The Impact of Microbiome Composition, Diversity, and Function on Enteric Disease

据估计，食源性感染每年在美国造成超过7600万人患病，30万人住院治疗和5,000人死亡。沙门氏菌、弯曲杆菌、志贺氏菌和肠出血性大肠杆菌（EHEC）引起大多数感染，特别是5岁以下的儿童。这四种病原体会导致多种疾病，包括出血性和非出血性腹泻，但在某些情况下也会导致肾衰竭，神经系统疾病和死亡。对于大多数肠道细菌病原体，疾病过程是通过传播到易感宿主，通过肠道，并附着到胃肠道衬里的宿主上皮细胞而开始的。大多数病原体已经进化出各种专门的机制来增强这一过程，并且在一些情况下，特定的基因型已经被证明比其他基因型引起更严重的疾病。虽然细菌的特性显然很重要，但宿主在疾病发病机制中的作用不应被忽视，因为不同病原体和宿主微生物群落之间的相互作用可能对疾病的发展很重要。在这里，我们建议使用焦磷酸测序结合宏基因组学来研究这四种常见的肠道病原体对肠道微生物组的组成和功能的影响。我们将分析来自200名未腹泻的健康个体的粪便DNA，并与800名由肠出血性大肠杆菌、沙门氏菌、弯曲杆菌和志贺氏菌引起的腹泻个体进行比较。具体目标是：（1）证明肠道微生物群落的组成、多样性和结构以及关键毒力和抗生素抗性基因的存在和表达影响由不同肠道细菌病原体引起的腹泻病;（2）确定肠道疾病深刻地影响群落成员的丰度、微生物群副产物的产生和表达，以及功能标记基因的分布和多样性（例如，短链脂肪酸）;和（3）证明不同肠道病原体的特定遗传和表型特征将更频繁和彻底地改变肠道疾病患者的微生物组。拟议的研究将提高我们对微生物组如何受到常见肠道病原体感染的影响的理解，同时控制性别，年龄，微生物群组成和功能概况，宿主免疫反应和细菌特征。将确定对预防肠道疾病重要的有益微生物群落、微生物和微生物产物，这反过来可以指导未来的预防和治疗策略。

Foodborne infections are estimated to cause >76 million illnesses, 300,000 hospitalizations and 5,000 deaths in the U.S. each year. Salmonella, Campylobacter, Shigella, and enterohemmorhagic Escherichia coli (EHEC) cause most infections, particularly in children <5 years of age. These four pathogens contribute to a wide range of illnesses including both bloody and non-bloody diarrhea, but also cause kidney failure, neurological disorders and death in some cases. For most enteric bacterial pathogens, the disease process is initiated by transmission to a susceptible host, passage through the gut, and attachment to host epithelial cells lining the gastrointestinal tract Most pathogens have evolved a variety of specialized mechanisms that enhance this process, and in several cases, specific genotypes have been shown to cause more severe disease than others. While bacterial characteristics are clearly important, the role of the host in disease pathogenesis should not be overlooked, as the interplay between different pathogens and host microbial communities is likely to be important for disease development. Here, we propose to use pyrosequencing combined with metagenomics to investigate the impact that these four common diarrheal pathogens have on the composition and function of the intestinal microbiome. We will analyze stool DNAs from 200 healthy individuals without diarrhea and make comparisons to 800 individuals with diarrhea caused by EHEC, Salmonella, Campylobacter, and Shigella. The specific aims are: (1) Demonstrate that the composition, diversity and structure of the intestinal microbial community and the presence and expression of key virulence and antibiotic resistance genes impacts diarrheal disease caused by different enteric bacterial pathogens; (2) Determine that enteric disease profoundly affects the abundance of community members, the production and expression of microbiota by-products, and the distribution and diversity of functional marker genes (e.g., short chain fatty acids); and (3) Demonstrate that specific genetic and phenotypic characteristics of different enteric pathogens will more frequently and drastically alter the microbiome in patients with enteric disease. The proposed study will enhance our understanding of how the microbiome is impacted by infection with common enteric pathogens while controlling for gender, age, microbiota compositional and functional profiles, host immune responses, and bacterial characterisfics. Beneficial microbial communities, microbes and microbial products important for preventing enteric disease will be identified, which in turn, could guide future prevention and treatment strategies.