Date of Award

May 2022

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Department

Anthropology

First Advisor

Patricia Richards

Committee Members

Ryan Newton, John Richards, Bettina Arnold

Keywords

ancient DNA, Historic cemeteries, oral microbiome, Paleomicrobiology

Abstract

Paleomicrobiological investigations of the human oral microbiome have primarily focused on samples of ancient origin, while fewer targeted studies of younger archaeological samples from the historic era have been conducted. However, the study of archaeological samples from the recent past, particularly the nineteenth century, can yield pertinent insights into the shifting temporal patterns of oral microbial diversity. For example, the sugar-rich diet associated with the Industrial Revolution of the mid-nineteenth century caused a shift in the composition of the oral microbiome towards a pathogenic state. Recent research has also demonstrated that the oral microbiomes derived from samples of modern and historic dental calculus, a form of fossilized dental plaque, are distinct, with modern oral ecosystems presenting with less diversity than their historic counterparts. Thus, further investigation of historic era samples is required to parse out the nuances of this nineteenth century shift and contextualize temporal patterns on both a phylogenetic and biocultural scale.With this in mind, the primary goal of this dissertation was to reconstruct the historic oral microbiome through identification of the microbes encased within the dental calculus of 80 individuals excavated from the Milwaukee County Poor Farm Cemetery (c. 1882-1925) (MCPFC). This cemetery was used for the burial of the institutionalized, indigent, and unidentified residents of Milwaukee County from approximately 1852 to 1974. 16S rRNA amplicon sequencing of the V4 hypervariable region and shotgun metagenome sequencing were used to generate taxonomic profiles for each individual. These two sequencing techniques are commonly applied in microbial community assessments, with the latter preferable for ancient DNA due to its fragmentary nature. A broad taxonomic comparison of these sequencing methods was conducted as part of a series of methodological inquiries explored within this dissertation. Other technical analyses included a comparison of DNA extraction protocols, assessment of environmental contamination, identification of DNA damage patterns, and evaluation of the influence of PCR amplification biases on taxonomic diversity. In addition, a correlation analysis including a variety of biological and paleopathological metadata was conducted and community-level trends were contextualized using a biocultural framework. The MCPFC is ideal for this type of molecular research due to the nature of its composition, which encapsulates key features of the nineteenth century population, notably allowing for an examination of the effects of poverty, immigration status, gender roles, and industrial labor on the expression of oral biodiversity. Statistically significant levels of individual biodiversity were observed, with the identified oral taxa possessing both commensal and pathogenic functionality. Based on the results of the correlation analysis, the composition of the historic oral microbiome within the MCPFC was driven by factors of health and lifestyle, such as the presence of oral and systemic infection, joint wear, and trauma, rather than biological differences (i.e., sex, age, and ancestry). An analysis of similarities confirmed these results, indicating that no statistically significant differences exist in the microbial structure of samples on the basis of sex, age, or ancestry. However, the significant drivers of oral biodiversity are different between males and females, suggesting that the gendered division of labor played an influential role. This was particularly apparent in the male population, where poor health and a lifestyle of arduous industrial labor appear to drive the taxonomic diversity present in the oral cavity. Additionally, the longer read length and minimal patterns of DNA decay identified in the historic-era samples from the MCPFC are distinct from those observed in older archaeological specimens. The observed differences and generalized definition of ancient source material underscore the need for further investigation of these trends, as they may aid in the refinement of temporal designations within the paleomicrobiological discipline. Lastly, this research demonstrates the applicability of both targeted marker gene and shotgun metagenome sequencing within samples of historic dental calculus. The comparatively analogous distribution of microbes suggests that the amplicon data provide a reasonable recreation of the “true” community composition as defined by the random sampling of shotgun metagenomes. In addition, expressions of taxonomy and abundance were nearly identical within the biological and technical duplicates, indicating that statistically quantifiable biases were not introduced as a product of DNA extraction or PCR amplification in this study. Since calculus samples from younger historic-era contexts do not appear to suffer from the same degradation and fragmentation as older archaeological samples, the applicability of 16S amplicon sequencing, which is more cost-effective, appears to be an appropriate analytical strategy for microbial community assessment. It is hoped that the results of this dissertation will increase the accessibility of paleomicrobiological analyses and encourage future research to further characterize the historic oral microbiome.

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