Doctoral Dissertation Research: Microbial Community Assembly in Primates

肠道是数万亿细菌的家园，这些细菌对营养消化、肠道发育和抵御疾病至关重要。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，以及它们如何在个体的一生中发生变化。本项目将描述和比较三种狐猴从出生到断奶的定植过程，每一种狐猴都有独特的肠道形态和生活史。从一种狐猴的断奶幼猴身上额外取样，将追踪感染隐孢子虫（一种肠道病原体）后的再定植过程。将比较出生后和疾病后的定植，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，研究结果可能对目前对微生物群在人类健康和发育中的作用的理解产生深远的影响。其他更广泛的影响包括培养一名STEM科学领域的女研究生，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群落结构的潜在不同影响，并研究相关的微生物特征对狐猴健康和营养摄取的潜在影响。杜克狐猴中心将收集vararecia variegata（果食性）、catta狐猴（通用型）和prothecus coquereli（叶食性）的粪便样本。DNA的提取和测序将使用两种不同的方法来确定哪些细菌种类存在，以及每个群落可以执行什么功能。首先，对16S基因的v4区进行测序和分析，确定细菌类群并测量其在每个群落中的频率。接下来，研究人员将对整个微生物组进行基因组测序，其中包括病毒、真菌、原生动物和除细菌外的其他生物。宏基因组读数将与NCBI数据库进行比较，以确定所有（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在一个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的组成和群落发展的项目，从而使肠道生态过程的建模能够应用于包括人类在内的其他灵长类动物。一种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。拟议的活动不仅将阐明微生物对灵长类动物进化和生态的贡献，而且还将通过地方宣传为公共教育提供跳板。

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.