Modulation of microbiome function by host-derived noncoding small RNA

总结： 许多研究报告了代谢性疾病等疾病中微生物群组成的变化， 综合征，炎症性肠病，高血压，哮喘，心血管疾病，类风湿性关节炎， 癌症和感染。其中一些联系已被证明是疾病的原因，通过使用特定的 将细菌引入临床前模型。例如，我们发现人类临床分离的C。空肠 （C. jejuni）81-176通过产生 细胞致死膨胀毒素（cdt）（He Z等人，Gut. 2019; 68（2）289-300）。更重要的是，C.空肠 81-176与C.缺乏cdtB毒素的空肠 组和不同的微生物群落，如通过16 S rDNA测序测量的（He Z等人，Gut.二〇一九年; 68（2）：289-300）。此外，我们证明了肠道微生物群可以防止C。空肠诱导肠 在ex-GF IllO-/-小鼠中，通过胆汁酸代谢的炎症（Sun X等人，Gastroenterology. 2018;154（6）：1751-1763）。因此，微生物组成和功能的破坏可能是微生物生长的重要方面。 由肠道病原微生物引起的疾病。在维持健康的大脑中， 宿主-微生物群平衡是复杂的，包括宿主来源的抗微生物肽、粘液 屏障和免疫球蛋白分泌等。我们实验室的最新发现表明， 从健康或结肠直肠组织获得的肠道微生物群改变了大肠杆菌来源的粪便中 小的RNA如miRNA，一些miRNA优先靶向细菌基因，如通过 生物信息学方法（Tomkovich S等人，mSystems. 2020; 5（1））。许多这些miRNAs被预测为 涉及调节运动性、分泌、外膜蛋白、应激反应、铁的靶细菌基因 获取和碳水化合物利用/运输。因此，宿主来源的小的非编码RNA的产生可能 代表宿主调节微生物群功能的另一种方式。这一令人兴奋的概念得到了 我们的初步数据表明，使用哺乳动物细胞外囊泡（EV）在细菌中进行基因敲除 装载有靶向原核基因的siRNA。这些发现表明，细菌对宿主的影响不同， 衍生的miRNA，这反过来又可以影响细菌的组成和基因表达。从这些 通过观察，我们假设细菌影响miRNA的产生，从而改变微生物群 社区功能和疾病表型。我们计划用以下两个例子来检验这个假设 具体目标： 目标1。确定EV在Il 10-/-小鼠中细菌诱导的miRNA中的作用。 目标2.定义EV介导的siRNA对微生物基因表达的影响。 这项研究将建立一个原则的证据，肠道病原体触发选择性EV含有miRNA 不同的影响微生物群。我们的方法使用微生物基因组学，转录组学，遗传操作， gnotobiotic技术代表了一个独特的机会，解决宿主，微生物群， 活动、宿主反应和炎症。该项目产生的调查结果将提供坚定的支持， 通过小的非编码RNA和开放的新的可能性， 将这一发现用于微生物基因操作和治疗目的。

Summary: A number of studies have reported changes in the composition of microbiota in diseases such as metabolic syndrome, inflammatory bowel diseases, hypertension, Asthma, cardiovascular diseases, rheumatoid arthritis, cancer and infection. Some of these links have been shown to be causative of diseases by using specific bacteria introduced into pre-clinical models. For example, we showed that the human clinical isolate C. jejuni (C. jejuni) 81-176 promote development of colitis-associated colorectal cancer through the production of cytolethal distending toxin (cdt) (He Z et al. Gut. 2019; 68(2) 289-300). Importantly, mice colonized with C. jejuni 81-176 had a significantly different microbial gene expression profile compared to C. jejuni lacking the toxin cdtB group, and different microbial communities as measured by 16S rDNA sequencing (He Z et al. Gut. 2019; 68(2):289-300). In addition, we demonstrated that the intestinal microbiota prevents C. jejuni-induced intestinal inflammation in ex-GF Il10-/- mice, through bile acid metabolism (Sun X et al. Gastroenterology. 2018;154(6):1751-1763). Thus, disruption of microbial composition and function may be an important aspect of disease mediated by enteropathogenic microorganisms. The mechanism implicated in maintaining a healthy host-microbiota balance is complex and included production of host-derived anti-microbial peptides, mucus barrier and immunoglobulin secretion among others. Recent findings from our laboratory suggest that human intestinal microbiota obtained from healthy or colorectal tissues altered expression of mammalian-derived fecal small RNAs such as miRNA, with some miRNAs preferentially targeting bacteria genes as predicted by bioinformatic approach (Tomkovich S et al. mSystems. 2020; 5(1)). Many of these miRNAs were predicted to target bacterial genes implicated in regulating motility, secretion, outer membrane proteins, stress response, iron acquisition, and carbohydrate utilization/transport. Thus, host-derived production of small non-coding RNA may represent another mean by which the host regulate microbiota function. This exciting concept is supported by our preliminary data demonstrating gene knockdown in bacteria using mammalian extracellular vesicles (EVs) loaded with siRNA targeting prokaryotic genes. These findings suggest that bacteria differentially impact host- derived miRNA, which in turn could influence bacterial composition and gene expression. From these observations, we hypothesize that bacteria influence the production of miRNA, which in turn modified microbiota community function and consequently disease phenotype. We plan to test this hypothesis with the following two specific aims: Aim 1. Define the role of EV in bacteria-induced miRNA in Il10-/- mice. Aim 2. Define the impact of EV-mediated siRNA on microbial gene expression. This study will establish a proof of principal that enteric pathogens triggers selective EV-containing miRNA differently affecting microbiota. Our approach using microbial genomics, transcriptomic, genetic manipulation, and gnotobiotic technology represents a unique opportunity to address the interplay between host, microbiota activities, host response and inflammation. The findings generated from this project will provide a firm support for the existence of an interkingdom communication through small non-coding RNA and open new possibilities to exploit this discovery for microbial gene manipulation and therapeutic purpose.