Study of Pathway-Dependent Effects of Luminal Microbial Metabolites Including Short Chain Fatty Acids and Bile Acids in Irritable Bowel Syndrome Through Meta-omics Analysis of Fecal Specimens

项目总结 肠道微生物及其代谢产物包括短链脂肪酸(SCFA)和胆汁酸(BA)的调节 胃肠(GI)生理学和携带巨大的潜力作为诊断和治疗工具应激 肠综合征(IBS)，一种常见的慢性肠道-大脑相互作用障碍(或功能性胃肠道功能障碍)。 然而，肠道微生物组及其中间体参与IBS的确切机制 症状尚不清楚。微生物组-代谢组-宿主相互作用的机械信息理解 对于制定新的和有针对性的战略以加强对IBS患者的护理至关重要。这 R03申请是根据PAR-19-365提交的。在这一应用中，PI提出了一种假设驱动的 研究策略：(1)确定与粪便SCFA和BA水平/谱相关的功能通路(基因) 和生理特性，以及(2)通过功能通路分析证实 非靶向粪便代谢物分析。这项研究将补充私人投资公司K23研究的目标 它们是为了(1)确定与SCFA和BA谱相关联的粪便微生物区系组成的变化 在IBS中，通过16S rRNA基因测序和靶向代谢产物分析，(2)建立可操作的SCFA IBS的生物标志物，以及(3)研究IBS中SCFA与BA的相互作用。本R03的具体目标 建议：(1)确定SCFA产生和BA的不同丰富的代谢途径(基因) IBS(IBS伴腹泻[IBS-D]，IBS伴便秘[IBS-C])和对照志愿者的生物转化 元基因组测序数据的功能图谱以及(2)比较基因组最终产物是否/如何- 关键微生物分类群的编码功能在IBS-D、IBS-C和对照中不同，通过非靶向代谢组学。 为了达到这些目标，私家侦探将利用她现有的K23队伍，这些人都是预期招聘的和优秀的 表型IBS和匹配对照志愿者。作为K23资助研究的一部分，所有参与者都提交了 使用标准化收集程序的2天粪便样本用于评估粪便微生物区系、粪便 SCFA和粪便BA。按照本R03中的说明，对剩余样本进行存档，以供进一步分析 求婚。本申请中提出的策略将补充PI目前的职业发展 并从多学科K23指导小组的持续指导中受益。调查结果将 通过确定粪便微生物区系的哪些特征可以改进，来指导后续R01的方法 转化为实用的基于微生物的工具(例如，第三代长期阅读技术)，可以在更大的 IBS和对照志愿者队列。或者，如果基因组编码的代谢潜力不能 新陈代谢组学证实，这些发现将告知需要测量基因表达(即代谢转录组学) 或定量微生物图谱，以在随后的R01中调查微生物对IBS病理生理学的影响。在… 项目结束后，PI将处于成为独立医生调查员的理想位置 研究新的微生物和代谢组学生物标志物和恢复IBS健康的有针对性的策略。

PROJECT SUMMARY The gut microbiome and its metabolites including short chain fatty acids (SCFA) and bile acids (BA) regulate gastrointestinal (GI) physiology and carry immense potential as diagnostic and therapeutic tools for irritable bowel syndrome (IBS), a common and chronic disorder of gut-brain interaction (or functional GI disorder). However, the precise mechanisms by which the gut microbiome and its intermediaries contribute to IBS symptoms are unclear. A mechanistically-informed understanding of microbiome-metabolome-host interactions will be essential to developing novel and targeted strategies to enhance the care of individuals with IBS. This R03 application is submitted in response to PAR-19-365. In this application, the PI proposes a hypothesis-driven research strategy to (1) identify functional pathways (genes) associated with fecal SCFA and BA levels/profiles and physiological traits in IBS and control volunteers and (2) confirm functional pathway analysis through untargeted fecal metabolite profiling. This study will complement the objectives of the PI's K23 research study which are to (1) identify changes in fecal microbiota composition that are associated with SCFA and BA profiles in IBS through 16S rRNA gene sequencing and targeted metabolite analysis, (2) establish SCFA as actionable IBS biomarkers, and (3) investigate interactions between SCFA and BA in IBS. The specific aims of this R03 proposal are to (1) identify differentially abundant metabolic pathways (genes) of SCFA production and BA biotransformation in IBS (IBS with diarrhea [IBS-D], IBS with constipation [IBS-C]) and control volunteers through functional profiling of metagenomic sequencing data and (2) compare if/how the end-products of the genomically- encoded functions of key microbial taxa differ in IBS-D, IBS-C, and controls through untargeted metabolomics. To achieve these aims, the PI will leverage her existing K23 cohort of prospectively-recruited and well- phenotyped IBS and matched-control volunteers. As part of the K23-funded study, all participants have submitted 2-day stool samples using standardized collection procedures for assessment of the fecal microbiota, fecal SCFA, and fecal BA. Residual specimens are archived and available for further analysis as described in this R03 proposal. The strategies proposed in this application will complement the PI's current career development activities and benefit from the continued mentorship from a multidisciplinary K23 mentorship panel. Findings will guide the approach for a subsequent R01 by identifying which features of the fecal microbiota could be refined into practical microbiota-based tools (e.g. third generation, long-read technology) that could be tested in a larger IBS and control volunteer cohort. Alternatively, if the genomically-encoded metabolic potential cannot be confirmed by metabolomics, findings will inform the need measure gene expression (i.e. metatranscriptomics) or quantitative microbial profiles to investigate microbial effects on IBS pathophysiology in a subsequent R01. At the conclusion of the project, the PI will be ideally positioned to become an independent physician investigator studying novel microbial and metabolomics biomarkers and targeted strategies to restore health in IBS.