Metabolic Syntrophy Between Human Gut Bacteria and Archaea

人类肠道细菌和古细菌之间的代谢协同

• 批准号: 10016363
• 负责人: Nicole R Buan
• 金额: $ 16.12万
• 依托单位: UNIVERSITY OF NEBRASKA LINCOLN
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2021-09-13
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10016363
• 关键词: Acetates; Affect; Anaerobic Bacteria; Anorexia; Archaea; Bacteria; Bacteroides; Bacteroides thetaiotaomicron; Biological Models; Carbohydrates; Carbon; Carbon Dioxide; Cecum; Cells; Chemicals; Citrobacter rodentium; Clinical Data; Coculture Techniques; Colorectal Cancer; Communicable Diseases; Communication; Complement; Complex; Consumption; Crohn' s disease; Data; Data Set; Diet; Dietary Carbohydrates; Digestive System Disorders; Disease; Diverticulosis; Fluorescence Microscopy; Food; Formulation; Gases; Genes; Genetic; Genetic Transcription; Goals; Growth; Habitats; Health; Human; Hydrogen; Intestines; Laboratories; Lead; Measures; Metabolic; Metabolism; Methane; Methanobrevibacter; Microbe; Microbiological Techniques; Modeling; Molecular; Morbidity - disease rate; Mus; Nebraska; Nutritional; Nutritional Requirements; Obesity; Optics; Organism; Outcome; Outcomes Research; Physiological; Population; Population Study; Probiotics; RNA; Research; Signal Transduction; Source; Surveys; System; Technology; Testing; Transcript; Waste Products; Work; base; biochemical tools; carbohydrate metabolism; dietary guidelines; experimental study; gastrointestinal epithelium; genetic manipulation; gut bacteria; gut microbes; gut microbiota; human disease; improved; in silico; innovation; insight; metabolomics; microbial; microbial community; microbiome; mouse model; next generation sequencing; novel; pathogen; predictive modeling; prevent; resilience; small molecule; transcriptome sequencing; transcriptomics

ABSTRACT The goal of the proposed research is to identify molecular metabolic signals of microbial syntrophy in the human gut, with the long-term goal of developing a predictive model relating host diet to healthy gut microbiota resiliency. Specifically, the research in the project leader's laboratory aims to identify and characterize the physiological function of metabolites and genes produced by human symbiotes Bacteroides thetaiotaomicron (B. theta), a bacterium, and Methanobrevibacter smithii (M. smithii), a methane-producing archaeon, in a novel co-culture system. B. theta and M. smithii are the dominant bacterium and archaeon in the human gut, respectively; their metabolisms are interdependent; and both are known to associate with gut epithelia. Perturbation of Bacteroides and/or Methanobrevibacter populations is associated with obesity, anorexia, irritable bowel disease, Crohn's disease, colorectal cancer, and diverticulosis. For these reasons, the project leader hypothesizes that metabolic syntrophy between both organisms is essential for healthy gut function and diet or pathogen challenge disrupts syntrophy, leading to digestive disorders and infectious disease. Three specific aims are proposed to test this hypothesis using a novel co-culture system. In Specific Aim 1, the project leader will optimize a B. theta/M. smithii co-culture system. Specifically, she will use anaerobic microbiology techniques to define the nutritional requirements of a syntrophic continuous co-culture in a chemostat and test nutritional enhancements under conditions encountered in the human gut. She will also use optical and confocal fluorescence microscopy to study the spatial organization (planktonic or associated in aggregates) of both organisms in co-culture. In Specific Aim 2, the project leader will create an integrated metabolic model of co-culture syntrophy based on metabolomic and transcriptomic data. Specifically, she will use next-generation sequencing technology (RNAseq) to identify gene transcripts upregulated by both organisms in syntrophic co-culture to improve accuracy of the metabolic system models. The system model will be validated with global and targeted metabolomics data. The refined system model, integrating transcriptomic and metabolomics datasets, will be used to predict how pathogen challenge affects syntrophic B.theta/M.smithii metabolism. Finally, in Specific Aim 3, the project leader will test co-culture resiliency to pathogen challenge. She will measure the metabolic and transcriptional changes that occur in the co-culture system when challenged by the mouse gut pathogen enterohemorrhagic Citrobacter rodentium. These experiments will be used to further refine and test the system model generated in Specific Aim 2. The innovative outcome of this research will be the demonstration that B. theta and M. smithiii in co-culture communicate through the two-way exchange of small molecule metabolites. Addition of a pathogen is expected to disrupt this communication system. This work is highly significant in that it will demonstrate syntrophy between common gut microbes that contribute to human health and disease.

摘要 这项研究的目的是确定微生物合成营养的分子代谢信号， 人类肠道，长期目标是开发一种将宿主饮食与健康肠道微生物群相关联的预测模型 恢复力具体而言，项目负责人实验室的研究旨在确定和表征 多形拟杆菌代谢产物和基因的生理功能 （B. theta）、细菌和史氏甲烷短杆菌（Methanobrevibacter smithii）（M. smithii），一种产生甲烷的古细菌，在一部小说中， 共培养体系。B。theta和M. Smithii是人类肠道中的优势细菌和古细菌， 它们的代谢是相互依赖的;并且已知两者都与肠上皮细胞相关。 拟杆菌和/或甲烷短杆菌种群的扰动与肥胖、厌食、 肠易激综合征、克罗恩病、结肠直肠癌和憩室病。由于这些原因，该项目 Leader假设，两种生物体之间的代谢互养对于健康的肠道功能至关重要， 饮食或病原体挑战破坏了合成营养，导致消化系统疾病和传染病。三 提出了具体的目标，以测试这一假设，使用一种新的共培养系统。具体目标1： 项目负责人将优化一个B。θ/M。Smithii共培养系统。具体来说，她会使用厌氧 微生物学技术，以确定营养需求的互养连续共培养， 恒化器和测试在人类肠道中遇到的条件下的营养增强。她还将使用 光学和共聚焦荧光显微镜来研究空间组织（在光学和共聚焦荧光显微镜中， 聚集体）。在具体目标2中，项目负责人将创建一个集成的 基于代谢组学和转录组学数据的共培养合成营养的代谢模型。具体来说，她将 使用下一代测序技术（RNAseq）来鉴定由两种基因上调的基因转录本。 在互养共培养物中的生物体，以提高代谢系统模型的准确性。该系统模型将 通过全球和目标代谢组学数据进行验证。完善的系统模型，整合了转录组学 和代谢组学数据集，将用于预测病原体挑战如何影响互养 B.theta/史氏甲烷短杆菌代谢。最后，在具体目标3中，项目负责人将测试共文化弹性， 病原体挑战她将测量共培养中发生的代谢和转录变化 系统时，由小鼠肠道病原体肠出血性柠檬酸杆菌啮齿类挑战。这些 实验将被用来进一步完善和测试在具体目标2中生成的系统模型。的 本研究的创新性成果将证明B. theta和M. Smithiii共培养 通过小分子代谢物的双向交换进行交流。添加病原体是 会破坏这个通讯系统这项工作意义重大，因为它将证明 共同的肠道微生物之间的合成营养有助于人类健康和疾病。