CAREER: Uncovering the strange biology of elusive Shigella phages and their roles in horizontal gene transfer

微生物很少孤立地存在。取而代之的是，他们在微生物群的更广泛背景下与多个其他伙伴互动。微生物群在与其相互作用的生物体的健康中发挥着重要作用。微生物群是复杂的有机体网络，通常包括噬菌体，噬菌体是感染细菌的病毒。由于噬菌体或噬菌体在塑造细菌进化中起着至关重要的作用，因此必须了解这些病毒在复杂微生物群落中的影响。该项目的目标是充分描述复杂微生物网络中噬菌体介导的进化机制(S)，并最终在模拟人类肠道的环境中检查这些网络。更广泛的影响活动包括一个噬菌体狩猎项目，该项目将让初中、高中和本科生参与发现新的噬菌体(这将涉及密歇根州立大学和格林内尔学院之间的合作)。博客文章和YouTube视频将使社区了解到新发现的噬菌体识别的进展情况。教师培训以及K-12课堂的课程开发是拟议工作计划的重要组成部分。一些噬菌体可以“转导”或打包宿主遗传信息，并在感染期间将其传递给下一宿主。这通过在群落内水平地调动和移动基因，深刻地影响了微生物群的进化。最近的一项发现揭示了志贺氏菌噬菌体内的新进化，这可能会增加细菌种群内的基因交换。为了真正了解噬菌体介导的进化机制，必须考虑复杂群落内的转导。这可以通过建立在传统的实验性微生物进化研究的基础上，只使用纯化的培养和非转导噬菌体，到包括转导噬菌体在内的多物种群落。这项研究的目的是确定噬菌体介导的遗传转移影响微生物组进化的机制。建立这些群落的第一步将是分离和鉴定不同的志贺氏菌噬菌体。PI将从不同的环境中分离志贺氏菌噬菌体，表征它们在不同宿主上的生命周期，并在噬菌体和宿主之间进行实验性的共同进化研究。这些共同进化实验最初将用于确定噬菌体如何进化以感染新宿主。综合起来，这些结果将有助于计算模型的参数化，这些模型将被用来建立日益复杂的实验网络。PI将决定影响快速进化的选择压力，以开发一种最终可应用于其他细菌的预测工具：噬菌体相互作用。然后，PI将使用产生有趣和新颖结果的条件，对通过计算预测的假设进行实验测试。最终细胞培养微流控(即“芯片上的肠道”)将被开发来模拟本地微生物群，并被用于研究噬菌体：哺乳动物肠道中的宿主相互作用。PI将使用分离株的基因测序来跟踪噬菌体和宿主细菌之间的进化和遗传流动性，这些基因序列是在这个本地但容易控制的环境中进化的。

Microbes rarely exist in isolation. Instead, they interact with multiple other partners in the broader context of a microbiome. Microbiomes play a large role in the health of the organisms with which they interact. Microbiomes are complex networks of organisms that frequently include bacteriophages, which are viruses that infect bacteria. Since bacteriophages, or phages, play essential roles in shaping bacterial evolution, it is imperative to understand the impact of these viruses within the context of complex microbial communities. The goal of this project is to fully characterize the mechanism(s) of phage-mediated evolution within complex microbial networks and ultimately examining these networks in an environment that mimics the human gut. The Broader Impact activities involve a phage hunting project that will involve middle school, high school and undergraduates in the discovery of new phages (this will involve a collaboration between MSU and Grinnell College). Blog posts, along with YouTube videos, will keep the community informed regarding progress in the identification of newly discovered phages. Teacher training, along with curriculum development in the K-12 classroom, are prominent components of the proposed workplan. Some phages can "transduce", or package host genetic information, and pass it along to the next host during infection. This profoundly affects microbiome evolution by mobilizing and moving genes horizontally within the community. A recent discovery has uncovered novel evolution within Shigella phages that potentially increases genetic exchange within bacterial populations. To truly understand mechanisms of phage-mediated evolution, it is imperative to consider transduction within complex communities. This can be done by building on traditional studies of experimental microbial evolution, which solely use purified cultures and non-transducing phages, to multi-species communities that include transducing phages. The objective of this research is to determine mechanisms by which phage-mediated genetic transfer affects microbiome evolution. The first step in building these communities will be to isolate and characterize diverse Shigella phages. The PI will isolate Shigella phages from diverse environments, characterize their life cycles on different hosts, and perform experimental co-evolution studies between phages and hosts. These co-evolution experiments will initially be used to determine how phages evolve to infect new hosts. Combined, these results will help parameterize computational models, which will be used to build experimental networks with increasing complexity. The PI will determine selection pressures that influence rapid evolution to develop a predictive tool that can ultimately be applied to other bacteria:phage interactions. The PI will then experimentally test computationally predicted hypotheses using conditions that resulted in interesting and novel outcomes. Ultimately cell culture microfluidics (i.e. "Gut-on-a-Chip") will be developed to mimic a native microbiome and be used to study phage:host interactions in the context of a mammalian gut. The PI will track evolution and genetic mobility between phages and host bacteria using genetic sequencing of isolates after a population has evolved in this native, but easily-controlled, environment.