How glycans shape gut microbiota function and assembly

描述（由申请人提供）：居住在人类远端肠道的微生物群落（微生物群）提供了人类尚未进化的生理属性，包括处理否则难以消化的膳食聚糖的能力。这个群落中的物种已经进化出了竞争几十种不同聚糖的策略，这些聚糖充斥着它们的环境。这些复杂的碳水化合物在化学结构和消化率上差异很大，这一特征可能决定了肠道（回肠、结肠近端或远端）的特定区域，每种聚糖在其中代谢。在不同的肠道区域聚糖可利用性和微生物生理之间的关系尚未探讨。然而，这些知识对于理解塑造微生物群的力量以及使用益生元（功能食品，最常见的是聚糖，旨在丰富有益微生物的丰度和/或生理）等方法设计操纵其功能的策略至关重要。我们将建立一个三方定植模型，使用1)无菌小鼠，2)完全测序的人类肠道细菌的合成群落，以及3)包含人类通常消耗的所有主要膳食聚糖的定义饮食。使用该模型，我们将验证我们的中心假设，即肠道中的聚糖存在于一系列梯度中（由它们的饮食或起源和生化特性决定），并且单个细菌物种将在它们首选聚糖丰富的区域富集。初步数据表明，保护性上皮黏液层是一个主要的聚糖生态位，它根据某些物种代谢黏液中宿主来源的聚糖的能力来选择肠道细菌亚群落。沿着肠道的长度直接收集管腔和黏液层的细菌群，或者使用激光捕获显微解剖（LCM）在显微镜下捕获。在Aim 1中，已知对特定聚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聚糖代谢的变化。随后，个体膳食聚糖的丰度将发生变化，以观察微生物群代谢的相应变化。在Aim 2中，我们将沿着肠道的长度和宽度在粘膜和管腔中测量44种不同的人类肠道拟杆菌属物种的丰度，我们已经经验地测量了几十种聚糖降解表型。该群落的聚集将在43种额外的细菌物种缺失和存在的情况下观察到，这些细菌物种代表了人类肠道中的其他优势门。尽管人类肠道菌群发挥着许多有益的作用，但该菌群的异常（生态失调）被认为是炎症性肠病和肥胖等病理状况的基础。拟议的实验将提供有关不同物种在何处以及为何聚集的数据，以响应一个重要的外部可操纵参数（膳食聚糖）。我们的研究结果将促进有意操纵人类微生物群来影响肠道健康的方法。

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.