Functional Metagenomic Reprogramming of the Human Microbiome through Mobilome Eng

通过 Mobilome Eng 对人类微生物组进行功能性宏基因组重编程

• 批准号: 8213003
• 负责人: Harris H Wang
• 金额: $ 42.25万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-20 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8213003
• 关键词: Address; Agar; Animal Model; Antibiotic Resistance; Bacteria; Bioremediations; Cell Separation; Chronic; Clinical; Codon Nucleotides; Complex; DNA Microarray Chip; DNA Transposable Elements; Dental caries; Development; Disease; Eczema; Elements; Engineered Gene; Engineering; Ensure; Environment; Escherichia coli; Failure; Food; Future; Gene Expression; Gene Transfer; Genes; Genetic; Genitourinary system; Genome engineering; Genomics; Gnotobiotic; Goals; Health; Horizontal Gene Transfer; Human; Human Microbiome; Human body; In Vitro; Individual; Infection; Kinetics; Lateral; Libraries; Life; Maps; Measures; Metabolism; Metagenomics; Methods; Microbe; Microscopy; Mobile Genetic Elements; Modeling; Monitor; Mus; Names; Natural Selections; Nose; Oral cavity; Organ; Outcome; Pathogenicity; Pharmaceutical Preparations; Probiotics; Production; Proteins; Public Health; Recombinants; Replicon; Reporter; Reporting; Research; Research Project Grants; Skin; Solid; Supplementation; Surface; Synthetic Genes; System; Techniques; Technology; Testing; Therapeutic; Time; Work; base; combat; design; gene synthesis; genetic element; genetic manipulation; genetic selection; gut microbiota; human disease; in vivo; in vivo Model; meetings; member; microbial; microbial community; microbiome; mouse model; new technology; novel therapeutics; prevent; programs; sensor; tool; trait; transcriptomics; transmission process; vector

DESCRIPTION (provided by applicant): The long-term goal of this research is to develop culture-independent strategies to effectively engineer and program the human microbiome in vivo. To this end, the objective of this proposal is to develop an enabling technology platform, named Genome Engineering by Self-Transmissible Replicons (GESTR), to allow the efficient delivery, propagation and expression of exogenous genes in the human microbiota, to characterize the kinetics of gene propagation in the microbiome, and to initially demonstrate the utility of such techniques in engineering the gut microbiota of mice. The specific goals of this work are i) to construct engineered self- transmitting conjugative transposons containing trackable payload genes and characterize their ability to mobilize into different strains typically found in the human gut microbiota; ii) to develop libraries of payload constructs to characterize transcriptional efficiency and codon adaptation for optimal payload gene expression in dominant gut microbes; and iii) to measure gene flow and transmission of exogenous genes by engineered self-mobilizable genetic elements in the gut microbiota of a murine model. Newly developed tools including Multiplex Automated Genome Engineering, de novo DNA-microarray-based gene synthesis, and meta- transcriptomics will be utilized to facilitate the development of this project. The proposed research will provide the first demonstration of key functionality and the development of sufficient new understanding to enable the broader use of this technology platform in future applications. Key questions in the dynamics of transmission and natural selection of laterally shared genes in the human microbiome will also be addressed. Engineering the human microbiome with augmented capabilities to report, prevent and reverse disease states and to modulate the metabolism of foods and drugs promises to be a critical avenue towards transforming human- associated microbes into micro-sensors, miniature protein-production factories, and adaptive bioremediation systems. This technology holds potential for development of clinical therapeutics of common microbial- associated diseases such as those of the gut (e.g. Crohn's, IBD, chronic maldigestion), oral cavity (e.g. dental caries), urogenital tract (e.g. infections, STDs), and skin (e.g. ectopic eczema). PUBLIC HEALTH RELEVANCE: The proposed research project aims to develop foundational technologies to enable the genetic manipulation of microbes that are commonly associated with the human body. These endeavors will facilitate the development of preventative measures and therapeutics to combat microbial-associated human diseases including those of the gut, mouth, nose, skin, and urogenital organs.

描述（由申请人提供）：本研究的长期目标是开发不依赖培养的策略，以有效地设计和编程体内人类微生物组。为此，该提案的目标是开发一种名为自传递复制子基因组工程（GESTR）的技术平台，以允许外源基因在人类微生物群中的有效递送、繁殖和表达，表征微生物群中基因繁殖的动力学，并初步证明此类技术在小鼠肠道微生物群工程中的实用性。这项工作的具体目标是i）构建含有可追踪的有效载荷基因的工程化的自传递接合转座子，并表征它们动员到通常在人肠道微生物群中发现的不同菌株中的能力; ii）开发有效载荷构建体的文库，以表征在优势肠道微生物中最佳有效载荷基因表达的转录效率和密码子适应;和iii）通过鼠模型的肠道微生物群中工程化的可自动员遗传元件测量外源基因的基因流和传递。新开发的工具，包括多重自动基因组工程，从头DNA微阵列为基础的基因合成，和Meta转录组学将被用来促进这个项目的发展。拟议的研究将首次演示关键功能并发展足够的新理解，以使该技术平台能够在未来的应用中更广泛地使用。还将讨论人类微生物组中横向共享基因的传播和自然选择动态中的关键问题。通过增强报告、预防和逆转疾病状态以及调节食物和药物代谢的能力来工程化人类微生物组有望成为将人类相关微生物转化为微传感器、微型蛋白质生产工厂和自适应生物修复系统的关键途径。该技术具有开发常见微生物相关疾病的临床治疗的潜力，所述常见微生物相关疾病例如肠道（例如克罗恩病、IBD、慢性消化不良）、口腔（例如龋齿）、泌尿生殖道（例如感染、STD）和皮肤（例如异位湿疹）的那些。 公共卫生关系：拟议的研究项目旨在开发基础技术，以实现对通常与人体相关的微生物的遗传操作。这些努力将促进预防措施和治疗方法的发展，以对抗微生物相关的人类疾病，包括肠道，口腔，鼻子，皮肤和泌尿生殖器官的疾病。