Doctoral Dissertation Research: The impact of microeukaryotes in human microbiome evolution

本论文项目将研究寄生虫对人类肠道微生物组（生活在人类消化道中的微生物群落）进化的作用，它们在这些微环境中的重要性，以及它们在现代工业化人口中损失的后果。最近的研究表明，工业化人群的肠道微生物组减少了物种多样性，包括有助于减少体内炎症的微生物物种的损失。这些人群中寄生虫感染的减少可能与工业化世界中肠道微生物组多样性减少和自身免疫性疾病患病率增加有关。该项目将促进我们对人类生物学和物种共同进化的理解，同时支持学生培训和在科学研究中纳入服务不足的群体。将通过美洲印第安人和阿拉斯加土著基因组研究中心举办一系列科学计算讲习班，并向公众提供，以鼓励继续进行科学教育。鉴于寄生虫感染仍然是全世界发病率和死亡率的主要来源，本项目制定的寄生虫检测和分析程序将通过国际伙伴关系在这些类型的感染构成重大公共卫生问题的区域传播。该项目调查工业化肠道中寄生虫的损失是否可以解释这些微生态系统中微生物多样性的损失。使用来自五个地理和文化可变人群的粪便样本，包括美国的工业化人群，以及南美洲和非洲的传统人群，本研究提出（1）描述寄生虫对人类肠道微生物组的影响，（2）记录生活方式的影响，包括生存策略对传统和工业化社会中寄生虫多样性的影响。将使用各种统计程序将从本研究采集的样本中测序的寄生虫DNA与细菌群落数据进行比较，以检测整个群落以及可能与寄生虫感染相关的功能变化。

This dissertation project will study the role of parasites on the evolution of the human gut microbiome (the community of micro-organisms that live in the human digestive tract), their importance in these micro-environments, and the consequences of their loss in modern industrialized populations. Recent research has shown that the gut microbiome of industrialized populations has reduced species diversity, including the loss of microbial species that can help to reduce inflammation in the body. The reduction of parasite infections in these populations may be related reduced gut microbiome diversity and the increased prevalence of autoimmune diseases in the industrialized world. This project will advance our understanding of human biology and the co-evolution of species, while supporting student training and inclusion of underserved groups in scientific research. A series of scientific computing workshops will be offered through the Center on American Indian and Alaska Native Genomic Research and made available to the general public to encourage continued scientific education. Given that parasite infection remains a major source of morbidity and mortality world-wide, procedures developed in this project for the detection and analysis of parasites will be disseminated through international partnerships in regions where these types of infections pose a major public health concern. This project investigates whether the loss of parasites in the industrialized gut can explain the loss of microbial diversity in these micro-ecosystems. Using fecal samples from five geographically and culturally variable populations including industrialized peoples in the United States, and traditional peoples in South America and Africa, this study proposes to (1) describe the impact of parasites on the human gut microbiome, and (2) document the influence of lifestyle including subsistence strategy on parasite diversity in traditional and industrialized societies. Parasite DNA sequenced from samples collected for this study will be compared to bacterial community data using a variety of statistical procedures to detect whole community as well as functional shifts that may be linked to parasite infection.