Supplement: Epigenetics of the Human Gut Microbiome

项目摘要 拟议的补充将扩大原来的研究，解决细菌表观遗传学的作用， 人类肠道微生物组及其与健康和疾病的机械联系。几乎所有的微生物都有DNA 修饰-表观基因组-遗传标记，调节基因表达和免疫功能， 系统，最常见的是限制修改（RM）。虽然基于DNA甲基化的特征很明显， RM系统已经很好地建立起来，现在在细菌和噬菌体中定义了>30种DNA修饰， 包括我们最近发现的硫代磷酸酯（PT）和7-脱氮鸟嘌呤修饰。DNA修饰 还调节基因表达以控制影响毒力和噬菌体的遗传基因表达 抗性以及非遗传基因表达。虽然这些细菌表观遗传学的例子 对于人类疾病，我们对DNA修饰如何决定或影响微生物种群知之甚少。 肠道，它们如何影响单个微生物物种的行为或生存，或者它们之间是否存在关系， 特定微生物组表观遗传学与人类健康和疾病。在这里，我们使用创新的分析，信息学， 和基因组学工具来探索这些问题，重点是在约15%的人中发现的细菌DNA修饰。 人类肠道微生物：PT修饰，其中氧化还原活性S取代DNA中的非键合氧 骨干这些研究是由PT在细菌病原体中的广泛分布驱动的， 此外，PT对炎症化学介质氧化的敏感性，以及已知的 炎症对肠道微生物群的影响，所有这些都表明炎症可以改变PT- 含有肠道微生物。然而，我们对微生物组表观遗传学几乎一无所知，更不用说 肠道细菌具有氧化还原敏感的PT和其他表观遗传标记。我们现在建议定义 健康人体肠道中含PT细菌的景观，阐明PT在微生物组变化中的作用 在肠道炎症过程中，并在肠道微生物组中发现新的表观遗传标记。我们从量化 PT和鉴定来自健康供体的粪便DNA样本中的含PT细菌 文库和从这些样本中培养的约7000株菌株（在15%中发现dnd基因）。然后，我们测试的想法， 氧化还原敏感性PT影响发炎肠道中的细菌适应性，定量PT水平和含PT的 在来自炎症性肠病（IBD）患者的20-30个粪便样品中的细菌。最后，我们将确定新的 肠道微生物中的DNA修饰，使用新技术发现库存粪便样本中的DNA标记 从BML供体和菌株，然后将它们与独特的微生物组表型和与 人类疾病该项目的意义在于含PT微生物在人类中的潜在作用 健康和疾病，含PT细菌对IBD的潜在临床影响，以及新的 发现新的微生物组表观遗传系统的工具。

Project Summary The proposed supplement will expand the original studies that address the role of bacterial epigenetics in the human gut microbiome and their mechanistic links to health and disease. Virtually all microbes possess DNA modifications – the epigenome -- inherited marks that regulate gene expression and function as immune systems, most commonly in restriction-modification (RM). While well-characterized DNA methylation-based RM systems are well established, there are now >30 DNA modifications defined in bacteria and bacteriophage, including our recent discovery of phosphorothioate (PT) and 7-deazaguanine modifications. DNA modifications also regulate gene expression to control heritable gene expression affecting virulence and bacteriophage resistance, as well as non-heritable gene expression. While these examples of bacterial epigenetics have links to human disease, we know little about how DNA modifications determine or affect microbial populations in the gut, how they affect the behavior or survival of individual microbial species, or if there is a relationship between specific microbiome epigenetics and human health and disease. Here we use innovative analytics, informatics, and genomics tools to explore these questions, with a focus on a bacterial DNA modification found in ~15% of human gut microbes: PT modifications, in which a redox-active S replaces a non-bonding oxygen in the DNA backbone. These studies are driven by the widespread distribution of PTs in bacterial pathogens and commensals, the susceptibility of PTs to oxidation by chemical mediators of inflammation, and the known effects of inflammation on gut microbiota, all of which suggest that inflammation could alter the balance of PT- containing gut microbes. However, we know virtually nothing about microbiome epigenetics, much less which gut bacteria possess redox-sensitive PTs and other epigenetic marks. We now propose to define the landscape of PT-containing bacteria in the healthy human gut, elucidate the role of PTs in microbiome changes during gut inflammation, and discover new epigenetic marks in the gut microbiome. We start by quantifying PTs and identifying PT-containing bacteria in fecal DNA samples from healthy donors to the Broad Microbiome Library and in ~7000 strains cultured from these samples (dnd genes found in 15%). We then test the idea that redox-sensitive PTs affect bacterial fitness in the inflamed gut, quantifying PT levels and PT-containing bacteria in 20-30 fecal samples from inflammatory bowel disease (IBD) patients. Finally, we will identify new DNA modifications in gut microbes, using novel technologies to discover DNA marks in banked fecal samples from BML donors and strains, and then link them to unique microbiome phenotypes and associations with human disease. The significance of this project lies in the potential role for PT-containing microbes in human health and disease, the potential clinical impact of PT-containing bacteria on IBD, and the development of new tools to discover new microbiome epigenetic systems.