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

职业：揭示难以捉摸的志贺氏菌噬菌体的奇怪生物学及其在水平基因转移中的作用

• 批准号: 1750125
• 负责人: Kristin Parent
• 金额: $ 79.43万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-15 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1750125&HistoricalAwards=false
• 关键词: CAREER; Uncovering; strange; biology; elusive

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.

微生物很少孤立存在。相反，它们在微生物组的更广泛背景下与多个其他伙伴相互作用。微生物组在与它们相互作用的生物体的健康中发挥着重要作用。微生物组是生物体的复杂网络，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背景下的影响。该项目的目标是充分表征复杂微生物网络中噬菌体介导的进化机制，并最终在模拟人类肠道的环境中检查这些网络。更广泛的影响活动涉及一个噬菌体狩猎项目，该项目将涉及中学，高中和本科生发现新的噬菌体（这将涉及密歇根州立大学和格林内尔学院之间的合作）。 博客帖子，沿着YouTube视频，将使社区了解新发现的蠕虫的识别进展。 教师培训，沿着K-12教室的课程开发，是拟议工作计划的重要组成部分。一些病毒可以“复制”，或者包装宿主的遗传信息，并在感染过程中将其沿着传递给下一个宿主。这通过在群落内水平调动和移动基因，深刻影响了微生物组的进化。最近的一项发现揭示了志贺氏菌内的新进化，可能会增加细菌种群内的遗传交换。为了真正理解噬菌体介导的进化机制，必须考虑复杂社区内的转导。这可以通过建立在实验微生物进化的传统研究的基础上来完成，传统研究仅使用纯化的培养物和非转导细菌，以包括转导细菌的多物种群落。本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。建立这些社区的第一步将是分离和表征不同的志贺氏菌。PI将从不同的环境中分离志贺菌，描述它们在不同宿主上的生命周期，并在志贺菌和宿主之间进行实验性的协同进化研究。这些共同进化实验最初将用于确定病毒如何进化以感染新的宿主。结合起来，这些结果将有助于参数化计算模型，这些模型将用于构建越来越复杂的实验网络。PI将确定影响快速进化的选择压力，以开发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将通过实验测试计算预测的假设，使用导致有趣和新颖结果的条件。最终，将开发细胞培养微流体（即“芯片上的肠道”）以模拟天然微生物组，并用于研究哺乳动物肠道背景下的噬菌体：宿主相互作用。PI将使用分离株的基因测序来跟踪细菌和宿主细菌之间的进化和遗传流动性，这些分离株是在一个种群在这种天然但易于控制的环境中进化后产生的。