Ancient DNA studies of dental calculus

Over the last 10 years, the human microbiota has been identified as a major force in human health and disease. Microbiota are the bacterial communities that live on the internal and external surfaces of the body, and comprise ~50% of the total cell count of a human individual. Recent studies have indicted the role of cultural and environmental factors on shaping these bacterial communities, including diet, interaction with people and animals, and medical treatments. However, the majority of microbiota studies are in modern human populations or animal models. Consequently, there is limited knowledge on the diversity of microbiota in the past, and how this diversity has been altered through time. Ancient DNA analyses of the oral microbiota preserved in dental calculus (calcified dental plaque) offer a way to examine historical microbiota composition. Thus, microbiota alterations through time can be mapped, and, with use of detailed archaeological and historical records, the cultural and environmental factors that trigger change identified. Further, elucidating fine scale population structure may be possible due to the rapid response of microbiota to changing environments. Results from ancient DNA studies are critical in understanding historical microbiota composition and population substructure, examining how microbiota change and adapt through time, defining the health status of historical and modern populations, and indicating routes of investigation for medical manipulation of microbiota in disease prevention. This thesis provides the most detailed analysis of historical microbiota to date, complemented with comprehensive metadata. Initially, I explored methods to minimize the impact of environmental contamination on analyses of ancient dental calculus collected from museums and archaeological sites. This allowed me to identify the optimum decontamination protocol and prepare over 250 British dental calculus samples from the Pre-Roman period to the Early Victorian period (~ 2,000 years). Utilizing high-throughput shotgun sequencing, I identified distinct, unique bacterial community structures present throughout history that are driven by the diets of different socio-economic classes and are not evident in the modern oral cavity. I then focused on an ~800-year period of London history (1066 – 1853) and identified the first associations of microbiota and disease in an ancient population. Ultimately, these studies alter our understanding of the modern oral microbiota and help define and calibrate ancient microbiota analysis as a powerful new tool for studying human history. Finally, I provided a framework for science communication within a research group that provides benefits and training to each member. I highlighted and demonstrated that science communication is a powerful tool for informing and engaging the public, and can provide direct research benefits. Moving forward, this framework should be utilized to disseminate research results to peers and the public with the aim to stimulate collaborations, and inform and engage public in new understandings of human biology, history, and medicine.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 2017