Identification and characterization of natural products from the human microbiota

摘要 来自微生物的小分子，即所谓的“天然产物”，一直是临床上-- 批准的药物和细胞生物探针，并为它们的发现开发新的战略将扩大 天然产品流进入美国国立卫生研究院和其他地方的化合物图书馆。使用生物信息学 我们最近开发的在微生物基因组中识别天然产物编码基因簇的算法 序列，我们在细菌中从一个令人惊讶的位置发现了大量的基因簇：人类 微生物组。在这里，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提纯并解决三类分子的结构。这个项目 将为更大的努力识别和表征人类的自然产品奠定基础 微生物组。 有三个原因说明，从人类微生物群中识别天然产品应该是优先事项： 1)未被开发的生态位和细菌门通常会产生新的天然产品。2)天然产物 来自人类的微生物群可能具有重要的生物活性，而且不太可能对 人类。3)对新天然产物的计算搜索变得越来越有成效， 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 我们的努力发现了具有异常重要生物活性的天然产品，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能够研究 人类与其微生物群之间的相互作用。虽然这项提案集中在确定三个类别 对于来自肠道和口腔细菌的分子，我们的长期目标是为系统化 从人类微生物组中计算寻找新的天然产物。 我们的努力分为三个具体目标：目标1：确定和描述 来自肠道细菌的NRPS基因簇家族。我们已经确定了一个&gt；50个NRPS基因簇家族 这一点突出有两个原因：1)90%的人中有一个或多个基因簇处于高水平 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)这个家族只在肠道细菌物种中发现，这增加了它发挥作用的可能性 在肠道定植的背景下发挥重要的生物学作用。目标2：确定和表征以下产品 口腔链球菌的NRPS和NRPS/PKS基因簇家族。通过分析 对285株口腔分离的链球菌进行基因组序列分析，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%。 元基因组和元转录组分析表明，在这些基因簇中，有8个是大的(最多12个- 模块)NRPS、PKS和NRPS/PKS杂交体；所有这些都广泛分布在人类群体中，并且大多数是 在牙齿上活跃地转录。目标3：鉴定和表征一类低聚糖的产物 来自类杆菌的基因簇。人类微生物群中最大的生物合成基因簇家族， 其中负责产生类杆菌壳多糖的，还没有得到充分的开发。这些分子 在肠道中含量很高，已知具有特定的配体-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.