THE DEVELOPMENTAL STOOL METATRANSCRIPTOME IN NEWBORNS

新生儿粪便发育元转录组

• 批准号: 7912794
• 负责人: William Estus Bennett
• 金额: $ 6.03万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7912794
• 关键词: Bacteria; Base Sequence; Biomass; Birth; Cells; Censuses; Computing Methodologies; Development; Disease; Elderly; Enteral; Epithelial; Feces; Functional disorder; Gene Expression Profile; Genes; Genomics; Goals; Health; Human; Human Biology; Human Microbiome; Infant; Inflammatory; Inflammatory Bowel Diseases; Intestines; Life; Maintenance; Messenger RNA; Metabolic; Methods; Microbe; Microbial Genome Sequencing; Necrotizing Enterocolitis; Neonatal; Newborn Infant; Nucleic acid sequencing; Obesity; Physiology; Population; Portraits; Process; Publishing; RNA Sequences; RNA analysis; Specimen; Time; Transcript; Work; computer science; insight; metagenomic sequencing; microbial; microbial host; microbiome; neonate; public health relevance; rRNA Genes

DESCRIPTION (provided by applicant): The interaction between the human microbiome and the host is of increasingly appreciated importance in human biology. The establishment and maintenance of gut microbes after birth assumes importance for many disorders in the neonatal period and later in life, including necrotizing enterocolitis, inflammatory bowel disease, and obesity. As such, the human neonate provides a unique opportunity to study the human intestinal microbiome. Previous attempts to study the developing newborn microbiome have included bacterial culture and 16S rRNA gene sequencing of nucleic acid in the stools of normal infants, but these approaches have limitations. The host and microbial transcriptome, and the aggregate metatranscriptome, can provide a more vivid and complete portrait of the precise metabolic activity of both host epithelial and inflammatory cells, and of the enteric microbial biomass. I propose to use RNA sequencing to characterize the intestinal microbial and host transcriptome in human neonates. We have recently published a new method to isolate and amplifiable host mRNA from human stool. We are also able to isolate and amplify bacterial transcripts. It is now appropriate to determine if RNA analysis in human stool, and most particularly RNA analysis by mass sequencing, illuminates host physiology and pathophysiology, and profiles the enteric microbiome. My first aim will be to develop a computational pipeline to process the mass-sequenced RNA in newborn stool. This will involve a stepwise process of alignment with both human and sequenced microbial genomes, as well as advanced computational methods to ascertain the identity of remaining sequence. My second aim will be to compare the resultant metatranscriptome with metagenomic sequence in the same specimen to verify the hypothesis that the transcript profile is sufficiently different than a genomic census. I will accomplish these goals with a combination of graduate course work in computer sciences and sequential study of a unique neonatal specimen set. PUBLIC HEALTH RELEVANCE: Development of the bacterial population in the intestinal tract is of major importance to human health and disease, both in the newborn period and in later life. Previous efforts have characterized this population by enumerating the bacterial species present and the genes they contain. We believe that a thorough understanding of which genes are expressed and at what times they are expressed, in bacteria and in the host will provide instructive new insights into how the bacterial population of the human gut becomes established, and how the gut matures.

描述(申请人提供)：人类微生物群和宿主之间的相互作用在人类生物学中越来越受到重视。出生后肠道微生物的建立和维持对新生儿期和以后生活中的许多疾病具有重要意义，包括坏死性小肠结肠炎、炎症性肠病和肥胖。因此，人类新生儿为研究人类肠道微生物群提供了一个独特的机会。以前研究发育中的新生儿微生物组的尝试包括细菌培养和正常婴儿粪便中核酸的16S rRNA基因测序，但这些方法都有局限性。宿主和微生物转录组以及集合转录组可以更生动和完整地描述宿主上皮细胞和炎性细胞以及肠道微生物生物量的精确代谢活动。我建议使用RNA测序来描述人类新生儿肠道微生物和宿主转录组的特征。我们最近发表了一种从人粪便中分离和扩增宿主mRNA的新方法。我们还能够分离和扩增细菌转录本。现在应该确定人类粪便中的RNA分析，尤其是通过大量测序进行的RNA分析，是否能够阐明宿主生理学和病理生理学，并描绘肠道微生物群。我的第一个目标将是开发一个计算管道来处理新生儿粪便中大量测序的RNA。这将涉及与人类和已测序的微生物基因组进行逐步比对的过程，以及确定剩余序列的同一性的先进计算方法。我的第二个目标将是在同一样本中比较得到的元转录组和元基因组序列，以验证转录谱与基因组普查足够不同的假设。我将结合计算机科学的研究生课程工作和对独特的新生儿样本集的连续研究来实现这些目标。 公共卫生相关性：肠道细菌种群的发展对人类健康和疾病具有重大意义，无论是在新生儿时期还是在以后的生活中都是如此。以前的努力通过列举存在的细菌物种和它们包含的基因来表征这一群体。我们相信，彻底了解哪些基因在细菌和宿主中表达，以及它们在什么时间表达，将为人类肠道的细菌种群如何建立，以及肠道如何成熟提供有启发性的新见解。