How glycans shape gut microbiota function and assembly

描述(由申请人提供)：生活在人类远端肠道的微生物群落(微生物区系)提供了人类尚未进化的生理属性，包括处理以其他方式无法消化的饮食多糖的能力。这个群落中的物种已经进化出了策略，以争夺淹没它们环境的数十种不同的糖类。这些复杂的碳水化合物在化学结构和可消化性上有很大的差异，这一特征可能决定了肠道(回肠、近端或远端结肠)中代谢每一种糖的特定区域。不同肠道区域的多糖利用率和微生物区系生理学之间的关系还没有被探索过。然而，这些知识对于理解塑造微生物区系的力量以及设计策略以利用益生菌(功能食品，通常是糖类，旨在丰富有益微生物的丰度和/或生理)等方法操纵其功能至关重要。我们将使用1)无菌小鼠，2)全序列人类肠道细菌的合成群落，以及3)包含人类典型消费的所有主要饮食多糖的可变数量的限定饮食，来建立一个三方定居模型。使用这个模型，我们将检验我们的中心假设，即肠道中的多糖存在于一系列梯度中(由它们的饮食或宿主来源和生化特性决定)，单个细菌物种将在它们首选的多糖丰富的地区得到丰富。初步数据表明，保护性的上皮粘液层是一个主要的糖基生态位，它根据只有一些物种代谢粘液中存在的宿主衍生的多糖的能力来选择肠道细菌的亚群落。肠腔和粘液层中的细菌种群将沿着肠道长度直接采集，或使用激光捕获显微解剖(LCM)进行显微镜捕获。在目标1中，已知对特定多糖有反应的细菌基因的转录将被用作生物传感器，以测量不同肠道区域之间细菌多糖代谢的差异。随后将改变个体饮食中多糖的丰度，以观察微生物区系代谢的相应变化。在目标2中，我们对44种不同的人类肠道拟杆菌进行了沿着肠道长度和宽度的粘膜和管腔的丰度测量，我们已经对这些物种进行了数十种降解多糖的表型的经验测量。在没有和存在代表人类肠道中另一个优势门的43个已测序细菌物种的情况下，将观察到这个群落的组装。虽然人类肠道微生物区系发挥了许多有益的作用，但这个群落中的异常(生物失调)被认为是炎症性肠病和肥胖等病理状况的基础。拟议的实验将提供关于不同物种在哪里以及为什么聚集在一起的数据，以响应一个重要的和外部可操纵的参数(饮食多糖)。我们的结果将为故意操纵人类微生物区系以影响肠道健康的方法提供便利。

DESCRIPTION (provided by applicant): The microbial community (microbiota) that inhabits the human distal gut provides physiologic attributes that humans have not evolved, including the ability to process otherwise indigestible dietary glycans. Species in this community have evolved strategies to compete for the dozens of different glycans that inundate their environment. These complex carbohydrates vary immensely in chemical structure and digestibility, a feature that likely dictates the particular region of the gut (ileum, proximal or distal colon) in which each glycan is metabolized. The relationship between glycan availability and microbiota physiology in different gut regions has not been explored. However, this knowledge will be essential to understand the forces that shape the microbiota as well as to design strategies to manipulate its function using approaches like prebiotics (functional foods, most often glycans, designed to enrich the abundance and/or physiology of beneficial microbes). We will establish a tripartite colonization model using 1) germfree mice, 2) synthetic communities of fully sequenced human gut bacteria, and 3) a defined diet that contains variable amounts of all major dietary glycans that are typically consumed by humans. Using this model, we will test our central hypothesis that glycans in the intestine are present in a series of gradients (determined by their diet or hos origin and biochemical properties) and that individual bacterial species will be enriched in regions where their preferred glycans are abundant. Preliminary data suggest that the protective epithelial mucus layer is a major glycan niche that selects for a sub-community of gut bacteria based on the ability of only some species to metabolize the host-derived glycans present in mucus. Bacterial populations from the lumen and the mucus layer will be directly harvested along the length of the intestine or captured microscopically using laser-capture microdissection (LCM). In Aim 1, transcription of bacterial genes that are known to respond to specific glycans will be used as biosensors to measure variation in bacterial glycan metabolism between separate gut regions. The abundance of individual dietary glycans will be subsequently varied to observe the corresponding changes in microbiota metabolism. In Aim 2, the abundance of 44 different human gut Bacteroidetes species, for which we have empirically measured several dozen glycan-degrading phenotypes, will be measured in the mucosa and lumen along the length and width of the gut. Assembly of this community will be observed in both the absence and presence of 43 additional sequenced bacterial species representing the other dominant phyla in the human gut. Although the human gut microbiota plays many beneficial roles, abnormalities in this community (dysbiosis) have been postulated to underlie pathological conditions such as inflammatory bowel disease and obesity. The proposed experiments will provide data regarding where and why different species assemble in response to one important and externally manipulable parameter (dietary glycans). Our results will facilitate approaches to intentionally manipulate the human microbiota to influence intestinal health.