From cells to communities: The multi-scale impacts of bacteriophages in the gut microbiome

项目总结/摘要 噬菌体是微生物群落中数量最多但了解最少的组成部分。 这在哺乳动物的胃肠道中尤其明显，在胃肠道中， 每克粪便中有100个细菌。尽管越来越多的证据表明， 人类微生物组，微生物组科学中常规使用的数据生成和分析方法被忽视 噬菌体生物学的重要方面。此外，缺乏基础知识和实验 了解微生物及其在微生物组中作用的工具。这种不理解尤其 当考虑到新兴的抗生素耐药性危机时，这一点很突出：许多重要的人类病原体 对我们的抗生素库越来越有抗药性。虽然越来越多的临床医生和科学家 相信“噬菌体疗法”（将噬菌体从宿主体内去除特定细菌的治疗应用）， 相关的微生物组）将是重要的，在我们从抗生素耐药性危机的恢复，噬菌体治疗是 不一致的有效。这在很大程度上是由于不完全了解网络如何影响他们的目标 细菌，它们对其他微生物组成员的脱靶效应，以及它们与哺乳动物宿主的相互作用。 如果没有这些知识，以噬菌体为中心的微生物群落动态的重要方面将仍然存在 模糊和阻碍稳健和可再现的噬菌体治疗应用。拟议研究的目标 计划是建立一个深刻的理解，在主机相关的微生物组中发挥的作用， 最终利用这种理解来告知基于噬菌体的治疗策略。我们将为此而努力 目的利用噬菌体分离物、细菌培养、细菌遗传学、无菌小鼠和系统生物学 接近。使用这些工具，拟议的研究计划将建立在我以前的工作， 拟杆菌thetaiotaomicron感染的细菌，并将重点放在一个突出的crAss样噬菌体的分离 家庭，DAC 15。我们将确定B中的表型异质性。多形核影响对 DAC 15，DAC 15与B的特异性相互作用。导致生产性感染的多形核，和 DAC 15如何影响微生物组-宿主相互作用。我们还将建立一个收藏夹， 感染模型人类肠道微生物组的其他成员以促进与不同细菌的类似工作， - 是的总之，这项工作将是一个急需的基础，以了解肠道的作用和身份， 常驻研究员，将建立持续和强大的以噬菌体为中心的肠道微生物组研究工具，并将 为开发稳健和可重复的噬菌体疗法提供信息。

PROJECT SUMMARY/ABSTRACT Bacteriophages (phages) are the most abundant but least understood constituents of microbial communities. This is especially evident in the mammalian gastrointestinal tract, where a diverse community of up to 1012 phages are present per gram of stool. Though mounting evidence suggests the importance of phages in human microbiomes, methods of data generation and analysis routinely used in microbiome science neglect important aspects of phage biology. Furthermore, there is a lack of foundational knowledge and experimental tools for understanding phages and the roles they play in microbiomes. This lack of understanding is especially salient when the burgeoning antibiotic resistance crisis is considered: many important human pathogens are becoming increasingly resistant to our antibiotic arsenal. While a growing number of clinicians and scientists believe that “phage therapy” (the therapeutic application of phages to remove specific bacteria from host- associated microbiomes) will be important in our recovery from the antibiotic resistance crisis, phage therapy is inconsistently effective. This is largely due to an incomplete understanding of how phages impact their target bacteria, their off-target effects on other microbiome members, and their interactions with the mammalian host. Without such knowledge, important facets of phage-centric microbiome community dynamics will remain obscure and hinder robust and reproducible phage therapy applications. The goal of the proposed research program is to build a deep understanding of the roles that phages play in host-associated microbiomes and to eventually exploit this understanding to inform phage-based therapeutic strategies. We will work towards this goal using phage isolates, bacterial culture, bacterial genetics, gnotobiotic mice, and systems biology approaches. Using these tools, the proposed research program will build on my previous work with Bacteroides thetaiotaomicron-infecting phages and will focus on an isolate of the prominent crAss-like phage family, DAC15. We will determine how phenotypic heterogeneity in B. thetaiotaomicron influences resistance to DAC15, the specific interactions between DAC15 and B. thetaiotaomicron that lead to productive infection, and how DAC15 influences microbiome-host interactions. We will additionally build a collection of phages that infect other members of a model human gut microbiome to facilitate similar work with diverse bacteria and phages. Together, this work will be a much-needed foundation to understand the roles and identities of gut- resident phages, will build tools for sustained and powerful phage-centric study of the gut microbiome, and will inform the development of robust and reproducible phage therapy.