Development of Engineered Native Bacteria as a Tool for Functional Manipulation of the Gut Microbiome

开发工程原生细菌作为肠道微生物组功能操纵的工具

• 批准号: 10737475
• 负责人: JEFF M HASTY
• 金额: $ 78.86万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-20 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10737475
• 关键词: Acceleration; Address; Affect; Antibiotics; Back; Bacteria; Bacteroides; Basic Science; Biological; Chronic Disease; Clinical; Communicable Diseases; Communities; Data; Development; Disease; Ecology; Engineering; Engraftment; Environment; Escherichia coli; Functional disorder; Gene Expression; Genetic; Gnotobiotic; Goals; Health; Human; Immune System Diseases; Individual; Intestines; Knock-in; Knowledge; Lactobacillus; Learning; Mediating; Mission; Modification; Mus; National Institute of Allergy and Infectious Disease; Nutrient; Organism; Outcome; Pathologic; Pathology; Phenotype; Physiological; Physiological Processes; Physiology; Production; Protein Secretion; Proteins; Public Health; Reporting; Research; Research Personnel; Role; Signal Transduction; Source; System; Testing; Therapeutic; Transgenes; combat; cost; curative treatments; design; gut microbiome; gut microbiota; host-microbe interactions; improved; in vivo; in vivo Model; innovation; interest; metabolomics; microbial community; microbial host; microbiome; microbiome composition; microbiome research; microbiome therapeutics; microorganism; novel strategies; patient stratification; prevent; quorum sensing; real world application; risk stratification; synthetic biology; targeted treatment; technology development; tool; tool development; transgene delivery; transgene expression; translational impact; Acceleration; Address; Affect; Antibiotics; Back; Bacteria; Bacteroides; Basic Science; Biological; Chronic Disease; Clinical; Communicable Diseases; Communities; Data; Development; Disease; Ecology; Engineering; Engraftment; Environment; Escherichia coli; Functional disorder; Gene Expression; Genetic; Gnotobiotic; Goals; Health; Human; Immune System Diseases; Individual; Intestines; Knock-in; Knowledge; Lactobacillus; Learning; Mediating; Mission; Modification; Mus; National Institute of Allergy and Infectious Disease; Nutrient; Organism; Outcome; Pathologic; Pathology; Phenotype; Physiological; Physiological Processes; Physiology; Production; Protein Secretion; Proteins; Public Health; Reporting; Research; Research Personnel; Role; Signal Transduction; Source; System; Testing; Therapeutic; Transgenes; combat; cost; curative treatments; design; gut microbiome; gut microbiota; host-microbe interactions; improved; in vivo; in vivo Model; innovation; interest; metabolomics; microbial community; microbial host; microbiome; microbiome composition; microbiome research; microbiome therapeutics; microorganism; novel strategies; patient stratification; prevent; quorum sensing; real world application; risk stratification; synthetic biology; targeted treatment; technology development; tool; tool development; transgene delivery; transgene expression; translational impact

PROJECT SUMMARY/ABSTRACT Most therapies that target microbiome composition do not have a detectable impact on the gut microbiome and are not robust to the interpersonal diversity and plasticity of the community in human hosts. To develop a better mechanistic understanding of the microbe-host relationship and more effective microbiome-mediated therapies, approaches based on functional modulation of the gut microbiome are necessary. However, these approaches have been difficult to develop. Attaining long-term engraftment in the luminal environment has proven to be quite difficult, and even once engraftment has been achieved, a change in physiology or improvement of pathologic phenotype has not yet been demonstrated. There is a critical need for a tool that will allow investigators to “knock-in” functions into the gut microbiome and investigate their effects on the luminal milieu and, ultimately, physiology in conventionally-raised hosts in non-sterile conditions. The investigators propose a novel approach to address this need by using native bacteria as chassis for the introduction of specific functions into the luminal environment. The proposal's innovation is a new strategy that allows the quick and effective “knock-in” of a beneficial function in a sustained manner into conventional hosts. To date they have demonstrated that tractable native bacteria can be engineered to express a beneficial function ex vivo, reintroduced to the host, engraft the entire gut of the host, and deliver an intended beneficial function. These functions can affect host physiology, help determine the effect of specific bacterial functions and potentially alleviate disease. The central hypothesis of this proposal is that long-term colonization and functional change in the gut microbiome of a conventional host can be performed effectively with engineered native bacteria. In the next five years, the investigators will continue the development of this technology and better understand the chassis-host interactions that will aid in the development of live bacterial therapeutics for clinical use. First, the investigators will engineer regulatory systems for the transgene of interest, including a sense and control, protein secretion, and biocontainment circuit. They will test whether these systems function in vivo in hosts that are in a non-sterile environment. In addition, they will assess the natural biocontainment of engineered native bacteria among co-housed hosts. Second, they will determine how the niche for a bacterial chassis affects function delivery and whether multiple functions can be delivered by the same chassis or whether different chassis are necessary for the delivery of multiple functions. Finally, the investigators will determine the role of microbial community in amplifying the effects of a transgene of interest in gnotobiotic mice. The expected outcome of the proposed studies is attainment of fundamental biological knowledge of how the gut microbiome can be functionally manipulated. These studies will have a positive translational impact because they will demonstrate that synthetic biology approaches can lead to the development of curative interventions to some of the most debilitating and costly chronic diseases.

项目摘要/摘要 靶向微生物组组成的大多数疗法对肠道微生物组没有可检测的影响 并且对人类主持人社区的人际关系多样性和可塑性并不强大。开发一个 更好地理解微生物宿主关系和更有效的微生物组介导的 疗法，基于肠道微生物组功能调节的方法是必要的。但是，这些 方法很难开发。在腔内环境中获得长期植入 事实证明，很难 尚未证明病理表型的改善。对于一个将要的工具迫切需要 允许研究人员将功能“敲击”到肠道微生物组中，并研究其对腔的影响 环境，最终在非疾病条件下传统饲养的宿主中的生理学。调查人员 提议一种新颖的方法来解决这种需求，通过将本机细菌作为底盘引入特定的底盘 功能进入腔环境。该提案的创新是一种新策略，可以快速且 有效的“敲击”有益的功能以持续的方式进入常规宿主。迄今为止，他们有 证明可以设计可牵引的天然细菌以表达有益的功能，即 重新引入宿主，植入宿主的整个肠道，并提供预期的有益功能。这些 功能可以影响宿主生理，有助于确定特定细菌功能的影响，并可能 减轻疾病。该提议的核心假设是长期定植和功能变化 常规宿主的肠道微生物组可以通过工程的天然细菌有效地进行。 在接下来的五年中，调查人员将继续开发这项技术，更好 了解将有助于开发实时细菌疗法的底盘 - 宿主相互作用 使用。首先，调查人员将设计监管系统，以转变感兴趣的转变，包括一种意义和 对照，蛋白质分泌和生物内在电路。他们将测试这些系统在体内是否在 在非紧密环境中的主机。此外，他们将评估工程的自然生物内在 共同宿主中的本地细菌。其次，他们将确定细菌底盘的利基市场如何影响 功能传递以及是否可以通过相同的底盘传递多个功能或是否不同 底盘对于传递多个功能是必需的。最后，调查人员将确定 微生物群落在扩大了对gnotobiotic小鼠兴趣转化的影响方面。预期 拟议研究的结果是获得有关肠道微生物组如何的基本生物学知识 可以在功能上操纵。这些研究将产生积极的翻译影响，因为它们将 证明合成生物学方法可以导致对某些的治疗干预措施的发展 最令人衰弱和昂贵的慢性疾病。