Impact of Diet on Intestinal Microbiota-Host Dynamics

描述（由申请人提供）：一个密集的微生物群落生活在每个人的胃肠道（GI）中。这种肠道微生物群由10-100万亿个微生物细胞组成，它影响着人类生物学的许多方面，包括免疫状态和代谢。异常的肠道微生物群组成与炎症性肠病和肥胖有关，但导致微生物群改变的因素目前尚未明确。这项建议的目标是深入了解肠道微生物群如何受到宿主饮食特定变化的影响。我们的长期目标是将微生物群整合到个性化医疗的新兴范例中，重点是针对微生物群的诊断和治疗，以治疗或预防肥胖、炎症性肠病和其他微生物群相关疾病。大量的肠道细菌，如拟杆菌（Bacteroides thetaiotaomicron），将其基因组的大部分用于利用未消化的膳食植物多糖（即膳食纤维）。将膳食多糖摄入与微生物群组成和功能的改变联系起来的机制是人类生物学不可或缺的一部分。本提案的目的是：(i)获得在拟杆菌类中保守的操纵子的功能机制，该功能是使用丰富的称为果聚糖的膳食植物多糖所必需的；（ii）确定由利用饲粮果糖和菊粉的相对能力不同的细菌种类组成的模型微生物如何在无糖生物小鼠肠道内适应饲粮中添加的菊粉；（iii）确定由B. theta和双歧杆菌组成的模型微生物群是否可以通过饮食诱导的改变来差异调节宿主上皮基因表达和全身或粘膜细胞因子水平。为了实现上述(i)，我们将使用遗传工具和生化分析来研究B. theta的果聚糖利用操纵子内基因的功能。比较基因组学和果聚糖生长分析将阐明存在于拟杆菌中的果聚糖利用能力谱的基因组基础。在目的（ii）中，缺乏肠道微生物群的无菌小鼠将用由B. theta菌株、拟杆菌种和/或直肠真杆菌（肠道优势厚壁菌门的一员）组成的简化模型微生物定殖。细菌基因表达、物种密度和肠道果聚糖含量的调查将阐明由不同于果聚糖使用的微生物群的优势成员组成的模型群落如何在组成和功能上适应膳食中增加的菊糖。在目的（iii）中，无菌小鼠与B. theta和两种不适合菊粉使用的双歧杆菌中的一种共定殖。如目的（ii）所述，将描述细菌在体内对膳食菊粉的功能和组成适应性。这些结果将决定我们是否可以根据基因组和功能数据预测饮食变化（胰岛素富集）如何影响模型微生物群。将监测宿主的反应，以确定上皮基因表达和全身和/或粘膜细胞因子反应是否可以通过饮食诱导的微生物群变化来调节。

DESCRIPTION (provided by applicant): A dense community of microbes lives within the gastrointestinal (GI) tract of each human. This intestinal microbiota is composed of 10-100 trillion microbial cells and it impacts numerous aspects of human biology including immune status and metabolism. Aberrant intestinal microbiota composition has been linked to inflammatory bowel diseases and to obesity, yet the factors contributing to microbiota alterations are currently ill defined. The goal of this proposal is to gain insight into how the intestinal microbiota is impacted by specified changes in host diet. Our long-term goal is to integrate the microbiota into the emerging paradigm of personalized medicine, with a focus on microbiota-targeted diagnostics and therapeutics to treat or prevent obesity, inflammatory bowel diseases, and other microbiota-relevant diseases. Species of abundant gut-dwelling bacteria, such as Bacteroides thetaiotaomicron (B. theta), devote vast portions of their genomes to the utilization of undigested dietary plant polysaccharides (i.e., dietary fiber). Mechanisms that link dietary polysaccharide intake to alterations in microbiota composition and function are integral to human biology. The aims of this proposal are to (i) gain mechanistic insight into the function of an operon conserved in Bacteroides required for use of abundant dietary plant polysaccharides called fructans; (ii) determine how model microbiotas composed of bacterial species with differing relative abilities to utilize the dietary fructan, inulin, adapt within the gnotobiotic mouse gut to dietary inulin supplementation; (iii) determine if host epithelial gene expression and systemic or mucosal cytokine levels can be differentially modulated by diet-induced alterations in model microbiotas composed of B. theta and Bifidobacterium species. To pursue (i) above, we will use genetic tools and biochemical assays to investigate the function of genes within B. theta's fructan utilization operon. Comparative genomics and fructan-growth assays will elucidate the genomic basis for the spectrum of fructan utilization capability that exists in the Bacteroides. In aim (ii), germ-free mice, which lack a gut microbiota, will be colonized with simplified model microbiotas composed of B. theta strains, Bacteroides species, and/or Eubacterium rectale, a member of the gut-dominant Firmicutes division. Surveys of bacterial gene expression, species density, and gut fructan content will illuminate how model communities composed of dominant members of the microbiota disparate for fructan use, adapt in composition and function to elevated dietary inulin. In aim (iii), germ-free mice are co-colonized with B. theta and one of two Bifidobacterium species discordant for inulin use. Functional and compositional adaptation of bacteria in vivo to dietary inulin will be characterized, as in aim (ii). These results will determine whether we can predict, based on genomic and functional data, how a change in diet (inulin-enrichment) will impact a model microbiota. Host responses will be monitored to determine if epithelial gene expression and systemic and/or mucosal cytokine responses may be modulated via diet-induced changes in the microbiota.