EFFECTS OF INFANT NUTRITION ON FECAL RESISTOME ESTABLISHMENT

婴儿营养对粪便抵抗力建立的影响

• 批准号: 9180554
• 负责人: Aimee M Moore
• 金额: $ 14.36万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2021-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9180554
• 关键词: Adolescent; Affect; Age-Months; Agriculture; Aliquot; Antibiotic Resistance; Antibiotic-resistant organism; Antibiotics; Applied Skills; Archives; Area; Bacteria; Bifidobacterium; Bioinformatics; Biometry; Breast Feeding; Carbapenems; Cattle; Cephalosporins; Child; Child health care; Childhood; Clinical; Collection; Communities; Community Developments; Complement; Complex; Computational Biology; Coupled; Data; Data Set; Databases; Development; Diet; Doctor of Philosophy; Enteral; Epidemiology; Exposure to; Feces; Food; Future; Gastroenterology; Generations; Genetic; Genome; Genomics; Genotype; Goals; Health; Human; Human Microbiome; Infant; Infection; Informed Consent; Institutional Review Boards; Investigation; Knowledge; Laboratories; Lead; Learning; Life; Link; Longitudinal Studies; Mentors; Mentorship; Metabolic; Metagenomics; Microbiology; Milk; Monobactams; Mothers; Neonatal; Neonatology; Organism; Outcome; Phenotype; Phylogenetic Analysis; Physicians; Property; Publications; Research; Research Personnel; Research Project Grants; Resistance; Resolution; Sampling; Science; Scientist; Shotgun Sequencing; Siblings; Soil; Solid; Source; Soy Milk; Structure; Surveys; Systems Biology; Taxon; Techniques; Testing; Time; Training; Translating; Translational Research; Twin Multiple Birth; Whole-Genome Shotgun Sequencing; Work; bacterial resistance; base; beta-Lactam Resistance; beta-Lactams; career; clinically actionable; clinically relevant; cohort; combat; computer framework; computer program; critical period; experience; feeding; gut microbiota; infancy; infant nutrition; innovation; interest; microbial; microbial community; microbiome; microbiota; next generation sequencing; novel; novel strategies; pathogen; programs; resistance gene; skills; soy; statistics; technology development; tool; trend

Project Summary My research interests include the development of the neonatal enteric microbiome, with a current focus on community-encoded functions such as antibiotic resistance or metabolic functions. I have worked since 2009 in the laboratory of Gautam Dantas, Ph.D.; during this time I have become proficient in a variety of benchtop techniques necessary for work in microbiology and genomics research, have taken classes in statistics and computer programming, and gained experience analyzing increasingly large and complex collections of metagenomic data. I have collaborated with colleagues with expertise in genetics, microbiology, gastroenterology, statistics, and neonatology, resulting in several publications. This proposal includes further didactic training in bioinformatics and computational biology, with a focus on enhancing my skills and knowledge in programming, statistics, and systems biology, as well as a research plan that will complement my formal coursework by providing ample opportunity for me to apply these skills. I will continue to work with my mentors Gautam Dantas, Ph.D., an expert in community-wide functions of human gut and soil bacteria and Phillip Tarr, MD, an physician-scientist who is a leader in the field of pediatric microbiome research, and has a track record of mentoring junior scientists to independence. My oversight committee includes Barak Cohen, Ph.D., an expert in computational and systems biology, William Shannon, Ph.D., an expert in biostatistics, and F. Sessions Cole, MD, an expert in genetics and translational research. The ongoing mentorship of these collaborators with diverse areas of expertise will enhance my didactic and hands-on training and, combined with my clinical experience as an academic neonatologist, will prepare me for an independent career as a physician scientist investigating the impact of the human microbiome on neonatal health. The research project described in this proposal is potentially clinically relevant, as bacterial resistance to all antibiotics urgently threatens human health. The antibiotic resistance genes harbored by the human gut microbiota (fecal resistome) are an epidemiologically important genetic reservoir that can potentially transfer resistance to human pathogens. Understanding the clinical determinants of fecal resistance gene carriage may lead to novel strategies to combat the spread of resistant organisms in human communities. Our recent work has indicated that the fecal resistome of healthy children is far more diverse than previously suspected, and suggests that the fecal resistome is established in early infancy, with infant resistomes being distinct from their mothers' in by 1-2 months of life and developing similarly to their twin siblings'. The goal of this proposal is to test the hypothesis that infant diet significantly influences fecal resistome and fecal microbial community development. Prior work by me and my mentors Dr. Dantas and Dr. Tarr has shown that functional metagenomic selections are an efficient means of broadly sampling pediatric fecal resistomes. We will use high-throughput functional metagenomic selections coupled with next-generation sequencing and a computational pipeline developed in our lab (Parallel Assembly and Annotation of Functional Metagenomic Selections, PARFuMS) to study longitudinal fecal resistome development in the first year of life in infants that are breastfed and formula fed (cow's milk and soy formula both represented) with an emphasis on changes associated with feeding transitions (e.g. from breastmilk to formula, initiating solid food). The samples to be used in this study have already been collected with informed consent for a separate IRB-approved study, and are stored in the Dantas lab. Functional metagenomic selections on a small subset of samples will be used to identify resistance genes that are clinically important and unique to this cohort. We will use the phenotype-linked data generated by functional metagenomic selections to quantify the correlation between specific resistance genes and genetic motifs and resistance phenotypes, which will enhance existing resistance gene databases with functional information and will provide a framework for identifying the most potentially dangerous resistance genes by statistically linking them with undesirable resistance phenotypes. Shotgun sequencing of a much larger sample set will allow high-resolution, quantitative data on the phylogenetic composition of the microbiota and predicted microbiome-encoded functions. We will use this rich dataset to correlate clinical variables with changes in the resistome, as well as to examine the effects of phylogenetic shifts on resistome development. This comprehensive research strategy is novel because it will be, to our knowledge, the first longitudinal study of the effects of early infant nutrition on fecal resistome and microbiome establishment, and will integrate functional metagenomic techniques and whole-genome shotgun sequencing with novel computational strategies developed expressly for longitudinal resistome study. The computational strategies developed for this study will provide a theoretical framework for future longitudinal investigations of other community-wide microbial functions. The work in this proposal will integrate with my clinical experience, my proposed didactic training in bioinformatics, and my mentored experience with metagenomics to prepare me for a career as an independent investigator conducting hypothesis-based research on thedevelopmental properties of the human microbiome and translating this knowledge to impact child health outcomes.

项目概要 我的研究兴趣包括新生儿肠道微生物组的发展，目前的重点是 关于社区编码的功能，例如抗生素耐药性或代谢功能。我从那时起就工作了 2009年在Gautam Dantas博士实验室；这段时间我已经熟练掌握了多种 微生物学和基因组学研究工作所需的台式技术，已参加过以下课程 统计和计算机编程，并获得了分析日益庞大和复杂的经验 宏基因组数据的集合。我与具有遗传学、微生物学专业知识的同事合作， 胃肠病学、统计学和新生儿学，发表了多篇出版物。该提案还包括 生物信息学和计算生物学的教学培训，重点是提高我的技能和 编程、统计学和系统生物学方面的知识，以及补充我的研究计划 正式的课程作业为我提供了充分的机会来应用这些技能。我将继续与我的 导师 Gautam Dantas 博士是人类肠道和土壤细菌全社区功能方面的专家， 菲利普·塔尔 (Phillip Tarr) 医学博士是一位医师科学家，是儿科微生物组研究领域的领导者，拥有 指导初级科学家独立的记录。我的监督委员会包括巴拉克·科恩， 博士，计算和系统生物学专家，威廉·香农博士，生物统计学专家，以及 F. Sessions Cole，医学博士，遗传学和转化研究专家。对这些人的持续指导 具有不同专业领域的合作者将加强我的教学和实践培训，并结合 凭借我作为学术新生儿科医生的临床经验，将为我作为一名独立的职业做好准备 医师科学家研究人类微生物组对新生儿健康的影响。 该提案中描述的研究项目具有潜在的临床相关性，因为细菌耐药性 所有抗生素都迫切威胁着人类健康。人类肠道携带的抗生素抗性基因 微生物群（粪便耐药组）是流行病学上重要的遗传库，可能会转移 对人类病原体的抵抗力。了解粪便抗性基因携带的临床决定因素可能 产生新的策略来对抗耐药生物在人类社区中的传播。我们最近的工作 表明健康儿童的粪便耐药组比之前怀疑的更加多样化，并且 表明粪便抵抗组是在婴儿早期建立的，婴儿抵抗组不同于婴儿时期的抵抗组。 母亲在出生后 1-2 个月内的发育与双胞胎兄弟姐妹相似。该提案的目标是 检验婴儿饮食显着影响粪便抗性组和粪便微生物群落的假设 发展。 我和我的导师 Dantas 博士和 Tarr 博士之前的工作表明，功能宏基因组 选择是广泛采样儿科粪便耐药组的有效方法。我们将使用高通量 功能宏基因组选择与下一代测序和计算流程相结合 我们实验室开发的（功能宏基因组选择的并行组装和注释，PARFuMS） 研究母乳喂养和配方奶粉喂养的婴儿第一年的纵向粪便抵抗组发育 喂养（牛奶和大豆配方奶粉均代表），重点是与喂养相关的变化 过渡（例如从母乳到配方奶、开始吃固体食物）。本研究中使用的样本有 已在知情同意的情况下收集用于 IRB 批准的单独研究，并存储在 Dantas 中 实验室。对一小部分样本的功能宏基因组选择将用于识别抗性基因 这些对于该队列来说具有临床重要性和独特性。我们将使用由以下方法生成的表型相关数据 功能宏基因组选择，以量化特定抗性基因与遗传之间的相关性 基序和抗性表型，这将增强现有抗性基因数据库的功能 信息，并将提供一个框架，通过以下方式识别最有潜在危险的抗性基因： 统计上将它们与不良的耐药表型联系起来。对更大样本进行鸟枪法测序 这套系统将提供有关微生物群系统发育组成的高分辨率定量数据，并预测 微生物组编码的功能。我们将使用这个丰富的数据集将临床变量与变化联系起来 抗性组，以及检查系统发育变化对抗性组发展的影响。这 综合研究策略是新颖的，因为据我们所知，这将是第一个纵向研究 早期婴儿营养对粪便抵抗组和微生物组建立的影响，并将整合 功能宏基因组技术和全基因组鸟枪法测序与新颖的计算 专门为纵向抗性组研究制定的策略。开发的计算策略 这项研究将为未来其他社区范围内的纵向调查提供理论框架 微生物功能。本提案中的工作将与我的临床经验、我提出的教学相结合 生物信息学方面的培训，以及我在宏基因组学方面的指导经验，为我的职业生涯做好了准备 独立调查员对人类的发育特性进行基于假设的研究 微生物组并将这些知识转化为影响儿童健康结果。