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

项目摘要/摘要 噬菌体是微生物群落中含量最丰富但知之甚少的组成成分。 这在哺乳动物的胃肠道中尤为明显，在那里有多达1012个多样化的群落 每克粪便中都有噬菌体。尽管越来越多的证据表明噬菌体在 人类微生物群，数据生成和分析方法，常规用于微生物群科学忽视 噬菌体生物学的重要方面。此外，还缺乏基础知识和实验 了解噬菌体及其在微生物群中扮演的角色的工具。这种缺乏理解的情况尤其是 当考虑到迅速增长的抗生素耐药性危机时，突出的是：许多重要的人类病原体 对我们的抗菌素变得越来越有抵抗力。虽然越来越多的临床医生和科学家 相信“噬菌体疗法”(用噬菌体从宿主体内清除特定细菌的治疗应用-- 相关微生物)对我们从抗生素耐药性危机中恢复将是重要的，噬菌体疗法是 效果参差不齐。这在很大程度上是因为对噬菌体如何影响他们的目标没有完全的理解。 细菌，它们对其他微生物组成员的非靶标效应，以及它们与哺乳动物宿主的相互作用。 如果没有这样的知识，以噬菌体为中心的微生物群落动态的重要方面将保留下来 遮蔽和阻碍健壮和可重复的噬菌体疗法应用。拟议研究的目标是 该计划是建立对噬菌体在宿主相关微生物群中所扮演的角色的深刻理解，并 最终利用这一理解为基于噬菌体的治疗策略提供信息。我们将为此而努力。 目标利用噬菌体分离、细菌培养、细菌遗传学、灵知生菌小鼠和系统生物学 接近了。使用这些工具，拟议的研究计划将建立在我之前与 类杆菌感染噬菌体，并将重点放在一个突出的粗糙状噬菌体的分离上 家人，DAC15。我们将确定B.thaiotaomicron的表型异质性如何影响对 DAC15，DAC15和B.thaiotaomicron之间导致产生性感染的特异性相互作用，以及 DAC15如何影响微生物群与宿主的相互作用。我们还将构建一个噬菌体集合， 感染模型人类肠道微生物组的其他成员，以促进与不同细菌和 噬菌体。总而言之，这项工作将成为理解Gut的角色和身份的迫切需要的基础- 常驻噬菌体，将建立持续和强大的以噬菌体为中心的肠道微生物群研究工具，并将 为发展健壮和可重复性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.