Symbiosis of E. coli and the Intestinal Microbiota in a Mouse Model

小鼠模型中大肠杆菌与肠道微生物群的共生

• 批准号: 8015175
• 负责人: TYRRELL CONWAY
• 金额: $ 38.58万
• 依托单位: UNIVERSITY OF OKLAHOMA
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-01-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8015175
• 关键词: Ablation; Address; Affect; Anaerobic Bacteria; Anaerobiosis; Animal Model; Attention; Bacterial Adhesins; Bacteroidetes; Cecum; Cells; Coculture Techniques; Communities; Complex; Coupled; Dietary Fiber; Digestion; Disease Resistance; Dissection; Ecosystem; Escherichia coli; Exhibits; Flagella; Fluorescent in Situ Hybridization; Food Webs; Foundations; Genetic; Genomics; Goals; Gram-Negative Bacteria; Growth; Health; Host resistance; Human; Human Microbiome; Image; In Situ; Individual; Intestines; K antigen; Kinetics; Lasers; Learning; Life; Lipopolysaccharides; Mass Spectrum Analysis; Measures; Metabolic; Metabolism; Microbe; Microscopic; Modeling; Molecular; Mucous body substance; Mus; Nutrient; Nutritional; Nutritional Study; O Antigens; Oklahoma; Organism; Oxygen; Oxygen measurement, partial pressure, arterial; Pathway interactions; Pattern; Phylogenetic Analysis; Phylogeny; Play; Polysaccharides; Population; Process; Property; Research; Research Design; Resources; Role; Sampling; Source; Specific qualifier value; Streptomycin; Structure; Surface; Surface Properties; Symbiosis; Techniques; Testing; Universities; bacterial H antigen; base; capsule; design; feeding; fitness; instrumentation; member; metabolomics; microbial; microbial community; microorganism; mouse model; new technology; novel; programs; rRNA Genes; research study; success; sugar; tool; trait

DESCRIPTION (provided by applicant): The microbial community composition of the human intestine is receiving a lot of attention and now is fairly well characterized. Yet the functional roles of individual microorganisms in the intestinal ecosystem and the dynamic interactions of its community members remain largely uncharacterized, including those interactions that drive competition for resources (i.e., the food web) and those that create conditions favorable for success of the community (e.g., anaerobiosis). Experiments that address these issues cannot be done in humans; they require an animal model that allows testing of the basic ecological principles that underpin the human microbiome. For over a decade, we have used the streptomycin-treated mouse model of intestinal colonization to characterize the functional role of Escherichia coli in the intestine. We learned that different E. coli strains execute different nutritional programs, allowing them to co-colonize the gut. Importantly, we learned that E. coli respires oxygen and thereby lowers the oxygen tension of the cecum, creating conditions that favor growth of the predominantly anaerobic microbial community. Therefore, we hypothesize that E. coli lives in symbiotic relationship with the anaerobes. Since anaerobes are sensitive to oxygen, we predict that the community composition of the intestine depends at least in part on the oxygen scavenging function contributed by E. coli. Since E. coli is unable to hydrolyze complex polysaccharides, which are the primary nutrient source in the gut, and because E. coli can grow only on the degradation products, we predict that anaerobic polysaccharide degradation releases simple sugars that cross-feed E. coli. And, since different E. coli strains execute different nutritional programs in the intestine, we predict that each E. coli strain will interact with distinct subpopulations of the microbial community. Here we outline a Research Plan designed to test these predictions. In Aim 1 we will use high-throughput sequencing of 16S rRNA gene tags and molecular phylogenetic analysis to examine the microbial composition of the streptomycin-treated mouse intestine as it is affected by E. coli colonization. Using isogenic E. coli strains that can and cannot respire oxygen, we will test the prediction that oxygen scavenging in the intestine affects the composition of the anaerobic microbial community. In addition, we will test the prediction that colonization of the intestine with different strains of E. coli, each of which consumes different nutrients in the intestine, will influence the microbial community composition. In Aim 2 we will test the prediction that different E. coli strains physically associate with different members of the microbial community by using 16S analysis of microbes sampled from the intestine by laser capture micro-dissection. Furthermore, we will characterize nutrient flow between E. coli and individual members of the intestinal microbial community in co-cultures. In Aim 3 we wil determine whether surface structures, including O-polysaccharides, flagella, and capsule, target E. coli to specific microhabitats where they could interact with different members of the microbiota. Thus we will characterize the interactions of E. coli with the microbial community in the intestine. PUBLIC HEALTH RELEVANCE: We will use a mouse model of intestinal colonization to explore and characterize the symbiotic relationship in which we hypothesize that E. coli generates anaerobic conditions to stimulate growth of anaerobes that degrade complex polysaccharides, which in turn release simple sugars that cross-feed E. coli. We will use the tools of genomics to determine the microbial community composition as it is impacted by scavenging of oxygen by E. coli and, in addition, we will couple the community analysis with sophisticated microscopic techniques to determine the specific organisms that E. coli physically associates with in the intestine and we will determine nutrient flow between these organisms in co-culture experiments. Our research represents an unprecedented step forward in the effort to characterize the functional roles of individual microbes in the human microbiome.

描述(申请人提供)：人体肠道的微生物群落组成受到了很大的关注，现在已经有了相当好的特征。然而，单个微生物在肠道生态系统中的功能作用及其群落成员的动态相互作用在很大程度上仍未确定，包括那些推动资源竞争的相互作用(即食物网)和那些为群落的成功创造有利条件的相互作用(例如厌氧)。解决这些问题的实验不能在人类身上进行；它们需要一种动物模型，允许测试支撑人类微生物组的基本生态原理。十多年来，我们一直使用链霉素处理的小鼠肠道定植模型来表征大肠杆菌在肠道中的功能作用。我们了解到，不同的大肠杆菌菌株执行不同的营养程序，使它们能够在肠道中共同定居。重要的是，我们了解到大肠杆菌呼吸氧气，从而降低盲肠的氧分压，创造有利于以厌氧为主的微生物群落生长的条件。因此，我们假设大肠杆菌与厌氧菌存在共生关系。由于厌氧菌对氧气很敏感，我们预测肠道的群落组成至少部分取决于大肠杆菌的氧气清除功能。由于大肠杆菌不能降解复杂的多糖，而复杂的多糖是肠道的主要营养来源，而且由于大肠杆菌只能在降解产物上生长，我们预测厌氧多糖降解会释放出与大肠杆菌交叉喂养的单糖。而且，由于不同的大肠杆菌菌株在肠道中执行不同的营养程序，我们预测每个大肠杆菌菌株将与微生物群落的不同亚群相互作用。在这里，我们概述了一项旨在测试这些预测的研究计划。在目标1中，我们将使用16S rRNA基因标签的高通量测序和分子系统发育分析来检测链霉素处理的小鼠肠道的微生物组成，因为它受到大肠杆菌定植的影响。使用可以和不能呼吸氧气的同基因大肠杆菌菌株，我们将测试肠道清除氧气会影响厌氧微生物群落组成的预测。此外，我们将测试不同菌株在肠道的定植预测，每种菌株在肠道中消耗不同的营养物质，将影响微生物群落组成。在目标2中，我们将通过使用激光捕获显微解剖从肠道采样的微生物的16S分析来测试不同的大肠杆菌菌株与微生物群落的不同成员之间的物理联系的预测。此外，我们将描述在共培养中，大肠杆菌和肠道微生物群落的个别成员之间的营养流动。在目标3中，我们将确定包括O-多糖、鞭毛和胶囊在内的表面结构是否针对特定的微生境，在那里它们可以与微生物区系的不同成员相互作用。因此，我们将描述大肠杆菌与肠道微生物群落的相互作用。 公共卫生相关性：我们将使用肠道定植的小鼠模型来探索和表征共生关系，在这种共生关系中，我们假设大肠杆菌产生厌氧条件来刺激厌氧菌的生长，厌氧菌降解复杂的多糖，而厌氧菌又释放与大肠杆菌交叉喂养的单糖。我们将使用基因组学工具来确定微生物群落组成，因为它受到大肠杆菌清除氧气的影响，此外，我们将把群落分析与复杂的显微技术结合起来，以确定大肠杆菌在肠道中与哪些特定生物物理相关，我们将在共培养实验中确定这些微生物之间的营养流动。我们的研究代表着在确定单个微生物在人类微生物群中的功能作用方面向前迈出了前所未有的一步。