THE DEVELOPMENTAL STOOL METATRANSCRIPTOME IN NEWBORNS

描述（由申请人提供）：人类微生物组与宿主之间的相互作用在人类生物学中的重要性日益受到重视。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，炎症性肠病和肥胖症。因此，人类新生儿提供了研究人类肠道微生物组的独特机会。以前研究新生儿微生物组发育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，但这些方法有局限性。宿主和微生物转录组以及聚集体元转录组可以提供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性的更生动和完整的描述。我建议使用RNA测序来表征人类新生儿的肠道微生物和宿主转录组。我们最近发表了一种从人粪便中分离和纯化宿主mRNA的新方法。我们还能够分离和扩增细菌转录物。现在可以确定人粪便中的RNA分析，特别是通过质量测序进行的RNA分析，是否阐明了宿主生理学和病理生理学，并描述了肠道微生物组。我的第一个目标是开发一个计算管道来处理新生儿粪便中的大规模测序RNA。这将涉及与人类和测序的微生物基因组进行逐步比对的过程，以及先进的计算方法来确定剩余序列的身份。我的第二个目标是将所得的元转录组与同一样本中的元基因组序列进行比较，以验证转录谱与基因组普查充分不同的假设。我将通过计算机科学的研究生课程和独特的新生儿标本集的连续研究来实现这些目标。 公共卫生相关性：肠道中细菌种群的发育对人类健康和疾病至关重要，无论是在新生儿时期还是在以后的生活中。以前的努力通过列举存在的细菌种类和它们所含的基因来表征这个群体。我们相信，彻底了解哪些基因在细菌和宿主中表达，以及它们在什么时候表达，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益的新见解。

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.