Targeted Killing of Bacteria in Communities

描述（由申请人提供）：人体肠道（肠道微生物群）中微生物的组成对健康有深远的影响。最近的研究表明，肠道微生物群与炎症性肠病、肥胖和药物代谢等疾病之间存在联系。人们对利用这些知识开发操纵肠道微生物群的方法非常感兴趣，这是治疗与微生物组成不当相关的疾病的新方法。然而，由于缺乏解决这些问题的工具，我们对社区的哪些操作将促进更好的健康的理解有限。尽管在阐明微生物群与健康之间的关系方面取得了相当大的进展，但目前的技术无法完全解决了解单个细菌贡献的挑战。拟议研究的目标是通过开发一种新的策略来解决这一挑战，该策略将允许从社区中选择性消除特定的细菌分类群。该方法涉及工程化广泛的宿主范围的酶，以递送选择性地切割靶细菌基因组特有的DNA序列的核酸内切酶，从而导致细胞死亡。这种靶向杀伤机制的有效性和特异性将在模型细菌大肠杆菌和人类肠道培养细菌中进行测试和改进。无菌小鼠系统与来自人类肠道的细菌定殖将被用作一个模型，以测试有关社区中特定细菌功能的假设。开发一种消除微生物群落个体成员的新技术，可能会对治疗与微生物失衡相关的疾病以及由特定细菌制剂引起的疾病产生深远影响。此外，这种策略可以广泛适用于微生物群落的基本方面的研究。

DESCRIPTION (provided by applicant): The composition of microorganisms that reside in the human intestine (gut microbiota) has a profound impact on health. Recent work has shown links between the gut microbiota and conditions such as inflammatory bowel disease, obesity, and drug metabolism. There is great interest in harnessing this knowledge to develop methods of manipulating the gut microbiota as a new way to treat diseases associated with an improper composition of microbes. However, we are limited by our understanding of what manipulations of the community would promote better health because tools to address these questions are lacking. Despite considerable advances in elucidating the relationships between the microbiota and health, the challenge of understanding the contributions of individual bacteria cannot be fully addressed by current technologies. The goal of the proposed research is to address this challenge by developing a novel strategy that would allow the selective elimination of specific bacterial taxa from a community. The approach involves engineering broad host range phages to deliver an endonuclease that selectively cleaves a DNA sequence unique to the genome of the target bacterium, leading to cell death. The effectiveness and specificity of this targeted killing mechanism will be tested and refined in the model bacterium Escherichia coli and in cultured bacteria from the human gut. The germ-free mouse system colonized with bacteria from the human gut will be used as a model to test hypotheses about the functions of specific bacteria in the community. The development of a new technology to eliminate individual members of a microbial community could have profound impacts on the treatment of diseases associated with an imbalance of microbes, as well as those caused by a specific bacterial agent. Furthermore, this strategy could be widely applicable to the study of fundamental aspects of microbial communities.