Metagenomic sequencing, microbiome reconstruction, and analysis of ancient North and Central American dental calculus
Zuckerman, Molly K.
Brown, Matthew W.
Thornton, Justin A.
Date of Degree
Original embargo terms
Visible to MSU only for 2 years||forever||5/15/2022
Dissertation - Open Access
Doctor of Philosophy
College of Arts and Sciences
Department of Biological Sciences
Analyses of human oral microbiomes reveal substantial amounts of information about health, diet, and diseases of individuals and their communities within the archaeological record. In order to examine bacterial genomes from the past, specific archaeological samples that contain remnants of the microbial communities in question must be utilized. Recent developments in high-throughput, next-generation DNA sequencing have enabled the characterization of entire oral microbiomes and genomes from the remains of the bacteria trapped in calcified dental plaque. This project analyzed samples of ancient human dental calculus from North and Central America, which were examined for the changes within the oral microbiome in relation to the adoption of agriculture. Additionally, the conditional presence of pathogens associated with an increasingly agricultural and carbohydrate-rich diet was examined. The overarching goal was to examine and determine the level of microbial shifts within the past oral microbiomes of North and Central America, and by virtue of using the associated archaeological reports and analyses, place the data into the proper context. Three distinct sets of dental calculus were used for this Dissertation; The first is from Indigenous samples (N=56), spanning from the Archaic to the Mississippian, recovered from excavations in the Guntersville Basin in Northern Alabama. The second set is from a Late-Terminal Classic Maya city center and satellite village in the Upper Belize Valley (N=11). The final sample set comes from an archaeologically recovered early 20th century Cemetery near Jackson Mississippi (N=12). After individual analyses, they are all examined along a temporal axis to examine the effect of agriculture on the human oral microbiome. The findings from this study have shown that oral microbiomes of the Americas were affected by the introduction of agriculture, but remained biologically diverse. Because various subsistence strategies can shape and affect the oral microbiome, the composition is seen to change over time. Our understanding of the evolution of oral microbiomes throughout human history is more complex than previously thought; there is no global trend for the oral microbiome, but is highly location dependent.
Belanich, Jonathan, "Metagenomic sequencing, microbiome reconstruction, and analysis of ancient North and Central American dental calculus" (2020). Theses and Dissertations MSU. 3069.