Microbial Ecology of the Zebrafish Intestine

斑马鱼肠道的微生物生态学

• 批准号: 8204620
• 负责人: Brendan Bohannan
• 金额: $ 34.83万
• 依托单位: UNIVERSITY OF OREGON
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-12-06 至 2014-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8204620
• 关键词: Address; Animals; Antibiotics; Bacteria; Cells; Communities; Complex; Defect; Development; Diabetes Mellitus; Diet; Digestive Physiology; Ecology; Environment; Fertility; Fertilization; Fishes; Gastrointestinal Diseases; Gastrointestinal tract structure; Genetic; Germ-Free; Gnotobiotic; Goals; Health; Human; Human Pathology; Image; Immune system; Individual; Inflammatory Bowel Diseases; Integration Host Factors; Intestines; Investigation; Knowledge; Larva; Life; Methods; Microbe; Microbial Taxonomy; Modeling; Monitor; Pattern; Play; Population; Probiotics; Relative (related person); Role; Sampling; Side; Staging; Standardization; Sterility; Stochastic Processes; Structure; Testing; Therapeutic; Time; Vaccinated; Vertebrates; Zebrafish; animal ecology; design; fitness; germ free condition; gut microbiota; in vivo; insight; member; microbial; microbial colonization; microbial community; microorganism; mutant; nutrition; prebiotics; pressure; prevent; public health relevance; research study; success; theories

DESCRIPTION (provided by applicant): All animals exist in intimate associations with communities of microorganisms, which play important roles in animal development and fitness. The most numerically abundant microbial communities associated with vertebrate animals are the assemblages of microbes in the gut, or the gut microbiota. The mechanisms by which animal-associated microbial communities assemble and persist inside the host are poorly understood. Fundamental unanswered questions about the ecology of animal-associated microbial communities include the extent to which these communities are assembled by host selection or by stochastic processes. If host selection is important, what mechanisms by which this selection occurs? Do selective forces change as a function of host developmental stage? Do the host selective pressures that influence community assembly also contribute to community robustness? An understanding of the assembly principles of these communities is essential for beginning to design therapeutic strategies for humans to safely and effectively promote beneficial microbial communities and prevent or correct pathogenic ones. We propose to apply ecological theory and modeling to understand the assembly and persistence of the gut microbiota in the model vertebrate zebrafish. We have established methods to rear zebrafish under sterile conditions ("germ-free") and associate them with defined microbial communities. The zebrafish offers many advantages for these studies. Their fecundity and rapid development allows us to rear thousands of germ-free individuals at a time and design experiments with a high degree of replication. The genetic tractability of zebrafish and their associated bacteria, permit experimental manipulation of host-microbiota associations from both sides of the interaction. The transparency of developing zebrafish allows us to monitor bacterial colonization of the gut in live animals and study spatial and temporal patterns of gut microbiota assembly. An overarching goal of this proposal is to advance the germ-free zebrafish model, through the improvement and standardization of germ-free nutrition and husbandry, and the development of defined zebrafish-associated microbial communities for reductionist analyses, such that this model can become widely used by microbial ecologists and developmental geneticists to study the dynamics of animal-associated microbial communities. In Aim 1, we propose to use ecological theory to calculate the relative importance of host selection and stochastic processes in the assembly of the zebrafish gut microbiota. We will ask whether host selection varies as a function of host developmental stage and microbial taxonomy. In Aim 2, we will determine the relative importance of diet and the immune system in host selection of the zebrafish microbiota. To address the role of diet, we will investigate gut microbiota assembly in fish reared on different diets. To address the role of the immune system, we will analyze gut microbiota assembly in zebrafish mutants with defect innate or adaptive immune systems, and in hosts vaccinated against members of their gut microbiota. In Aim 3 we will investigate the mechanisms that underlie host selection. We will use defined microbial communities to determine the size of the initial colonizing population. We will use in vivo imaging to examine the spatial and temporal patterns of gut colonization. Finally we will determine how diet and immune system contribute to community robustness by monitoring invasion of established microbiota as a function of these host factors. Collectively these studies will provide a deeper mechanistic understanding of how host- associated microbial communities are established and sustained. Such knowledge is essential for the rational design of prebiotics, probiotics, and antibiotics to treat human pathologies associated with imbalances of the microbiota such as inflammatory bowel diseases and diabetes. PUBLIC HEALTH RELEVANCE: The human gastrointestinal tract is colonized by approximately ten trillion microbial cells. This complex microbial community is important for normal human health and digestive physiology and is disrupted in many gastrointestinal disorders such as inflammatory bowel disease. The proposed experiments will provide new insights into the factors that direct the assembly and persistence of the gut microbial community. Such knowledge will advance the design of therapeutic strategies for humans to safely and effectively promote beneficial microbial communities and prevent or correct pathogenic ones.

描述(申请人提供)：所有动物都与微生物群落密切相关，微生物群落对动物的发育和健康起着重要作用。与脊椎动物相关的数量最丰富的微生物群落是肠道中的微生物组合，即肠道微生物区系。与动物相关的微生物群落在宿主体内聚集并持续存在的机制尚不清楚。关于动物相关微生物群落生态学的基本悬而未决的问题包括，这些群落在多大程度上是通过宿主选择或随机过程组装起来的。如果宿主选择很重要，那么这种选择是通过什么机制进行的？选择性力量会随着寄主发育阶段的变化而变化吗？影响社区集会的东道主选择压力是否也有助于社区的稳健性？理解这些群落的组装原理对于开始为人类设计治疗策略至关重要，以安全有效地促进有益微生物群落的发展，并预防或纠正致病微生物群落。我们建议应用生态学理论和模型来理解模式脊椎动物斑马鱼肠道微生物区系的组装和持久性。我们已经建立了在无菌条件下饲养斑马鱼的方法，并将它们与特定的微生物群落联系在一起。斑马鱼为这些研究提供了许多优势。它们的繁殖力和快速发展使我们能够一次饲养数千个无菌个体，并设计具有高度复制性的实验。斑马鱼及其相关细菌的遗传易操纵性，允许从相互作用的两端对宿主-微生物区系关联进行实验操作。斑马鱼发育的透明度使我们能够监测活体动物肠道细菌的定植，并研究肠道微生物区系组装的空间和时间模式。这项建议的一个总体目标是通过改进和标准化无菌营养和养殖业，以及开发用于简化论分析的已定义的斑马鱼相关微生物群落，来推进无菌斑马鱼模型，使该模型可被微生物生态学家和发育遗传学家广泛用于研究动物相关微生物群落的动态。在目标1中，我们建议使用生态学理论来计算宿主选择和随机过程在斑马鱼肠道微生物区系组装中的相对重要性。我们将询问寄主选择是否随着寄主发育阶段和微生物分类的不同而不同。在目标2中，我们将确定饲料和免疫系统在斑马鱼微生物区系寄主选择中的相对重要性。为了解决饮食的作用，我们将调查不同饲料饲养的鱼的肠道微生物区系组装。为了解决免疫系统的作用，我们将分析具有先天或适应性免疫系统缺陷的斑马鱼突变体的肠道微生物群组装，以及针对其肠道微生物群成员接种疫苗的宿主。在目标3中，我们将研究宿主选择的基础机制。我们将使用已定义的微生物群落来确定初始定居种群的大小。我们将使用活体成像来检查肠道定植的空间和时间模式。最后，我们将通过监测作为这些宿主因素的已建立的微生物区系的入侵来确定饮食和免疫系统如何有助于群落的稳健性。总的来说，这些研究将提供对寄主相关微生物群落如何建立和维持的更深层次的机械理解。这些知识对于合理设计益生菌、益生菌和抗生素来治疗与微生物区系失衡相关的人类病理疾病，如炎症性肠道疾病和糖尿病至关重要。 与公共卫生相关：人类胃肠道中有大约10万亿个微生物细胞。这种复杂的微生物群落对正常的人类健康和消化生理很重要，在许多胃肠道疾病中都会受到干扰，例如炎症性肠病。拟议的实验将为指导肠道微生物群落的组装和持久性的因素提供新的见解。这些知识将推动人类治疗策略的设计，以安全和有效地促进有益微生物群落，并预防或纠正致病微生物。