Functional Analysis of a Digestive-Tract Microbiome During Dietary Changes

饮食变化期间消化道微生物组的功能分析

• 批准号: 8197896
• 负责人: JOERG GRAF
• 金额: $ 36.76万
• 依托单位: UNIVERSITY OF CONNECTICUT STORRS
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-12-01 至 2014-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8197896
• 关键词: Address; Adolescent; Aeromonas; Affect; Albumins; Alleles; Amaze; Animals; Bacteria; Biochemical Process; Blood; Cell Separation; Cells; Clostridium; Communities; Complex; Cytolysis; Data; Diet; Flow Cytometry; Food; Functional RNA; Gastrointestinal tract structure; Gene Expression; Gene Expression Profile; Genes; Genetic; Genome; Human; Human Microbiome; Individual; Lectin; Leeches; Location; Mammals; Measures; Metabolic; Metabolism; Microelectrodes; Minor; Molecular; Monitor; Mucins; Nutrient; Oxidants; Personal Satisfaction; Phase; Physiology; Population; Population Heterogeneity; Reporter Genes; Ribosomal RNA; Solutions; Sorting - Cell Movement; Source; Structure; System; Techniques; Technology; Time; Volatile Fatty Acids; Work; animal data; hatching; improved; insight; mature animal; member; microbial community; microbiome; next generation; public health relevance; sugar; tool

DESCRIPTION (provided by applicant): In humans, the digestive-tract microbiota is a complex community composed out of hundreds of species. This microbiome provides humans with an amazing repertoire of biochemical processes that far exceed those encoded by the animal's genome. As an animal matures or switches diets the microbiome can change in composition. How this change affects the overall physiology of the microbiome and its contribution to the host is poorly understood. The information gained from the Human Microbiome Project has produced a wealth of genome information and is providing insight into possible functions, but functional data from animals with their native microbiome are lacking. The sheer complexity of the microbiome has hindered identifying the genes that the microbiome expresses, the metatranscriptome. This application investigates a naturally occurring simple microbiome that resides in the digestive tract of the medicinal leech. Two bacteria dominate the microbial community and for one genetic tools are available. The composition of the microbiome changes during the first two weeks after the leeches hatch from the cocoon and also after they consume a blood meal. If the blood was partially lysed, a Clostridium species that is minor member of the microbiome became very abundant. Massively parallel sequencing will be used to monitor changes in the composition and in the metatranscriptome of the microbiome as the animals mature and change diet. This will be confirmed using qPCR and qRT-PCR, respectively. This analysis allows one to determine if under specific conditions a particular allele or strain is more abundant. Using gfp-fusions, the exact location of the cells expressing the genes will be determined. Environmental parameter such as electron acceptors, sugars and short chained fatty acids will be measured. Because the bacteria are present both in pelagic and microcolony phases, compare niche specific gene expression can be determined by using Illumina sequencing of FACS sorted cells. This work will determine new principles using a simple system that are applicable to the more complex human system and apply technologies that will become more feasible to use in highly complex systems as the sequencing throughput and computational power increase. PUBLIC HEALTH RELEVANCE: The digestive-tract microbiome is essential for the well-being of humans, but the complexity of the community has hindered a direct assessment of its function. In this application, we utilize a naturally occurring, simple microbiome to establish techniques that identify the transcriptomes of the microbiome and allow one to elucidate its functions as it changes in composition of subpopulations occupying different niches.

描述（由申请人提供）：在人类中，消化道微生物群是一个由数百个物种组成的复杂群落。这种微生物组为人类提供了一系列令人惊叹的生化过程，远远超过了动物基因组编码的过程。当动物成熟或改变饮食时，微生物组的组成可能会发生变化。这种变化如何影响微生物组的整体生理学及其对宿主的贡献尚不清楚。从人类微生物组项目获得的信息产生了丰富的基因组信息，并提供了对可能功能的深入了解，但缺乏来自具有天然微生物组的动物的功能数据。微生物组的复杂性阻碍了微生物组表达的基因（元转录组）的识别。该应用研究了存在于药用水蛭消化道中的天然存在的简单微生物组。两种细菌在微生物群落中占主导地位，其中一种细菌是可用的遗传工具。水蛭从茧中孵化后的前两周以及吸食血粉后，微生物组的组成会发生变化。如果血液被部分溶解，作为微生物组次要成员的梭状芽胞杆菌物种就会变得非常丰富。随着动物成熟和饮食改变，大规模并行测序将用于监测微生物组的组成和宏转录组的变化。这将分别使用 qPCR 和 qRT-PCR 进行确认。该分析允许人们确定在特定条件下特定等位基因或菌株是否更丰富。使用 gfp 融合，将确定表达基因的细胞的确切位置。将测量电子受体、糖和短链脂肪酸等环境参数。由于细菌同时存在于中上层和小菌落阶段，因此可以通过使用 FACS 分选细胞的 Illumina 测序来确定比较生态位特异性基因表达。这项工作将使用一个简单的系统来确定适用于更复杂的人类系统的新原理，并应用随着测序通量和计算能力的增加而在高度复杂的系统中使用变得更加可行的技术。 公共卫生相关性：消化道微生物群对于人类的福祉至关重要，但群落的复杂性阻碍了对其功能的直接评估。在这一应用中，我们利用一种天然存在的简单微生物组来建立识别微生物组转录组的技术，并允许人们阐明其在占据不同生态位的亚群组成发生变化时的功能。