How glycans shape gut microbiota function and assembly

描述（由申请方提供）：栖息在人类远端肠道中的微生物群落（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争夺淹没其环境的数十种不同聚糖的策略。这些复杂的碳水化合物在化学结构和消化率方面差异很大，这一特征可能决定了每种聚糖代谢的肠道特定区域（回肠、近端或远端结肠）。尚未探索不同肠道区域中聚糖可用性与微生物群生理学之间的关系。然而，这些知识对于理解塑造微生物群的力量以及设计策略以使用益生元（功能性食品，最常见的是聚糖，旨在丰富有益微生物的丰度和/或生理学）等方法来操纵其功能至关重要。我们将使用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可变量的定义饮食建立三方定植模型。使用该模型，我们将检验我们的中心假设，即肠道中的聚糖以一系列梯度存在（由其饮食或来源和生化特性决定），并且单个细菌物种将在其首选聚糖丰富的区域富集。初步数据表明，保护性上皮粘液层是主要的聚糖生态位，其基于仅某些物种代谢粘液中存在的宿主来源聚糖的能力选择肠道细菌亚群落。将沿肠的长度沿着直接采集来自管腔和粘液层的细菌群体，或使用激光捕获显微切割（LCM）显微捕获。在目标1中，已知响应特定聚糖的细菌基因的转录将用作生物传感器，以测量不同肠道区域之间细菌聚糖代谢的变化。随后将改变单个膳食聚糖的丰度，以观察微生物群代谢的相应变化。在目标2中，我们已经凭经验测量了几十种聚糖降解表型的44种不同的人肠道拟杆菌属物种的丰度，将在沿着肠道长度和宽度的粘膜和管腔中测量。在不存在和存在代表人类肠道中其他优势门的43种额外测序细菌物种的情况下，将观察到该群落的组装。尽管人类肠道微生物群发挥着许多有益的作用，但该群落的异常（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哪里以及为什么会对一个重要的外部可操作参数（膳食聚糖）做出反应的数据。我们的研究结果将有助于有意操纵人体微生物群以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.