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

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 大多数针对微生物群组成的疗法对肠道微生物群没有可检测到的影响 并且对人类宿主社区的人际多样性和可塑性不是很健壮。要开发一种 更好地从机制上理解微生物-宿主关系和更有效地由微生物组介导 基于肠道微生物群功能调节的治疗方法是必要的。然而，这些 开发方法一直很困难。在流明环境中实现长期嫁接具有 事实证明，这是相当困难的，即使一旦实现了植入，生理或 病理表型的改善尚未得到证实。迫切需要一种能够 允许研究人员在肠道微生物群中“敲入”功能，并调查它们对管腔的影响 环境，并最终在非无菌条件下的常规饲养的宿主中的生理学。调查人员 提出一种新的方法来解决这一需求，通过使用本地细菌作为底盘引入特定的 在发光环境中发挥作用。该提案的创新是一种新的战略，可以让快速和 以持续的方式将有益的功能有效地“敲入”到传统的宿主中。到目前为止，他们有 证明了易驯服的本地细菌可以被改造成在体外表达有益的功能， 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。这一建议的中心假设是，长期的殖民和功能变化 传统宿主的肠道微生物组可以用工程的本地细菌有效地执行。 在未来的五年里，调查员将继续发展这项技术，并更好地 了解底盘与宿主的相互作用，这将有助于临床活菌疗法的开发 使用。首先，调查人员将为感兴趣的转基因设计监管系统，包括感官和 控制、蛋白质分泌和生物抑制回路。他们将测试这些系统是否在体内发挥作用 处于非无菌环境中的主机。此外，他们还将评估人工合成的天然生物容器。 合住宿主中的本地细菌。其次，他们将确定细菌底盘的利基环境如何影响 功能交付以及同一底盘是否可以交付多种功能，或者是否不同 底盘是交付多种功能所必需的。最后，调查人员将确定 微生物群落，放大感兴趣的转基因对诺生菌小鼠的影响。预期中的 拟议研究的结果是获得了关于肠道微生物群如何产生的基本生物学知识 可以在功能上被操纵。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疾病的治疗干预措施的发展 最让人虚弱和代价高昂的慢性病。