Doctoral Dissertation Research: Microbial Community Assembly in Primates

博士论文研究：灵长类微生物群落组装

• 批准号: 1455848
• 负责人: Anne Yoder
• 金额: $ 2.96万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-03-15 至 2017-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1455848&HistoricalAwards=false
• 关键词: Doctoral; Dissertation; Research; Microbial; Community

The gut is home to tens of trillions of bacteria that are integral for nutrient digestion, gut development, and defense against disease. But it is not clear how these communities of microbes are established, how they respond to diet and disease, and how they may change through an individual's life. This project will characterize and compare the colonization process from birth to weaning in infants of three lemur species, each with a unique gut morphology and life history. Additional sampling from the weaned infants of one lemur species will track the re-colonization process after infection with Cryptosporidium, an intestinal pathogen. Colonization after birth and disease will be compared to elucidate the rules governing gut community development. Because lemurs and humans are both primates, the study findings may have a profound impact on current understanding of the role of microbiota in human health and development. Additional broader impacts include training of a female graduate student in the STEM sciences, and extensive public science education and outreach efforts. This two-year project will analyze bacterial 16S rDNA and metagenomic profiles to tease apart the potentially divergent effects of host phylogenetic history and diet on the gut microbiota community structure and to examine the associated microbial signatures for potential effects on lemur health and nutritional uptake. Fecal samples will be collected at the Duke Lemur Center from Varecia variegata (frugivorous), Lemur catta (generalist), and Propithecus coquereli (folivorous). DNA will be extracted and sequenced using two different approaches to determine which bacterial species are present and what functions each community can perform. First, the v4 region of the 16S gene will be sequenced and analyzed to identify bacterial taxa and measure their frequencies in each community. Next, the investigators will sequence genomic reads from the entire microbiome, which includes viruses, fungi, protozoans, and other organisms in addition to bacteria. Metagenomic reads will be compared to NCBI databases to identify all (bacterial and non-bacterial) community members, as well as the functions encoded by the genes from each community. This will be the first project to intensively and longitudinally study the composition and community development of gut microbiota across multiple species within a phylogenetically related but ecologically diverse group of mammals, thus enabling modeling of ecological processes in the gut for application to other primates, including humans. A novel bioinformatics pipeline for metagenomic data analysis will be made publicly available as an open source tool through an online repository. The proposed activities will not only shed light on microbial contributions to primate evolution and ecology, but the results will provide a springboard for public education through local outreach.

肠道是数万亿细菌的家园，这些细菌对于营养消化、肠道发育和防御疾病至关重要。但目前尚不清楚这些微生物群落是如何建立的，它们如何对饮食和疾病做出反应，以及它们如何在个人的生活中发生变化。该项目将描述和比较三种狐猴物种婴儿从出生到断奶的定植过程，每种狐猴物种都有独特的肠道形态和生活史。对一种狐猴的断奶婴儿进行额外取样，将追踪感染隐孢子虫（一种肠道病原体）后的重新定殖过程。将比较出生后的定植和疾病，以阐明控制肠道群落发展的规则。由于狐猴和人类都是灵长类动物，该研究结果可能对目前对微生物群在人类健康和发展中的作用的理解产生深远的影响。其他更广泛的影响包括对女研究生进行 STEM 科学培训，以及广泛的公共科学教育和推广工作。这个为期两年的项目将分析细菌 16S rDNA 和宏基因组图谱，以梳理宿主系统发育历史和饮食对肠道微生物群落结构的潜在不同影响，并检查相关微生物特征对狐猴健康和营养吸收的潜在影响。杜克狐猴中心将从 Varecia variegata（果食性）、Lemur catta（多面性）和 Propithecus coquereli（叶食性）采集粪便样本。将使用两种不同的方法提取 DNA 并进行测序，以确定存在哪些细菌物种以及每个群落可以执行哪些功能。首先，将对 16S 基因的 v4 区域进行测序和分析，以识别细菌分类单元并测量它们在每个群落中的频率。接下来，研究人员将对整个微生物组的基因组读数进行测序，其中包括病毒、真菌、原生动物和除细菌外的其他生物体。宏基因组读数将与 NCBI 数据库进行比较，以识别所有（细菌和非细菌）群落成员，以及每个群落基因编码的功能。这将是第一个深入和纵向研究系统发育相关但生态多样化的哺乳动物群体中多个物种肠道微生物群组成和群落发展的项目，从而能够对肠道生态过程进行建模，以应用于包括人类在内的其他灵长类动物。用于宏基因组数据分析的新型生物信息学管道将通过在线存储库作为开源工具公开提供。拟议的活动不仅将揭示微生物对灵长类动物进化和生态学的贡献，而且其结果还将通过当地推广为公共教育提供跳板。