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.

项目摘要 我的研究兴趣包括新生儿肠道微生物组的开发，目前的重点是 关于社区编码的功能，如抗生素耐药性或代谢功能。从那以后我一直在工作 2009年在Gautam Dantas的实验室获得博士学位；在此期间，我精通了各种 微生物学和基因组研究工作所需的台式技术已经在 统计和计算机编程，并获得了分析日益庞大和复杂的经验 元基因组数据的集合。我与在遗传学、微生物学、 胃肠病学、统计学和新生儿学，出版了几本书。这项提议还包括 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，以及一个研究计划，这将补充我的 正规的课程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，人类肠道和土壤细菌的社区功能专家，以及 菲利普·塔尔，医学博士，内科科学家，儿科微生物组研究领域的领导者，拥有 指导初级科学家走向独立的记录。我的监督委员会包括巴拉克·科恩， 威廉·香农博士，生物统计学专家，以及 F·塞申斯·科尔，医学博士，遗传学和翻译研究专家。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授课和实践培训，并结合 以我作为一名学术新生儿专家的临床经验，我将为独立的职业生涯做好准备 研究人类微生物群对新生儿健康影响的内科科学家。 这项建议中描述的研究项目具有潜在的临床意义，因为细菌耐药性 对所有抗生素的使用严重威胁着人类的健康。人类肠道中蕴藏的抗生素耐药基因 微生物区系(粪便耐药组)是流行病学上重要的遗传库，可以潜在地转移 对人类病原体的抵抗力。了解粪便耐药基因携带的临床决定因素可能 导致新的战略，以打击抗药性生物在人类社区的传播。我们最近的工作 已经表明，健康儿童的粪便抵抗力比之前怀疑的要多样化得多。 说明粪便抵抗体是在婴儿早期建立的，婴儿的抵抗体与他们的 母亲出生1-2个月，发育与她们的双胞胎兄弟姐妹相似。这项提议的目标是 检验婴儿饮食显著影响粪便抵抗力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之前的工作表明，功能元基因组学 选择是广泛抽样儿科粪便耐药菌的有效方法。我们将使用高吞吐量 结合下一代测序和计算流水线的功能元基因组选择 我们实验室开发的(功能元基因组选择的并行组装和注释，Parfum)以 研究母乳喂养和配方奶婴儿在出生第一年的纵向粪便抵抗力发展 饲料(牛奶和大豆配方都代表)，强调与喂养相关的变化 过渡(例如，从母乳到配方奶粉，开始吃固体食物)。这项研究中使用的样本包括 已在知情同意下为IRB批准的单独研究收集，并存储在Dantas中 实验室。在一小部分样本上的功能性元基因组选择将被用于鉴定抗性基因 在临床上很重要，对这个队列来说是独一无二的。我们将使用由生成的表型关联数据 功能元基因组选择用于量化特定抗病基因与遗传的相关性 基序和抗病表型，这将加强现有的抗病基因数据库与功能 信息，并将提供一个框架，通过以下方式识别最具潜在危险的抗性基因 从统计上看，它们与不良耐药表型有关。对大得多的样本进行鸟枪测序 SET将允许提供关于微生物区系系统发育组成和预测的高分辨率、定量数据 微生物组编码的功能。我们将使用这个丰富的数据集来将临床变量与 以及研究系统发育变化对抗性组发育的影响。这 综合研究策略是新颖的，因为据我们所知，它将是第一个纵向研究 婴幼儿早期营养对粪便抵抗力和微生物组建立的影响 功能元基因组学技术与全基因组鸟枪式测序 专门为纵向电阻组研究开发的策略。为以下目的开发的计算策略 这项研究将为今后社区范围内其他纵向调查提供理论框架 微生物的功能。这项建议中的工作将与我的临床经验、我建议的教义相结合 生物信息学培训，以及我在元基因组学方面的指导经验，为我的职业生涯做好了准备 对人类发育特性进行基于假设的研究的独立调查者 并将这一知识转化为影响儿童健康结果的知识。