Biological validation of phage host-range identified by proximity guided metagenomics

通过邻近引导宏基因组学鉴定噬菌体宿主范围的生物学验证

• 批准号: 10761394
• 负责人: Ivan Liachko
• 金额: $ 29.91万
• 依托单位: PHASE GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10761394
• 关键词: Affect; Amendment; Bacteria; Bacteriophages; Benchmarking; Bioinformatics; Biological; Clinical; Communicable Diseases; Communities; Complex; Confidence Intervals; Culture-independent methods; Data; Data Set; Detection; Development; Disease; Environment; Filtration; Genome; Genomics; High-Throughput Nucleotide Sequencing; Infection; Investments; Ligation; Machine Learning; Measures; Metagenomics; Methods; Nature; Performance; Phase; Predictive Value; Process; Research; Sampling; Sensitivity and Specificity; Small Business Innovation Research Grant; Specificity; Speed; Techniques; Technology; Testing; Therapeutic; Therapeutic Studies; Translating; Validation; Virus; clinical application; clinical development; cost; crosslink; experimental study; fecal microbiome; fecal microbiota; gut dysbiosis; gut microbiome; human disease; improved; in vivo; microbial community; microbial disease; microbiome; microbiota; microorganism; novel therapeutics; pathogenic bacteria; preclinical development; research and development; timeline; tool; virtual

Abstract Phages are viruses that infect bacteria and have the potential to be used as a clinical tool for treating infectious diseases and gut microbiome-related disorders. Understanding phage-host interactions can improve the ability to use phages as a treatment option, and potentially lead to the development of new therapies. However, current methods for studying these interactions are low-throughput and culture-based, limiting progress in phage therapy research. Proximity ligation sequencing, which uses in vivo crosslinking between phage and host genomes, is a high-throughput sequencing tool which can be used to read out these associations. However, no rigorous experimental validation has yet been performed to verify these interactions, nor to characterize the analytical performance of this approach. The objective of this project is to establish proximity ligation sequencing as a reliable scientific tool for studying phage-host associations. We propose to use a combination of gold-standard microbiological methods and advanced sequencing tools to rigorously validate and define the performance of proximity ligation sequencing for studying phage-host interactions. We will determine the sensitivity and specificity of proximity ligation sequencing using both defined microbial communities and natural fecal microbiome communities. In addition, we will estimate the positive predictive value of proximity ligation-identified phage-host associations in complex microbial communities using phage isolation techniques. These experiments will provide key statistical parameters of reliability, unlocking a high-throughput, culture-independent method of characterizing phage-host interactions. This approach would enable new avenues in phage-based applications, including the development of phage-based therapies for infectious disease, gut dysbiosis, and the targeted manipulation of microbiomes.

抽象的 噬菌体是感染细菌的病毒，有潜力用作治疗感染性的临床工具 疾病和肠道微生物组相关疾病。了解噬菌体与宿主的相互作用可以提高能力 使用噬菌体作为治疗选择，并可能导致新疗法的开发。然而， 目前研究这些相互作用的方法是低通量和基于文化的，限制了研究进展 噬菌体治疗研究。邻近连接测序，利用噬菌体和噬菌体之间的体内交联 宿主基因组是一种高通量测序工具，可用于读出这些关联。 然而，尚未进行严格的实验验证来验证这些相互作用，也没有进行 描述该方法的分析性能。 该项目的目标是建立邻近连接测序作为研究的可靠科学工具 噬菌体-宿主关联。我们建议结合使用金标准微生物方法和 先进的测序工具可严格验证和定义邻近连接测序的性能 用于研究噬菌体-宿主相互作用。我们将确定邻近连接的敏感性和特异性 使用定义的微生物群落和天然粪便微生物群落进行测序。此外， 我们将估计复杂的邻近连接鉴定的噬菌体-宿主关联的阳性预测值 使用噬菌体分离技术的微生物群落。这些实验将提供关键的统计数据 可靠性参数，解锁一种高通量、独立于培养物的噬菌体宿主表征方法 互动。这种方法将为基于噬菌体的应用开辟新途径，包括 开发基于噬菌体的传染病、肠道菌群失调疗法以及靶向操纵 微生物组。