作用的基本机制。

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.