Fecal Phage: Exposing Unknown in the Dark Matter of the Human Gut

粪便噬菌体：暴露人类肠道暗物质中的未知物质

• 批准号: 8532486
• 负责人: FOREST L ROHWER
• 金额: $ 38.17万
• 依托单位: SAN DIEGO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-23 至 2014-08-22
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8532486
• 关键词: Address; Affect; Amino Acid Sequence; Antibiotic Resistance; Back; Bacteria; Bacterial Genes; Bacteriophages; Biodiversity; Bioinformatics; Biological; Biological Assay; Biological Neural Networks; Biological Process; Capsid Proteins; Cells; Cholera Toxin; Communities; Computer Simulation; Crohn' s disease; DNA Sequence; Data; Digestion; Employee Strikes; Escherichia coli; Family; Family health status; Gastrointestinal tract structure; Genbank; Genes; Genetic; Genetic Variation; Goals; Health; Homologous Gene; Human; Hypersensitivity; Immune System Diseases; Immunity; Individual; Insulin-Dependent Diabetes Mellitus; Knowledge; Light; Link; MHC Class II Genes; Mass Spectrum Analysis; Metabolic; Metabolic Diseases; Metabolism; Metagenomics; Methods; Mothers; Nature; Obesity; Oceans; Open Reading Frames; Pathogenicity; Peptide Sequence Determination; Persons; Phenotype; Population; Proteins; Proteomics; Publishing; Reading; Research; Research Project Grants; Sampling; Sequence Homology; Structural Genes; Structural Protein; Structure; Techniques; Time; Training; Twin Multiple Birth; Variant; Viral; Viral Genes; Viral Genome; Viral Packaging; Viral Physiology; Virion; Virus; analog; base; gene function; human data; immune function; improved; metagenome; metagenomic sequencing; microbial community; novel; programs; protein aminoacid sequence; research study; trait; virome

DESCRIPTION (provided by applicant): Viruses are the most abundant, most diverse, and least understood biological entities on Earth. Humans contain at least several trillion viruses, largely phage (bacteriophage) infecting the bacteria in the gastrointestinal tract. Because viruses use their host cells to reproduce, they can impact the host populations. Gut phage possess genes which are integral to the biological functions of both their bacterial hosts and the humans they inhabit. While they potentially affect digestion, pathogenicity and immune function, currently, very little is known about this critical community. The goal of this research project isto develop novel high- throughput methods to rapidly reveal and characterize the diversity of this biological "dark matter." In the preliminary study of fecal viral communities from four pairs of twins and their mothers, we showed that 80% of viral genomes have little similarity to known sequences. Viral genes evolve rapidly, making homology- based searches for sequence function difficult. The focus of our research will be to characterize this unknown community using existing techniques, including the elucidation of the phenotype and structure of 100 unknown viral genes. In Aim 1, the genetic and functional diversity of the viral metagenomes will be characterized. Viral genes which are present in multiple people or stable through time will be examined, with a focus on those which are likely to have metabolic functions affecting the host. In Aim 2 proteomics of samples enriched for viral capsid and structural proteins will be used to link those protein sequences with the DNA sequences, and artificial neural networks will be used to search for similar sequences in the metagenomes. Aim 3 focuses on characterizing the function of metabolic genes that may affect the host. The 100 selected sequences will be expressed in E. coli, their effect on phenotype will be assayed with metabolic arrays and mass spectrometry of metabolites, and their 3D crystal structures will be determined in order to search for structural homology rather than sequence homology. The link between the presence of a predicted metabolic gene and human host health traits, such as obesity, will be evaluated. Combined, these approaches will greatly increase our knowledge of the nature of these unexplored viral communities. An understanding of uncharacterized viral gene function in the human gut will not only shed light on the twin- and-mother communities we are studying directly, it will also address questions about the known correlations between human health and gut viruses. This research will likely improve our fundamental understanding of the interactions of viruses, bacteria, human metabolism and immunity. Discoveries related to the progression of auto-immune diseases, metabolic disorders, allergies and many other conditions may become possible.

描述（由申请人提供）：病毒是地球上最丰富、最多样化且最不为人所知的生物实体。人类体内至少含有数万亿病毒，其中大部分是感染胃肠道细菌的噬菌体（噬菌体）。由于病毒利用宿主细胞进行繁殖，因此它们会影响宿主群体。肠道噬菌体拥有对其细菌宿主及其所居住的人类的生物功能不可或缺的基因。虽然它们可能影响消化、致病性和免疫功能，但目前，人们对这个关键群落知之甚少。该研究项目的目标是开发新颖的高通量方法来快速揭示和表征这种生物“暗物质”的多样性。在对四对双胞胎及其母亲的粪便病毒群落的初步研究中，我们发现 80% 的病毒基因组与已知序列几乎没有相似性。病毒基因快速进化，使得基于同源性的序列功能搜索变得困难。我们研究的重点将是利用现有技术来表征这个未知的群落，包括阐明 100 个未知病毒基因的表型和结构。在目标 1 中，将表征病毒宏基因组的遗传和功能多样性。将检查存在于多人体内或随时间稳定的病毒基因，重点关注那些可能具有影响宿主代谢功能的病毒基因。在目标 2 中，富含病毒衣壳和结构蛋白的样品的蛋白质组学将用于将这些蛋白质序列与 DNA 序列连接起来，人工神经网络将用于搜索宏基因组中的相似序列。目标 3 侧重于表征可能影响宿主的代谢基因的功能。 100个选定的序列将在大肠杆菌中表达，通过代谢阵列和代谢物质谱分析它们对表型的影响，并确定它们的3D晶体结构，以寻找结构同源性而不是序列同源性。将评估预测代谢基因的存在与人类宿主健康特征（例如肥胖）之间的联系。结合起来，这些方法将极大地增加我们对这些未经探索的病毒群落性质的了解。了解人类肠道中未表征的病毒基因功能不仅可以揭示我们正在直接研究的双胞胎和母亲群体，还可以解决有关人类健康与肠道病毒之间已知相关性的问题。这项研究可能会提高我们对病毒、细菌、人体新陈代谢和免疫相互作用的基本了解。与自身免疫性疾病、代谢紊乱、过敏和许多其他疾病的进展相关的发现可能成为可能。