Discovery of Antibiotics from Soil Microbiomes Using Metagenomics

利用宏基因组学从土壤微生物组中发现抗生素

• 批准号: 9906905
• 负责人: SEAN F BRADY
• 金额: $ 67.8万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-01 至 2022-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9906905
• 关键词: Anabolism; Antibiotics; Bacteria; Bacterial Antibiotic Resistance; Base Sequence; Biological; Biological Assay; Categories; Clinical; DNA Sequence; Drug resistance; Environment; Gene Cluster; Genes; Genome; Harvest; High-Throughput Nucleotide Sequencing; Individual; Infection; Laboratories; Laboratory culture; Lead; Libraries; Metagenomics; Methods; Natural Products; Phenotype; Planet Earth; Protocols documentation; Recording of previous events; Rewards; Sampling; Series; Soil; Source; Structure; Surface; Time; United States; Work; base; clinical development; clinically relevant; combat; cost effective; design; improved; interest; metagenome; microbiome; novel; pathogenic bacteria; screening; small molecule

Project summary: Drug-resistant infections kill more than 65,000 people in the United States per year and the identification of new antibiotics capable of combating antibiotic resistant bacterial pathogens is desperately needed. Bacterial natural products have a long proven history of being good lead structures for the development of clinically useful antibiotics but, unfortunately, the discovery of novel natural products from cultured bacteria has dramatically slowed in recent years. During the same time, the advent of cost effective high-throughput sequencing and an increasingly sophisticated understanding of bacterial secondary metabolite biosynthesis have led to two important revelations with respect to the search for new natural products: first, that the biosynthetic potential of most cultured bacteria, as judged by the number of biosynthetic gene clusters observed in sequenced genomes, is far greater than previously estimated; second, that the number of bacterial species in most environments is at least one hundred times greater than the number of species that is readily cultured. These observations indicate that conventional natural product screening approaches, which rely on laboratory culturing of random bacterial strains from the environment, have not come close to realizing the full biosynthetic potential of the earth's microbiome and that a fundamental change in the approach to bacterial natural products discovery is therefore needed. Consequently, my laboratory has sought to develop methods to allow natural product discovery from environmental samples, without the need for strain isolation and cultivation. The approaches I propose to use to harvest small molecules from metagenomic libraries are divided into two general categories: 1) Sequence-based metagenomics, which relies on DNA sequence similarity to identify clones containing a specific gene of interest and 2) Function-based metagenomics, which relies on the random, unbiased screening of individual eDNA clones in phenotypic assays to identify clones producing bioactive metabolites. Using sequence-based approaches we can interrogate metagenomes for novel gene clusters (i.e., new antibiotics), as well as clusters that encode congeners of clinically relevant natural product (i.e., improve the utility of clinically important classes of antibiotics). Our functional screening studies will focus on developing methods for creating metagenomic libraries that are enriched in natural product gene clusters to facilitate more efficient screening for novel antibiotics. For this proposal, we will use our existing pipelines and improved protocols, as they come on-line, to identify novel natural products with improved activities against antibiotic resistant bacterial pathogens. We have undoubtedly just begun to scratch the surface of what lies hidden in the genomes of environmental bacteria. The work here will greatly increase access to the natural products that remain hidden in the environment and ultimately yield a series of novel natural antibiotics with the potential to better treat antibiotic resistant bacterial pathogens. !

耐药性感染每年在美国造成超过65，000人死亡， 能够对抗抗生素抗性细菌病原体的新抗生素的鉴定迫切需要 needed.细菌天然产物具有长期被证明是用于微生物的良好先导结构的历史。 开发临床有用的抗生素，但不幸的是，发现新的天然产物， 近年来，培养细菌的速度急剧下降。与此同时，成本效益的出现 高通量测序和对细菌次级代谢产物日益复杂的理解 生物合成导致了关于寻找新的天然产物的两个重要启示：首先， 大多数培养细菌的生物合成潜力，根据生物合成基因簇的数量来判断， 在测序的基因组中观察到的，远远大于先前的估计;第二，细菌的数量 在大多数环境中，物种的数量至少是容易找到的物种数量的一百倍。 有教养这些观察结果表明，传统的天然产品筛选方法依赖于 从环境中随机细菌菌株的实验室培养，还没有接近实现全面的 地球微生物组的生物合成潜力，以及细菌生物合成方法的根本变化， 因此，需要发现天然产物。因此，我的实验室一直在寻找方法 允许从环境样品中发现天然产物，而不需要菌株分离， 修为我建议从宏基因组文库中收获小分子的方法是 分为两大类：1）基于序列的宏基因组学，它依赖于DNA序列 与识别包含特定感兴趣基因的克隆的相似性，以及2）基于功能的宏基因组学，其 依赖于在表型分析中对单个eDNA克隆进行随机、无偏筛选来鉴定克隆 产生生物活性代谢物。使用基于序列的方法，我们可以询问宏基因组， 新的基因簇（即，新抗生素），以及编码临床相关抗生素同源物的簇 天然产物（即，提高临床上重要类别的抗生素的效用）。我们的功能筛选 研究将集中于开发用于创建富含天然高分子的宏基因组文库的方法。 产生基因簇，以促进更有效地筛选新型抗生素。对于本提案，我们将使用 我们现有的管道和改进的协议，因为他们上线，以确定新的天然产品， 提高了对抗生素抗性细菌病原体的活性。毫无疑问，我们才刚刚开始 隐藏在环境细菌基因组中的表面。这里的工作量将大大增加 获取隐藏在环境中的天然产物，并最终产生一系列新颖的 天然抗生素具有更好地治疗抗生素耐药性细菌病原体的潜力。 !