Comparative Community Genomics of the Gut Microbiota

描述（由申请人提供）： 该项目的全球目标是增加我们对栖息在人类胃肠道（GI）的多种微生物群落的了解。这种微生物群在人类健康中起着至关重要的作用，包括对消化过程的重要贡献，促进肠道成熟和完整性以及免疫系统的调节。此外，微生物群以几种复杂的方式与病原体相互作用。一方面，常驻细菌对肠道病原体发挥保护性屏障作用;但另一方面，它们可以通过参与宿主-微生物相互作用或抗生素耐药性的基因的水平传播来丰富传入病原体的武库。此外，许多正常良性的胃肠道菌群有可能在受损宿主中成为机会致病菌。因此，阐明胃肠道微生物群的组成和编码能力对于全面分析传染病至关重要。 为了实现这一目标，我们将从直接从粪便样品中分离的基因组DNA中产生大插入细菌人工染色体（BAC）文库。BAC文库的可用性将允许通过提供广泛的基因组序列来深入表征GI微生物群，所述基因组序列将用于阐明该群落成员的编码能力以及系统发育位置。鉴于GI微生物群的组成随年龄和饮食而变化很大，我们选择从微生物群发育的两个非常不同的阶段生成BAC库：成人和母乳喂养的婴儿，如母亲和儿童所代表的。由于广泛使用小鼠作为实验系统来研究一般的感染性疾病和特别是GI微生物群，我们还将为小鼠母亲和哺乳幼崽生成BAC文库。为了最大限度地了解传染病的进化和生态学，我们将把测序工作的重点放在与致病性和其他生态相互作用相关的基因组区域，包括微生物群落成员之间以及微生物与宿主之间。

DESCRIPTION (provided by applicant): The global aim of this project is to increase our understanding of the diverse microbial community that inhabits the human gastrointestinal (GI) tract. This microbiota plays essential roles in human health, including a significant contribution to the digestive process, promotion of gut maturation and integrity and modulation of the immune system. Moreover, the microbiota interacts with pathogenic agents in several complex ways. On one hand, resident bacteria exert a protective barrier effect against enteropathogens; but, on the other, they could contribute to enrich the arsenal of incoming pathogens through horizontal transmission of genes involved in host-microbe interaction or antibiotic resistance. In addition, many normally benign GI commensals have the potential to become opportunistic pathogens in compromised hosts. Elucidating the composition and coding capabilities of the GI microbiota is therefore crucial for a comprehensive analysis of infectious disease. To advance towards this goal, we will produce large-insert bacterial artificial chromosome (BAC) libraries from genomic DNA isolated directly from fecal samples. The availability of BAC libraries will allow for a deep characterization of the GI microbiota by providing extensive genomic sequences that will serve to elucidate the coding capabilities as well as the phylogenetic positions of the members of this community. Given that the composition of the GI microbiota varies greatly with age and diet, we have chosen to generate BAC libraries from two very distinct stages of microbiota development: adults and breast-feeding infants, as represented by mother and child. Because of the widespread use of mice as an experimental system to study both infectious diseases in general and the GI microbiota in particular, we will also generate BAC libraries for mouse mother and suckling pup. To maximize our insight into the evolution and ecology of infectious disease, we will focus our sequencing efforts towards genomic regions relevant to pathogenicity and other ecological interactions, both among the microbial community members and between microbes and host.