CAREER: Population and evolutionary dynamics of bacteriophage-symbiont-host interactions: Development of a multi-layered model microbiome

该项目的总体目标是建立一个易于处理的主机共生体噬菌体系统，在其中询问的机制，表型的结果，和多伙伴相互作用的进化动力学。该系统的结果可以为这些相互作用如何在更大范围内发挥作用提供基本见解，例如在哺乳动物肠道微生物组中。结果还可以通过阐明噬菌体给药的长期后果来告知基于噬菌体的治疗。随着抗生素耐药性的上升威胁到我们治疗细菌感染的能力，使用噬菌体作为天然抗生素的兴趣显着增加。因此，这项研究符合NSF的使命，因为它促进了科学的进步。该系统和实验方法的多学科性质是连接教学和研究的理想选择。它可以有效地整合到多个生物课程中，并根据技术和概念复杂性的规模水平进行定制。这个项目的研究和教学课程之间的交织元素将提供新颖的动手研究经验，以生物学学生的大池。因此，除了提供深入了解生物过程和多伙伴协会的结果，该项目为学生提供了发展研究技能的能力。这些更广泛的影响服务于国家科学基金会的使命，通过培养学生进入生物经济工作队伍，促进国家繁荣。噬菌体可能对细菌共生体及其宿主生物的适应性和进化产生强大的影响。然而，内共生体的宿主内位置可以保护它们免受噬菌体感染或改变感染结果。尽管它们具有潜在的意义，但很少有研究探讨了细菌对宿主-共生体相互作用的影响，或者研究了宿主生态系统在介导共生体-噬菌体相互作用中的作用。该项目的目标是建立一个易于处理的宿主-共生体-噬菌体生态系统，以询问这些相互作用的机制，表型结果和进化动力学。该研究策略利用了社会阿米巴Dictyosteelium discoideum和Paraburkholderia细菌之间的自然微生物共生。兼性副伯克霍尔德氏菌共生体在阿米巴宿主中建立细胞内感染，并且感染特征在共生体菌株之间变化。该项目将通过分析Paraburkholderia和相关细菌基因组的前噬菌体和噬菌体防御元件来调查共生体进化和性状的历史影响，而正在进行的基于土壤的筛选噬菌体分离将阐明共生体特异性共生体的相对环境丰度和多样性。最终，副伯克霍尔德氏菌感染的阿米巴将暴露于微生物中并连续培养，以通过1）量化种群丰度和共生体感染模式以及2）分析进化和祖先分离株的表型和基因组特征来评估所有各方的动态，适应性结果和进化轨迹。该系统的结果可能为了解这些相互作用如何在其他共生系统和更大规模上发挥作用提供基本见解，有助于为基于噬菌体的治疗提供信息，并与微生物生态学，病毒学，进化生物学和细菌发病机制相关。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

The overarching goal of this project is to establish a tractable host-symbiont-bacteriophage system in which to interrogate the mechanisms, phenotypic outcomes, and evolutionary dynamics of multi-partner interactions. Results from this system may provide fundamental insight into how these interactions play out on larger scales, such as within the mammalian gut microbiome. Results may also inform phage-based therapies by illuminating long-term consequences of phage administration. As the rise of antibiotic resistance threatens our ability to treat bacterial infections, interest in using bacteriophages as natural antibiotics has significantly increased. As such, this research meets the mission of the NSF in that it promotes the progress of science. This system and the multidisciplinary nature of the experimental approach is ideal for linking teaching and research. It can be effectively integrated into multiple biology courses and tailored to scale levels of technical and conceptual complexity. Interweaving elements of this project between research and teaching courses will provide novel hands-on research experiences to a large pool of biology students. Thus, in addition to providing insight into the biological process and outcomes of multi-partner associations, this project provides students the ability to develop research skill sets. These Broader Impacts serve the NSF mission of advancing national prosperity by training students for entry into the bioeconomy work force.Bacteriophages are likely to have powerful impacts on the fitness and evolution of bacterial symbionts and their host organisms. However, the intra-host location of endosymbionts may shield them from phage infection or modify infection outcomes. Despite their potential significance, few studies have explored the impact of phages on host-symbiont interactions or investigated the role of the host ecosystem in mediating symbiont-phage interactions. The goal of this project is to establish a tractable host-symbiont-phage ecosystem to interrogate the mechanisms, phenotypic outcomes, and evolutionary dynamics of these interactions. The research strategy utilizes a natural microbial symbiosis between the social amoeba Dictyostelium discoideum and Paraburkholderia bacteria. Facultative Paraburkholderia symbionts establish intracellular infections in amoeba hosts and infection characteristics vary across symbiont strains. This project will investigate the historical impact of phages on symbiont evolution and traits by analyzing Paraburkholderia and related bacterial genomes for prophage and phage defense elements, while ongoing phage isolation from soil-based screening will illuminate relative environmental abundance and diversity of symbiont specific phages. Ultimately, Paraburkholderia infected amoeba will be exposed to phages and continuously cultured to assess the dynamics, fitness outcomes, and evolutionary trajectory of all parties by 1) quantifying population abundances and symbiont infection patterns and 2) analyzing phenotypic and genomic characteristics of evolved and ancestral isolates. Results from this system may provide fundamental insight into how these interactions play out in other symbiosis systems and on larger scales, help inform phage-based therapeutics, and be of relevance to microbial ecology, virology, evolutionary biology, and bacterial pathogenesis.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.