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: 9918341
• 负责人: Aimee M Moore
• 金额: $ 15.49万
• 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 2020-09-15
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9918341
• 关键词: Adolescent; Affect; Age-Months; Agriculture; Aliquot; Antibiotic Resistance; Antibiotic-resistant organism; Antibiotics; Archives; Area; Bacteria; Bifidobacterium; Bioinformatics; Biometry; Breast Feeding; Breastfed infant; Carbapenems; Cattle; Cephalosporins; Child; Child Health; Childhood; Clinical; Collection; Communities; Community Developments; Complement; Complex; Computational Biology; Coupled; Dangerousness; Data; Data Set; Databases; Development; Diet; Doctor of Philosophy; Epidemiological trend; Epidemiology; Exposure to; Feces; Food; Future; Gastroenterology; Generations; Genetic; Genetic Research; Genomics; Genotype; Goals; Health; Human; Human Microbiome; Human Milk; Infant; Infant formula; 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; Scientist; Shotgun Sequencing; Siblings; Soil; Solid; Source; Structure; Surveys; Systems Biology; Techniques; Testing; Time; Training; Translating; Translational Research; Twin Multiple Birth; Whole-Genome Shotgun Sequencing; Work; bacterial community; bacterial resistance; base; beta-Lactam Resistance; beta-Lactams; career; clinically actionable; clinically relevant; cohort; combat; computational pipelines; computer framework; computer program; critical period; experience; fecal microbiota; feeding; genome sciences; gut microbiome; gut microbiota; human pathogen; infancy; infant nutrition; innovation; interest; microbial; microbial community; microbiome; microbiome research; microbiota; next generation sequencing; novel; novel strategies; resistance gene; skills; soy; statistics; technology development; tool

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.

项目摘要 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 在社区编码的功能上，例如抗生素抗性或代谢功能。从那以后我工作过 2009年在Gautam Dantas博士学位的实验室中；在这段时间里，我已经精通多种 微生物学和基因组学研究所必需的台式技术已上课 统计和计算机编程，并获得了分析越来越大而复杂的经验 宏基因组数据的集合。我曾与同事合作，具有遗传学，微生物学专业知识， 胃肠病学，统计和新生儿学，导致了几个出版物。该建议包括进一步 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，统计和系统生物学方面的知识以及将补充我的研究计划 正式的课程为我提供了充分的机会运用这些技能。我将继续与我的 导师Gautam Dantas博士，人类肠道和土壤细菌的社区范围范围专家 医学博士菲利普·塔尔（Phillip Tarr），医师科学家，他是小儿微生物组研究领域的领导者 指导初级科学家到独立的记录。我的监督委员会包括Barak Cohen， 博士学位，计算与系统生物学专家，威廉·香农（William Shannon）博士，生物统计学专家， F. Sessions Cole，医学博士，遗传学和转化研究专家。这些持续的指导 具有不同专业知识领域的合作者将增强我的教学和动手培训，并结合 凭借我作为学术新生儿学家的临床经验，我将为我做好独立职业的准备 医师科学家研究了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可能在临床上与细菌抗性有关 对所有抗生素迫切威胁人类健康。人类肠道含有的抗生素抗性基因 微生物群（粪便抵抗组）是一个流行病学上重要的遗传储层，可以潜在地转移 对人类病原体的抗性。了解粪便抗性基因运输的临床决定因素可能 导致新的策略与抗性生物在人类社区中的传播作用。我们最近的工作 已经表明，健康儿童的粪便抵抗比以前的怀疑要多样化， 表明粪便抗性是在婴儿早期建立的，婴儿抗药性与其不同 母亲“到1-2个月的生命中，与双胞胎兄弟姐妹的发展类似”。该提议的目的是 检验婴儿饮食会显着影响粪便抗粪便和粪便微生物群落的假设 发展。 我和我的导师丹塔斯博士和塔尔博士的先前工作表明，功能性宏基因组 选择是对小儿粪便抗性的有效方法。我们将使用高通量 功能性宏基因组选择，结合下一代测序和计算管道 在我们的实验室中开发（功能性元基因组选择，parfums的平行组装和注释） 研究母乳喂养的婴儿的第一年纵向粪便抵抗体的发展 美联储（牛奶和大豆配方均代表），重点是与喂养相关的变化 过渡（例如从母乳到配方奶粉，启动固体食品）。本研究中要使用的样品 已通过知情同意书收集了一项由IRB批准的研究，并存储在Dantas中 实验室。一小部分样品中的功能性宏基因组选择将用于识别抗性基因 该队列在临床上很重要且独特。我们将使用由表型连接的数据生成的 功能性宏基因组选择，以量化特异性抗性基因与遗传之间的相关性 主题和抗性表型，它将增强具有功能性的现有抗药性基因数据库 信息并将提供一个框架，以识别最可能的危险抗性基因 从统计上将它们与不良抗性表型联系起来。更大样本的shot弹枪测序 集合将允许有关菌群的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。我们将使用此丰富的数据集将临床变量与变化相关联 抵抗组以及检查系统发育转移对抵抗组发育的影响。这 综合研究策略是新颖的，因为据我们所知，它将是首次纵向研究 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 具有新型计算的功能性宏基因组技术和全基因组shot枪测序 明确制定了用于纵向抵抗组研究的策略。为 这项研究将为未来对其他社区的纵向调查提供一个理论框架 微生物功能。该提案中的工作将与我的临床经验相结合，我提出的教学 在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，为我做好准备 独立研究者对人类的开发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。