Comprehensive characterization of parasite and commensal assemblages in humans

项目总结/摘要 寄生虫引起的疾病在全球范围内造成大量的发病率和死亡率。然而， 证据表明，人类和共生体（这里定义为所有宿主依赖的真核生物）之间的关系， 生物体，包括寄生虫和寄生虫）并不总是有害的，事实上，有时可能会赋予 重要的健康优势。共生体集合体可能有助于消化，赋予保护性免疫，或者， 矛盾的是，提供保护免受病原性寄生虫感染和疾病。我们目前了解到， 引起人类疾病的真核寄生虫的生物学和生态学，但我们对它们的整体生物学和生态学知之甚少。 原生动物和寄生在人类身上的蠕虫群落的结构和功能。这 与细菌学和真菌学领域相比， 通过对细菌和真菌的研究， 微生物群事实上，目前大多数寄生虫学方法都是为了一个不同的目的而设计的： 特定的致病微生物虽然无偏见的社区分析方法已经得到验证， 对于原核生物和真菌的标准化，对于真核生物共生体，目前不存在这样的方法，包括 寄生虫由于没有标准化的方法，研究真核生物的有益作用 共生体群落及其在寄生虫病中的潜在作用是一个关键的知识空白。 这项工作的最终目标是创建一个统一的，有效的研究工具， 人类共生体组合，可与细菌和真菌 微生物群落为此，我们开发了一种新的全面（能够识别所有生物体） 无论先前的表征如何，包括新生物）真核共生体聚集的测定 基于新设计的PCR引物，新的降噪策略和用户- 友好的生物信息学管道。我们开发该测定法的目标是：1）创建一个“行业标准”， 共生体群落评估，类似于其他标准化微生物组测定，2）开发广泛的- 适用于所有生物体和所有样品类型的研究方法，3）有助于我们了解 人类真核生物共生体群落的基础生物学和生态学; 4）为未来的发展提供信息， “通用”诊断工具和有针对性的抗寄生虫疗法。我们将通过计算机模拟优化测定， 定制数据库，体外使用“模拟社区”，以及离体使用来自实验感染的 动物然后，我们将通过分析两个人的样本来验证管道并评估其性能。 不同的人群，其中肠道寄生虫先前已通过显微镜和PCR表征。 通过这个项目的完成，我们希望提供一个急需的研究工具，将改善我们的 了解人类共生体社区，反过来，这将为人类健康和 药

PROJECT SUMMARY/ABSTRACT Diseases attributed to parasites cause substantial morbidity and mortality globally. However, there is mounting evidence that the relationship between humans and symbionts (defined here as all host-dependent eukaryotic organisms, including parasites and commensals) is not always detrimental and, in fact, may sometimes confer important health advantages. Symbiont assemblages may aid in digestion, confer protective immunity, or, paradoxically, provide protection from pathogenic parasite infection and disease. We currently understand the biology and ecology of eukaryotic parasites that cause human disease, but we know very little about the overall structure and function of communities of protozoans and helminths that also colonize humans. This shortcoming hinders progress in the field of parasitology, compared to the fields of bacteriology and mycology, which have revolutionized our understanding of human health through the study of bacterial and fungal microbiota. Indeed, most current parasitological methods are designed for a different purpose: to target specific, pathogenic organisms. Although methods for unbiased community analysis have been validated and standardized for prokaryotes and fungi, no such methods currently exist for eukaryotic symbionts, including parasites. With no standardized methods in place, research into the beneficial effects of eukaryotic symbiont communities and their potential role in parasitic disease represents a critical knowledge gap. The ultimate objective of this work is to create a uniform, validated research tool for the study of human symbiont assemblages, comparable to what has been achieved for the bacterial and fungal microbiomes. To this end, we have developed a novel comprehensive (able to identify all organisms regardless of prior characterization, including novel organisms) assay for eukaryotic symbiont assemblage characterization that is based on newly-designed PCR primers, a novel noise reduction strategy, and a user- friendly bioinformatic pipeline. Our goals in developing this assay were to 1) create an “industry standard” for symbiont community assessment, analogous to other standardized microbiome assays, 2) develop a broadly- applicable research method useful for all organisms and all sample types, 3) contribute to our understanding of the basic biology and ecology of human eukaryotic symbiont communities and 4) inform future development of “universal” diagnostic tools and targeted anti-parasitic therapeutics. We will optimize the assay in silico using custom databases, in vitro using a “mock community”, and ex vivo using samples from experimentally-infected animals. We will then validate the pipeline and assess its performance by analyzing human samples from two different populations in which intestinal parasites have previously been characterized by microscopy and PCR. Through completion of this project, we hope to provide a critically-needed research tool that will improve our understanding of human symbiont communities, and that, in turn, will inform advances in human health and medicine.