Population genomic analysis of gut microbial colonization in premature infants.

许多对人类微生物组的研究低估了菌株水平遗传多样性的复杂性，部分原因是 由于计算方面的挑战。这是一个重要的问题，因为微妙的基因组变化可能会急剧 影响微生物行为，例如抗生素耐药性。需要进行紧张程度的调查，以了解 基因组随着时间的推移而变化，也是为了准确地描述微生物群落如何组装、响应 对扰动的影响，并且因人而异。我们的工作集中在婴儿肠道微生物群上，以解决这些问题 基本的生物学问题，并确定婴儿健康和早期模式之间的联系 殖民主义。该项目的目标是使用菌株分解的元基因组分析来监测微生物 在婴儿出生的头三年内在肠道内的定植。我们将检验这一假说 婴儿微生物组的配置会对稍后肠道微生物组的成熟产生负面影响 童年。如果这一假设是正确的，那么在高危个体中操纵微生物组，特别是 早产儿，可能会提供改善健康结果的机会。我们提议的工作将以 在婴儿肠道和肠道定植期间发展的微生物群落的种群结构 研究菌株持久性、菌株迁移、原位基因组多样化和移动基因的作用 元素。为了了解菌株或物种丰度的主要时间变化，我们将利用一种新的 方法推断微生物生长速度以及社区范围的基因表达。我们将进行应变- 100例新生儿及其母亲出生后三年粪便样本水平分析 我们将包括40名没有重大健康问题的早产儿，其中一半是通过剖腹产出生的；40名早产儿 发生坏死性小肠结肠炎(NEC)或迟发性败血症(LOS)的婴儿，一半是通过剖腹产出生的 以及20名足月婴儿，其中一半是通过剖腹产出生的。微生物DNA的深度测序将 能够从共存的细菌、古生菌(如果存在)、噬菌体和质粒群中重建基因组。 这将使我们能够跟踪物种成员、群落结构、代谢潜力和种群水平 遗传异质性。我们将使用这些数据来检验一些早期建立的菌株的假设 持续到最初的定殖期(目标1)；检验肠道微生物稳定的假设 群落比不稳定的肠道微生物群落拥有更高的菌株水平多样性(目标2)；并测试 新生儿期临床变量影响前三种菌株获得模式的假说 寿命年数(目标3)。提高对婴儿肠道中群落聚集和多样化的理解可能 通过揭示疾病预防和治疗战略，转化为更好的结果。这项研究 还将揭示微生物群落动力学的普遍原理，这将对其他 人类健康和科学的各个方面。

Many studies of the human microbiome underemphasize the complexity of strain-level genetic diversity, partly due to computational challenges. This is an important problem because subtle genomic alterations can sharply impact microbial behavior, e.g. antibiotic resistance. Strain-level investigations are needed to understand how genomes change over time, and also to accurately characterize how microbial communities assemble, respond to perturbations, and vary among individuals. Our work focuses on the infant gut microbiome to address these fundamental biologic questions and to identify connections between infant health and early patterns of colonization. The objective of this project is to use strain-resolved metagenomic analyses to monitor microbial colonization in the infant gut during the first three years of life. We will test the hypothesis that early configurations of the infant microbiome can negatively impact maturation of the gut microbiome later in childhood. If this hypothesis is true, then manipulation of the microbiome in at-risk individuals, particularly premature infants, may provide opportunities to improve health outcomes. Our proposed work will characterize the population structure of microbial communities that develop during colonization of the infant gut and examine the roles of strain persistence, strain immigration, in situ genome diversification, and mobile genetic elements. To understand major temporal changes in strain or species abundance, we will utilize a novel method to infer microbial growth rates as well as community wide gene expression. We will conduct strain- level analyses of fecal samples from 100 newborn infants and their mothers during the first three years of life. We will include 40 preterm infants with no major medical problems, half born via caesarean section; 40 preterm infants that develop either necrotizing enterocolitis (NEC) or late-onset sepsis (LOS), half born via caesarean section; and 20 full term infants, half born via caesarean section. Deep sequencing of microbial DNA will enable genome reconstruction from coexisting bacterial, archaeal (if present), 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 hypothesis that some early-establishing strains persist beyond the initial colonization period (Aim 1); to test the hypothesis that stable gut microbial communities possess higher strain-level diversity than unstable gut microbial communities (Aim 2); and to test the hypothesis that clinical variables in the newborn period impact patterns of strain acquisition in the first three years of life (Aim 3). Improved understanding of community assembly and diversification in the infant gut could translate to improved outcomes by uncovering strategies for disease prevention and treatment. This research will also reveal universal principles of microbial community dynamics that will have implications for other aspects of human health and science.