Identification and characterization of natural products from the human microbiota

摘要 来自微生物的小分子被称为“天然产物”，是临床- 批准的药物和细胞生物探针，并为他们的发现开发新的策略将扩大 一系列天然产物进入NIH和其他地方的化合物库。使用生物信息学 我们最近开发了一种算法，用于识别微生物基因组中的天然产物编码基因簇 序列，我们已经发现了细菌中的许多基因簇来自一个令人惊讶的位置：人类 微生物组在此，我们建议使用化学，遗传学和生物信息学的组合来分离， 从人体肠道和口腔细菌中纯化并解析三类分子的结构。这个项目 将为更大的努力奠定基础，以确定和表征来自人类的天然产品。 微生物组 从人体微生物组中识别天然产物应该成为优先事项的原因有三个： 1)未充分开发的生态位和细菌门通常产生新的天然产物。2)天然产物 可能具有重要的生物活性，并且不太可能对人体有毒。 人类3)对新的天然产物的计算搜索已经变得越来越富有成效， 人类微生物组计划将为人类相关细菌提供丰富的序列数据。不仅会 我们的努力揭示了具有异常重要的生物活性的天然产物，它们也将验证 人类微生物组作为天然产物的新来源，并使未来的分子基础的研究 人类和微生物之间的相互作用。虽然这项建议的重点是确定三类 从肠道和口腔细菌的分子，我们的长期目标是奠定基础，系统化， 计算搜索来自人类微生物组的新天然产物。 我们的努力分为三个具体目标：目标1：识别和表征产品的 来自肠道细菌的NRPS基因簇家族。我们已经确定了一个家族的>50 NRPS基因簇 这有两个原因：1）这些基因簇中的一个或多个在90%的人中以高水平存在。 健康的人类受试者，使其成为人类中分布最广泛的基因簇家族之一 人口2)这个家族只存在于肠道细菌物种中，这增加了它在肠道中发挥作用的可能性。 在肠道定植的背景下重要的生物学作用。目标2：确定和表征 来自口腔链球菌菌株的NRPS和NRPS/PKS基因簇家族。通过分析 285个口腔链球菌分离株的基因组序列，我们发现主要的遗传差异 在这些物种的菌株中，有14个生物合成基因簇，占基因组的8%。 宏基因组学和元转录组学分析表明，在这些基因簇中，有8个是大的（多达12个）。 模块）NRPS、PKS和NRPS/PKS杂交体;所有这些都广泛分布于人群中，并且大多数是 活跃地转录在牙齿上。目的3：鉴定和表征寡糖家族的产物 拟杆菌属的基因簇。人类微生物组中最大的生物合成基因簇家族， 其负责产生拟杆菌荚膜多糖，但研究不足。这些分子 以高丰度存在于肠道中，并且已知具有特异性配体-受体相互作用， 调节宿主的免疫反应。

Abstract Small molecules from microbes known as `natural products' have been an important source of clinically- approved drugs and cell biological probes, and developing new strategies for their discovery will expand the stream of natural products entering compound libraries at the NIH and elsewhere. Using a bioinformatic algorithm we recently developed to identify natural product-encoding gene clusters in microbial genome sequences, we have found numerous gene clusters in bacteria from a surprising location: the human microbiome. Herein, we propose to use a combination of chemistry, genetics, and bioinformatics to isolate, purify, and solve the structures of three classes of molecules from human gut and oral bacteria. This project will lay the groundwork for a larger effort to identify and characterize natural products from the human microbiome. There are three reasons why identifying natural products from the human microbiome should be a priority: 1) Underexplored ecological niches and bacterial phyla usually yield new natural products. 2) Natural products from the human microbiome are likely to have important biological activities, and are unlikely to be toxic to humans. 3) Computational searches for new natural products have become increasingly fruitful, and the Human Microbiome Project will provide a wealth of sequence data for human-associated bacteria. Not only will our efforts uncover natural products with unusually important biological activities, they will also validate the human microbiome as a new source of natural products and enable future studies of the molecular basis of interactions between humans and their microbiome. While this proposal is focused on identifying three classes of molecules from gut and oral bacteria, our long-term goal is to lay the groundwork for systematizing a computational search for new natural products from the human microbiome. Our efforts are organized into three Specific Aims: Aim 1: Identify and characterize the products of a family of NRPS gene clusters from gut bacteria. We have identified a family of >50 NRPS gene clusters that stands out for two reasons: 1) One or more of these gene clusters is present at a high level in 90% of healthy human subjects, making this one of the most widely distributed gene cluster families in the human population. 2) This family is only found in gut-dwelling bacterial species, raising the possibility that it plays an important biological role in the context of gut colonization. Aim 2: Identify and characterize the products of a family of NRPS and NRPS/PKS gene clusters from oral strains of Streptococcus. By analyzing the genome sequences of 285 oral isolates of Streptococcus, we have found that the major genetic differences among strains of these species are 14 biosynthetic gene clusters that occupy up to 8% of the genome. Metagenomic and metatranscriptomic analyses suggest that of these gene clusters, eight are large (up to 12- module) NRPS, PKS, and NRPS/PKS hybrids; all are widely distributed in the human population, and most are actively transcribed on teeth. Aim 3: Identify and characterize the products of a family of oligosaccharide gene clusters from Bacteroides. The largest family of biosynthetic gene clusters in the human microbiome, which are responsible for producing Bacteroides capsular polysaccharides, is underexplored. These molecules are present at high abundance in the gut and are known to have specific ligand-receptor interactions that modulate the host immune response.