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Establishing the feasibility of editing the human gut microbiome

建立编辑人类肠道微生物组的可行性

基本信息

批准号：
10621772
负责人：
Peter James Turnbaugh
金额：
$ 40.38万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-08-01 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10621772
关键词：
Actinobacteria class BCAR1 gene Bacteria Bacterial Genes Bacterial Genome Bacteriophage Genetics Bacteriophages Biochemical Biological Biomedical Research Cardiac Cell Death Cells Clustered Regularly Interspaced Short Palindromic Repeats Communities Complex Custom Cytoprotection DNA DNA delivery Development Plans Devices Digoxin Discipline Disease Dissection Engineering Exposure to Family Foundations Gastrointestinal tract structure Gene Combinations Gene Deletion Gene Targeting Genes Genetic Genome Genomic DNA Genotype Gnotobiotic Goals Growth Guide RNA Habitats Health Human Human Microbiome Immune system In Situ In Vitro Individual Knowledge Link Medicine Metabolic Pathway Metabolism Methods Modeling Molecular Genetics Mus Pathogenesis Pharmaceutical Preparations Physiology Planets Plants Plasmids Predisposition Prevalence Process Reagent Regulation Research System Technology Testing Therapeutic Toxin Validation Variant bacterial genetics clinical application fitness gene discovery gut bacteria gut microbiome high reward high risk host microbiome human disease in vivo evaluation insight interest knockout gene microbial microbial community microbial host microbiome microbiome research mutant novel nuclease programs protein complex technology development technology research and development tool

项目摘要

PROJECT SUMMARY Definitive links between the remarkable inter-individual genotypic variation in the human microbiome and disease are still limited due to the lack of generalizable methods to precisely remove microbial genes from complex microbial communities in situ. Not only would such a technology help transform the microbiome field from a descriptive to a mechanistic discipline, but it would also have immediate clinical applications. The goal of this Focused Technology Research and Development (PAR-19-253) application is to establish a generalizable toolkit to program the endogenous CRISPR-Cas systems in human gut bacteria to knockout genes of interest with unprecedented precision. CRISPR-Cas is a bacterial immune system, composed of RNA-guided nucleases, that protect the cell against bacteriophage and other foreign DNA. Endogenous CRISPR-Cas systems can be programmed to target their own genomic DNA using custom guide RNAs (gRNAs) homologous to a gene of interest. As an initial proof-of-principle we will target a single gut bacterial gene that we discovered is responsible for the inactivation of the cardiac drug digoxin, but if successful this approach could be readily extended to the numerous bacterial species that have now been implicated in host physiology and the predisposition to and treatment of disease. We will pursue the following Specific Aims: (Aim I) the functional validation of a novel CRISPR-Cas system in Eggerthella lenta, a prevalent gut Actinobacterium with multiple links to metabolism and microbial pathogenesis; (Aim II) the isolation and rebooting of bacteriophages that infect human gut bacteria; and (Aim III) the engineering of bacteriophage to program an endogenous gut bacterial CRISPR-Cas system. Our long-term goal is to establish the first modular tools for engineering the gut microbiome to delete one gene, combinations of genes, or even entire metabolic pathways. Importantly, by focusing on endogenous CRISPR-Cas systems, we anticipate that along the way we will uncover basic insights into the diversity, regulation, and function of these systems, with broad implications for our understanding of the complex interactions between bacteriophages, their bacterial hosts, and their shared mammalian habitat. While our early results provide support for feasibility, this high-risk, high- reward technology development plan would have broad implications for the study of microbial communities and host-microbiome interactions while bringing the promise of microbiome-based therapeutics within reach.

项目摘要人类微生物组中显着的个体间基因型变异与由于缺乏可推广的方法来精确地从细菌中去除微生物基因，复杂的微生物群落。这种技术不仅有助于改变微生物领域，从一个描述性的学科到一个机械性的学科，但它也会有直接的临床应用。目标该重点技术研究与开发（PAR-19-253）申请的目的是建立一个可推广的工具包，用于在人类肠道细菌中编程内源性CRISPR-Cas系统，以前所未有的精确度敲除目标基因CRISPR-Cas是一种细菌免疫系统，由RNA引导的核酸酶组成，保护细胞免受噬菌体和其他外来DNA的侵害。内源性CRISPR-Cas系统可以编程为使用自定义指南靶向其自身的基因组DNA 与感兴趣的基因同源的RNA（gRNA）。作为初步的原理验证，我们将针对单个肠道我们发现的细菌基因负责心脏药物地高辛的失活，但如果成功的这种方法可以很容易地扩展到许多细菌物种，与宿主生理学和疾病的易感性和治疗有关。我们将继续努力具体目的：（目的I）在迟缓蛋孢（Eggerthella lenta）中对新型CRISPR-Cas系统进行功能验证，与代谢和微生物发病机制有多重联系的肠道放线菌;（目的II）分离和感染人类肠道细菌的噬菌体的重新启动;以及（目标III）噬菌体的工程改造，对内源性肠道细菌CRISPR-Cas系统进行编程。我们的长期目标是建立第一个用于工程化肠道微生物组的模块化工具，以删除一个基因，基因组合，甚至整个代谢途径重要的是，通过关注内源性CRISPR-Cas系统，我们预计沿着我们将揭示这些系统的多样性，监管和功能的基本见解，对我们理解噬菌体，它们的细菌宿主，以及它们共同的哺乳动物栖息地虽然我们的早期结果为可行性提供了支持，但这种高风险，高- 奖励技术开发计划将对微生物群落的研究产生广泛的影响，宿主-微生物组相互作用，同时使基于微生物组的治疗有望实现。

项目成果

期刊论文数量（3）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli.

DOI：
10.1128/mbio.01573-23
发表时间：
2023-10-31
期刊：
mBio
影响因子：
6.4
作者：
通讯作者：

Microbiome single cell atlases generated with a commercial instrument.

使用商业仪器生成的微生物组单细胞图谱。

DOI：
10.21203/rs.3.rs-3253785/v1
发表时间：
2023
期刊：
Research square
影响因子：
0
作者：
Abate,Adam;Li,Xiangpeng;Xu,Linfeng;Demaree,Benjamin;Noecker,Cecilia;Bisanz,Jordan;Weisgerber,Daniel;Modavi,Cyrus;Turnbaugh,Peter
通讯作者：
Turnbaugh,Peter

Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors.

多种果实，蔬菜和酒精摄入量与结直肠癌幸存者中的肠道微生物物种以及基因丰度有关。