Epigenetics of the human gut microbiome

人类肠道微生物组的表观遗传学

• 批准号: 10405552
• 负责人: Eric John Alm
• 金额: $ 36.81万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-20 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10405552
• 关键词: 7-deazaguanine; Address; Adenine; Affect; Bacteria; Bacterial DNA; Bacterial Genome; Bacteriophages; Behavior; Cell Cycle; Chemicals; Chemistry; Chromatography; Clinical; Collaborations; Colon Carcinoma; Consumption; Coupled; DNA; DNA Methylation; DNA Modification Process; DNA Restriction-Modification Enzymes; Development; Disease; Epigenetic Process; Equilibrium; Etiology; Gene Expression; Genes; Genetic Engineering; Genome; Genomic Instability; Genomics; Goals; Health; Heritability; Human; Human Microbiome; Immune system; In Vitro; Individual; Inflammation; Inflammation Mediators; Inflammatory Bowel Diseases; Inherited; Libraries; Link; Maps; Mass Spectrum Analysis; Metagenomics; Methyltransferase; Microbe; Modification; Mus; Mycobacterium abscessus; Oxidation-Reduction; Oxidative Stress; Oxygen; Patients; Phenotype; Play; Population; Predisposition; Program Research Project Grants; Proteins; Pseudomonas aeruginosa infection; Research; Resistance; Role; Sampling; Sulfur; System; Testing; Vertebral column; Virulence; Wound Infection; analytical tool; bacterial fitness; base; computerized tools; epigenome; gene function; genomic tools; gut bacteria; gut inflammation; gut microbes; gut microbiome; gut microbiota; human disease; human microbiota; informatics tool; innovation; innovative technologies; microbial; microbiome; microbiome research; neutrophil; new technology; next generation sequencing; novel; oxidation; pathogen; pathogenic bacteria; phosphorothioate; tool; virtual

Project Summary The proposed studies 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 have been known since the 1970s, 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, such as the DNA adenine methyltransferase, DAM, and cell cycle-regulated methylase, CcrM, which 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 an initial 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. The proposed 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.

项目摘要 拟议的研究涉及细菌表观遗传学在人类肠道微生物组中的作用以及它们的 与健康和疾病的机械论联系。几乎所有的微生物都有DNA修饰--表观基因组-- 调节基因表达并发挥免疫系统功能的遗传标记，最常见的是限制性- 修改(Rm)。虽然基于DNA甲基化的RM系统的特征已经很好，但自从 20世纪70年代，现在有30种DNA修饰定义在细菌和噬菌体中，包括我们最近的 硫代磷酸(PT)和7-去氮鸟嘌呤修饰的发现。DNA修饰也调节基因 表达，如DNA腺嘌呤甲基转移酶，DAM，和细胞周期调节甲基酶，CCRM， 它们控制影响毒力和噬菌体抗药性的可遗传基因表达，以及非 可遗传的基因表达。虽然这些细菌表观遗传学的例子与人类疾病有关，但我们 对DNA修饰如何确定或影响肠道中的微生物种群，以及它们如何 影响单个微生物物种的行为或生存，或者是否与 特定微生物组表观遗传学与人类健康和疾病。这里我们使用创新的分析方法， 信息学和基因组学工具来探索这些问题，最初的重点是细菌DNA 在约15%的人肠道微生物中发现的修饰：PT修饰，其中具有氧化还原活性的S取代了 DNA主干中的非键氧。拟议的研究是由广泛分布的 在细菌病原体和共生体中，PTS对化学介体氧化的敏感性 炎症，以及炎症对肠道微生物区系的已知影响，所有这些都表明炎症 可能会改变含有PT的肠道微生物的平衡。然而，我们对微生物群几乎一无所知 表观遗传学，更不用说肠道细菌具有氧化还原敏感的PTS和其他表观遗传学标记。我们现在 建议定义健康人肠道中含PT细菌的格局，阐明其作用 肠道炎症过程中微生物组的变化，并在肠道中发现新的表观遗传标记 微生物组。我们首先对PTS进行量化，并在粪便DNA样本中鉴定含有PT的细菌 广泛微生物组文库的健康捐赠者和从这些样本培养的约7000株菌株(DND基因 发现在15%)。然后，我们测试氧化还原敏感型PT会影响发炎肠道中细菌的适合性， 炎症性肠病患者20-30份粪便标本中PT水平及含PT细菌的定量检测 (IBD)患者。最后，我们将使用新技术在肠道微生物中识别新的DNA修饰 在储存的BML捐献者和菌株的粪便样本中发现DNA标记，然后将它们与独特的 微生物组表型及其与人类疾病的关系。这个项目的意义在于 含PT微生物在人类健康和疾病中的潜在作用，PT-2的潜在临床影响 在IBD上含有细菌，以及开发新的工具来发现新的微生物组表观遗传系统。