Evolution and Ecology of the Human Oral Microbiome

人类微生物群是生活在人体内外的细菌的总和，拥有我们90%的细胞和99%的基因，在执行许多基本的人类生命功能中起着至关重要的作用。然而，我们对它的多样性、变异和进化知之甚少。仅人类口腔就拥有一个包含1000多种微生物物种的复杂生态系统，而这种口腔微生物群与蛀牙、心血管疾病和一系列呼吸系统疾病有关。最近，人们发现牙结石（钙化的牙菌斑）包含了保存了数千年的口腔微生物组的丰富记录。本研究的目的是利用宏基因组学和元蛋白质组学方法系统地表征从旧石器时代到现在的黑猩猩和人类的口腔微生物组。这项研究将有助于通过时间重建人类口腔微生物组，并了解常见口腔病原体和疾病的起源。这项研究的结果也将有助于学生培训、公共科学推广和教育。很少有研究对人类口腔微生物群的自然变异或口腔微生物群随时间的变化进行基础研究。因此，人们对人类口腔微生物群的起源和进化生态学知之甚少。最近，人们发现牙结石（钙化牙菌斑）包含了保存数千年的口腔微生物组的丰富生物分子记录。该项目将使用最先进的宏基因组学和元蛋白质组学技术，对从黑猩猩和已灭绝和现存的人身上采集的口腔微生物进行表征：古代海德堡人（约430,000 BP）、旧石器时代智人（约23,000 BP和20,000 BP）、铜石器时代智人（约4,000 BP），以及现代人类和黑猩猩。这些样本将为在人类进化过程中重建人类口腔微生物群提供一条途径。

The human microbiome, the sum total of bacteria that live in and on the human body, harbors 90% of our cells and 99% of our genes, and plays a critical role in performing many basic human life functions. And yet, we know very little about its diversity, variation, and evolution. The human oral cavity alone harbors a complex ecosystem containing more than 1,000 microbial species, and this oral microbiome has been associated with tooth decay, cardiovascular disease and a range of respiratory illnesses. Recently it has been discovered that dental calculus (calcified dental plaque) entraps a rich record of the oral microbiome that preserves for thousands of years. The objective of this study is to use metagenomic and metaproteomic approaches to systematically characterize the oral microbiome of chimpanzees and humans from the Paleolithic to the present. This study will contribute to reconstructing the human oral microbiome through time and understanding the origins of common oral pathogens and diseases. Findings from this study will also contribute to student training, and public science outreach and education. Few studies have conducted basic research on the natural variation of the human oral microbiome or on changes in the oral microbiome through time. As a result little is known about the origins and evolutionary ecology of the human oral microbiome. Recently it has been discovered that dental calculus (calcified dental plaque) entraps a rich biomolecular record of the oral microbiome that preserves for thousands of years. This project will use state-of-the-art metagenomic and metaproteomic technologies to characterize the microbes of the oral cavity collected from chimpanzees and extinct and extant members of Homo: archaic Homo heidelbergensis (ca. 430,000 BP), Paleolithic H. sapiens (ca. 23,000 BP and 20,000 BP), Chalcolithic H. sapiens (ca. 4,000 BP), and present-day humans and chimpanzees. These samples will provide a path to reconstructing the the human oral microbiome over the course of hominin evolution.