Molecular mechanisms underlying the host range of bacteriophages infecting Shiga toxin-producing Escherichia coli strains

噬菌体（噬菌体）是所有栖息地中最丰富的实体，也是遗传多样性的主要库，影响微生物结构和生态系统动态。尽管假设所有细胞生物体都会受到病毒攻击，但对宿主与病毒相互作用的范围知之甚少。产志贺毒素大肠杆菌 (STEC) 是多种人畜共患病原体，在世界范围内引起食源性疾病。新的致病性血清群不断出现，但牛及其环境仍然是 STEC 的主要储存库。有效的收获前干预对于最大限度地减少食品供应链中的 STEC 污染至关重要。内源噬菌体在牛及其环境中普遍存在，通过未知机制调节 STEC 的多样性。获得有关噬菌体如何适应牛环境并捕食各种 STEC 的机制见解对于了解 STEC 生态并增强噬菌体生物防治效果以减少牛中 STEC 脱落至关重要。支持噬菌体-细菌相互作用的分子机制是在噬菌体和宿主基因组中编码的。我的研究计划的长期目标是了解环境噬菌体基因组如何变化并与细菌共同进化，以及它如何塑造细菌群落结构和种群。我的研究项目结合使用基因组学、生物信息学、基因组适应性测定和合成生物学等方法，研究噬菌体的基因多样性和特化以及与 STEC 识别和感染性的相关联系。 3 个家族中超过 70 个 STEC 噬菌体的可用性使我们能够解决其与宿主相互作用组中的各种关键问题。我们将确定噬菌体尾部基因如何多样化和模式化以响应不同的 STEC 表面结构。我们还将从基因角度鉴定参与噬菌体结合的 STEC 表面结构。对于广泛的宿主范围噬菌体，我们将探索它们是否能够识别并附着到保守的宿主表面结构以引发感染。最后，我们将使用基因组编辑来修改噬菌体尾部基因，试图改变其宿主特异性。该计划是第一个系统地研究噬菌体的各种基因型和 STEC 不同血清群之间的初始相互作用的项目，产生了关于 STEC 噬菌体宿主识别和感染的分子机制的新知识。解决这些研究目标应该大大提高对噬菌体基因组如何适应自然环境以及这些变化如何促进新环境中的适应和专业化的理解。此外，拟议的计划旨在通过阐明初级生产水平的基础知识来解决加拿大致病性大肠杆菌面临的紧迫食品安全挑战。该计划将培养训练有素的噬菌体生物学高级人才，精通尖端技术和其他基本技能，使他们能够在学术界、工业界和其他领域脱颖而出。

Bacteriophages (phages) are the most abundant entities across all habitats, and a major reservoir of genetic diversity, affecting microbial structure and ecosystem dynamics. The scope of host-viral interactions is poorly understood, although hypothetically all cellular organisms are prey to viral attack. Shiga-toxigenic Escherichia coli (STEC) are a diverse group of zoonotic pathogens, causing foodborne disease worldwide. New pathogenic serogroups keep emerging, but cattle and their environment continue to be the primary reservoir for STEC. Effective pre-harvest interventions are critical to minimize STEC contamination in the food supply chain. Endogenous phages are ubiquitous in cattle and their environment, regulating diversity of STEC via unknown mechanisms. Gaining mechanistic insights regarding how phages adapt to the cattle environment and prey on a variety of STEC is imperative to understand STEC ecology, and enhance phage biocontrol outcomes to mitigate STEC shedding in cattle. Molecular mechanisms that support phage-bacteria interactions are encoded in phage and host genomes. The long-term objectives of my research program are to understand how environmental phage genomes change and co-evolve with bacteria and how this shapes bacterial community structures and populations. Using a combination of approaches, including genomics, bioinformatics, genome-fitness assays and synthetic biology, my research program examines gene variety and specialization of phages and associated linkage to STEC recognition and infectivity. Availability of >70 STEC phages across 3 families enable us to address various key questions in their interactome with their host. We will determine how phage tail genes are diversified and patterned in response to divergent STEC surface structure. We will also genetically identify STEC surface structures involved in phage binding. For broad host-range phages, we will explore whether they can recognize and attach to conserved host surface structures to initiate infection. Finally, we will use genome editing to modify phage tail genes in an attempt to alter their host specificity. The proposed program is the first to systematically investigate initial interplays between various genotypes of phages and diverse serogroups of STEC, generating new knowledge on molecular mechanisms underlying host recognition and infection of STEC phages. Addressing these research objectives should greatly improve understanding of how phage genomes adapt in response to natural environments and how these changes promote adaptation and specialization in new environments. In addition, the proposed program aims to address Canada's urgent food safety challenges of pathogenic E. coli by elucidating fundamental knowledge at the primary-production level. This program will generate well trained HQP specialized in phage biology and proficient in cutting-edge technologies and other essential skills, enabling them to excel in academia, industry and elsewhere.