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肠道微生物组及其的作用 与健康和疾病的机械联系。几乎所有微生物都具有DNA修饰 - 表观基因组 - 遗传标记的标记调节基因表达和作为免疫系统的功能，最常见于限制 - 修改（RM）。自从以来，虽然已经知道了良好的基于​​DNA甲基化的RM系统 1970年代，现在在细菌和噬菌体中定义了30个DNA修饰，包括我们的最新 发现磷酸盐酸盐（PT）和7-二瓜氨酸修饰。 DNA修饰还调节基因 表达，例如DNA腺嘌呤甲基转移酶，大坝和细胞周期调节的甲基化酶CCRM，CCRM， 控制病毒和细菌耐药性的遗传基因表达以及非 - 可遗传的基因表达。尽管这些细菌表观遗传学的例子与人类疾病有联系，但我们 几乎了解DNA修饰如何确定或影响肠道中的微生物种群，它们如何 影响单个微生物物种的行为或生存，或者是否存在关系 特定的微生物组表观遗传学以及人类健康与疾病。在这里，我们使用创新分析， 信息和基因组学工具以探索这些问题，最初关注细菌DNA 在〜15％的人肠道微生物中发现的修改：PT修饰，其中氧化还原活性S替代A DNA主链中的非键氧。拟议的研究是由宽度分布驱动的 细菌病原体和共生中的PT，PT对PTS对化学介质氧化的敏感性 炎症以及炎症对肠道菌群的已知影响，所有这些都表明炎症 可以改变含PT的肠道微生物的平衡。但是，我们几乎对微生物组一无所知 表观遗传学，肠道细菌具有对氧化还原敏感的PT和其他表观遗传学标记的要少得多。我们现在 建议在健康人肠道中定义含PT细菌的景观，阐明该作用 肠道注射过程中微生物组变化中的Pts的PT，并在肠道中发现新的表观遗传标记 微生物组。我们首先量化PT并鉴定来自粪便DNA样品中的含PT的细菌 宽阔的微生物组文库的健康供体，在这些样品中培养的约7000种菌株中（DND基因） 发现15％）。然后，我们测试了氧化还原敏感的PT会影响肠发炎的细菌适应性的观念， 量化炎症性肠病的20-30个粪便样品中的PT水平和含PT的细菌 （IBD）患者。最后，我们将使用新技术来确定肠道微生物中的新DNA修饰 从BML供体和菌株中发现库存的粪便样品中的DNA标记，然后将其链接到独特 微生物组表型和与人类疾病的关联。该项目的意义在于 含PT的微生物在人类健康和疾病中的潜在作用，PT-的潜在临床影响 在IBD上含有细菌，以及开发新工具以发现新的微生物组表观遗传系统。