Population genomic analysis of gut microbial colonization in premature infants.

许多关于人类微生物组的研究都没有充分强调菌株水平遗传多样性的复杂性， 由于计算的挑战。这是一个重要的问题，因为细微的基因组改变可以 影响微生物行为，例如抗生素耐药性。需要进行应变水平的调查，以了解 基因组随着时间的推移而变化，同时也准确地描述了微生物群落如何组装，反应， 的干扰，并在个体之间变化。我们的工作重点是婴儿肠道微生物组，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， 殖民化本项目的目的是使用菌株分辨宏基因组分析来监测微生物 在婴儿出生后的前三年内在婴儿肠道中定植。我们将检验早期 婴儿微生物组的构型可能对婴儿后期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，那么在高危人群中操纵微生物组， 早产儿，可以提供改善健康结果的机会。我们提出的工作将体现 在婴儿肠道定植期间发育的微生物群落的群体结构， 研究菌株持久性、菌株迁移、原位基因组多样化和移动的遗传的作用 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 方法来推断微生物生长速率以及社区范围内的基因表达。我们将进行应变- 对100名新生儿及其母亲在生命的头三年期间的粪便样本进行水平分析。 我们将纳入40名没有重大医疗问题的早产儿，其中一半通过剖腹产出生; 40名早产儿， 发生坏死性小肠结肠炎（NEC）或迟发性脓毒症（LOS）的婴儿，一半通过剖腹产出生 20名足月婴儿，其中一半通过剖腹产出生。微生物DNA的深度测序将 能够从共存的细菌、古细菌（如果存在）、噬菌体和质粒群体进行基因组重建。 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 遗传异质性我们将用这些数据来检验一个假设，即一些早期建立的菌株 持续超过初始定植期（目标1）;为了检验稳定的肠道微生物 群落比不稳定的肠道微生物群落具有更高的菌株水平多样性（目标2）;并测试 假设新生儿期的临床变量影响前三个阶段的应变获得模式 寿命（目标3）。提高对婴儿肠道中群落组装和多样化的理解， 通过揭示疾病预防和治疗战略，转化为更好的结果。本研究 还将揭示微生物群落动态的普遍原则，这将对其他生物学领域产生影响。 人类健康和科学方面。

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.