Population genomic analysis of gut microbial colonization in premature infants

描述（由申请人提供）：与人体相关的微生物群落，特别是胃肠道，在健康和疾病中起着关键作用。本提案的目的是了解肠道微生物演替的特定模式如何与健康和疾病相关，特别是与新生儿坏死性小肠结肠炎（NEC）相关。虽然现有的证据表明，肠道微生物有助于NEC的发病机制，这种关系的细节仍然知之甚少。目前，对早产儿肠道定植过程以及有无NEC早产儿肠道定植过程的差异知之甚少。我们提出了互补的高通量系统发育和宏基因组分析来研究出生后前三周内早产儿肠道的微生物定植。我们提出的工作将阐明，在高分辨率，在早产儿肠道定植过程中发展的微生物群落的人口结构，并研究早期殖民者的作用，胃肠道介导的选择，移民，移动的元素对基因组变异和微生物生存的影响，并研究这些过程如何与NEC的发病。我们将使用“下一代”测序来解决物种和人口水平的社区演替模式在关键的初始时期的肠道定植在婴儿做和不继续发展NEC。我们将使用出生后前三周每天收集的粪便样本的高通量16S rRNA标签测序来描述社区发展。然后，我们将对这些粪便时间序列样本中的一半进行微生物DNA的深度宏基因组测序，以重建共存细菌，古细菌，噬菌体和质粒群体的基因组。这将使我们能够跟踪物种成员，社区结构，代谢潜力和种群水平的遗传异质性。我们将使用这些数据来测试初始聚生体预测后续群落多样性的程度[目标1]，噬菌体介导的原位多样化的重要性，插入元件，和质粒与移民在确定人口结构和代谢潜力[目标2]，并定义与健康和疾病相关的生态轨迹[目标3]。我们的初步宏基因组数据最终证明，所提出的方法可以用来重建近完整的基因组共存的生物体从早产儿肠道粪便样本有足够的人口深度来分析人口异质性和动态。对早产儿肠道中定植过程的更好理解可以通过提出更有效的疾病预防和治疗策略来改善早产儿的结局。更广泛地说，这项研究将揭示生态系统殖民动态的各个方面，这些方面对人类健康和环境的其他方面有影响。!

DESCRIPTION (provided by applicant): Microbial communities associated with the human body, in particular the gastrointestinal tract, play crucial roles in health and disease. The objective of this proposal is to understand how specific patterns in gut microbial succession are related to health and disease, and specifically to neonatal necrotizing enterocolitis (NEC). Although available evidence suggests that intestinal microbes contribute to the pathogenesis of NEC, the details of this relationship remain poorly understood. At present, relatively little is known about the gut colonization process in premature newborns, and about differences between this process in premature infants with and without NEC. We propose complementary high-throughput phylogenetic and metagenomic analyses to study microbial colonization of the premature infant gut during the first three weeks after birth. Our proposed work will elucidate, at high resolution, the population structure of microbial communities that develop during colonization of the premature infant gut and examine the roles of early colonists, gastrointestinal tract-mediated selection, immigration, the effects of mobile elements on genomic variation and microbial survival, and examine how these processes relate to onset of NEC. We will use "next-generation" sequencing to resolve species- and population-level community succession patterns during the critical initial period of gut colonization in babies that do and do not go on to develop NEC. We will profile community development using high-throughput 16S rRNA tag sequencing of stool samples collected daily during the first three weeks after birth. We will then carry out deep metagenomic sequencing of microbial DNA from half of these fecal time series samples to reconstruct genomes for coexisting bacterial, archaeal, phage, and plasmid populations. This will allow us to track species membership, community structure, metabolic potential, and population-level genetic heterogeneity. We will use these data to test the extent to which initial consortia predict succeeding community diversity [Aim 1], the importance of in situ diversification mediated by phage, insertion elements, and plasmids vs. immigration in determining population structure and metabolic potential [Aim 2], and to define ecological trajectories that correlate with health and disease [Aim 3]. Our preliminary metagenomic data conclusively demonstrate that the proposed approach can be used to reconstruct near-complete genomes of coexisting organisms from premature infant gut fecal samples with sufficient population depth to analyze population heterogeneity and dynamics. Improved understanding of the colonization process in the premature infant gut could translate to improved outcomes for premature babies by suggesting more effective strategies for disease prevention and treatment. More broadly, this research will uncover aspects of ecosystem colonization dynamics that have implications for other aspects of human health and the environment. !