Impact of Diet on Intestinal Microbiota-Host Dynamics

 描述（由申请人提供）：人体肠道内有一个密集而复杂的微生物群落，称为肠道微生物群。这种微生物生态系统与人类健康生物学的许多方面有关，但也可能导致多种疾病，包括炎症性肠病，肥胖和结肠癌。饮食是一个主要的决定因素的微生物物种，或微生物类型，栖息在一个人的微生物群，以及这些物种进行的功能。具体而言，膳食微生物群可获得的碳水化合物（MAC），膳食纤维的主要成分，作为肠道微生物群的主要代谢输入。与传统社会相比，现代饮食中的膳食纤维明显较少，这一观察结果与微生物群多样性的减少有关（例如，微生物种类较少）。低多样性微生物群反过来又与代谢综合征和炎症的标志物相关，增加膳食纤维似乎可以改善微生物群的多样性和健康。然而，在理解膳食MAC如何影响微生物群多样性以及膳食MAC消耗是否会导致微生物群中的微生物类型的不可逆损失方面仍然存在很大的差距。该提案旨在确定膳食MAC对微生物群多样性和微生物代谢的影响，并确定如何将灭绝的微生物群落类型成功地重新引入低多样性群落。在目标1中，将使用食用规定饮食的携带人类微生物群（“人源化”）的小鼠来确定限制饮食MAC对肠道内代谢物、基因和物种的主要后果。为了确定饮食诱导的微生物群多样性的减少是否可以在重新引入MAC时逆转，将剥夺小鼠的MAC，然后重新引入MAC，并定义它们的微生物群组成和功能。还将确定多代MAC耗尽对分集损失的影响。将通过宏基因组、短链脂肪酸和代谢组学分析评估微生物群功能。在目标2中，将评估使用纤维补充剂进行饮食干预的人类的微生物群。微生物群组成和功能的改变将使用结构复杂性不同的纤维补充剂进行比较。将使用宏基因组、短链脂肪酸和代谢组学分析类似地定义基因含量和小分子代谢物。目标3的目标是确定引入细菌微生物群类型以恢复具有低多样性微生物群的人源化小鼠的多样性的最佳方法。微生物群重编程策略包括移植（i）来自高多样性供体的完整微生物群，（ii）来自高多样性粪便的复杂可培养微生物群，或（iii）由可培养型菌株组成的限定群落。成功的策略，定义为那些显着增加微生物群多样性，将被跟踪超过 确定新菌株建立的动力学的时间。

 DESCRIPTION (provided by applicant): The human gut harbors a dense and complex community of microbes known as the intestinal microbiota. This microbial ecosystem is connected to many facets of human biology in health, but can also contribute to several diseases including inflammatory bowel diseases, obesity, and colon cancer. Diet is a major determinant of both the microbial species, or phylotypes, that inhabit one's microbiota, as well as the functions carried out by these species. Specifically, dietary microbiota-accessible carbohydrates (MACs), the main component of dietary fiber, serve as the primary metabolic input for the gut microbiota. Modern diets have significantly less dietary fiber relative to those from traditional societies, an observation that has been linked to the decrease in microbiota diversity (e.g., less microbial species) in individuals from industrialized countries. Low diversit microbiotas, in turn, have been correlated with markers of metabolic syndrome and inflammation, and increased dietary fiber appears to improve microbiota diversity and health. Yet large gaps still exist in understanding how dietary MACs influence microbiota diversity and whether dietary MAC depletion can result in irreversible loss of phylotypes within the microbiota. This proposal aims to define the influence of dietary MACs on microbiota diversity and microbial metabolism and to determine how extinct microbial phylotypes can be successfully reintroduced into low diversity communities. In Aim 1, mice harboring a human microbiota (`humanized') eating defined diets will be used to determine the major consequences that restricting dietary MACs has on metabolites, genes, and species within the gut. To determine whether a diet- induced reduction in microbiota diversity can be reversed upon re-introduction of MACs, mice will be deprived of MACs, followed by reintroduction of MACs, and their microbiota composition and function will be defined. The effect of MAC depletion over multiple generations on diversity loss will also be determined. Microbiota functionality will be assessed by metagenomic, short-chain fatty acid, and metabolomic analyses. In Aim 2, the microbiota of humans undergoing a dietary intervention with fiber supplements will be assessed. Alterations in microbiota composition and functionality will be compared using fiber supplements that vary in structural complexity. Gene content and small molecule metabolites will be similarly defined using metagenomic, short-chain fatty acid, and metabolomic analyses. The goal of Aim 3 is to identify the best method to introduce bacterial phylotypes to restore diversity into humanized mice that harbor a low diversity microbiota. Microbiota reprogramming strategies include transplanting (i) an intact microbiota from a high- diversity donor, (ii) a complex culturable microbiota from high-diversity stool, or (iii) defined communities composed of culturable type strains. Successful strategies, defined as those that significantly increase microbiota diversity, will be tracked over time to determine the kinetics of new strain establishment.