Oral Microbiome Evolution
Much of my research investigates how the human oral microbiome evolves in response to migration, lifeways, and behavior.
To understand how the human oral microbiome has changed over long evolutionary timescales, I use dental calculus, which is the calcified form of dental plaque (tartar). Dental calculus is commonly found in archaeological skeletal remains and serves as an excellent source of ancient biomolecules (DNA, proteins, and metabolites), which can remain well-preserved inside calculus for thousands of years.
To understand how the human oral microbiome has changed over long evolutionary timescales, I use dental calculus, which is the calcified form of dental plaque (tartar). Dental calculus is commonly found in archaeological skeletal remains and serves as an excellent source of ancient biomolecules (DNA, proteins, and metabolites), which can remain well-preserved inside calculus for thousands of years.
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Recovering ancient human mitogenomes from dental calculus
In 2016, I was part of the team that published the first complete human mitochondrial genomes reconstructed from archaeological dental calculus samples (Ozga et al. 2016). In this study, we recovered complete mitogenomes for six individuals from the 700-year old Norris Farms cemetery in Illinois. We used ancient DNA extracted from dental calculus in conjunction with target enrichment and next-generation sequencing methods. Our study showed that dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains, especially in cases where conventional samples, such as bone, are not available or are not sufficiently well-preserved for ancient DNA analyses. |
Dental calculus deposits on mandibular dentition (Ozga et al. 2016)
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CHOMPER: Calculus and Hominid Oral Metagenomes for Pathogen Evolution Research
In 2021, Dr. Cecil Lewis and I were awarded a grant from the National Science Foundation (NSF) to study how oral microbiome communities and oral pathogen genomes differ depending on host species, geographic location, time, and dietary lifestyle. Under the CHOMPER project, we have studied the oral microbiomes of Native American Ancestors in collaboration with their descendant or stakeholder communities. For example, our partnership with The Wichita and Affiliated Tribes in Oklahoma led to the recovery of oral microbiomes from their Ancestors dating back to more than 600 years ago (Honap et al. 2023). Another partnership with the Anson Street African Burial Ground Project, has led to the recovery of oral microbiomes from 17th - 18th century African descended individuals from Charleston, South Carolina (Fleskes et al. 2024).
Together, these oral microbiome data have helped elucidate the impact of European Contact and the changes brought about during the colonial era on the oral microbiome. Our research has shown that pre-European Native American populations carried oral microbial strains different from the ones carried by Europeans. The interactions between these strains led to different evolutionary outcomes for oral microbes. In case of the oral pathogen, Tannerella forsythia, the pre-contact era American strains were completely replaced by European strains, whereas for the oral commensal, Pseudoramibacter alactolyticus, the pre-contact era American strains continue to be prevalent today.
My research on this topic continues in collaboration with Dr. Keith Prufer (University of New Mexico) and Maya stakeholder communities in Belize, Dr. Cara Monroe (University of Oklahoma Health Science Center) and the Muwekma Ohlone Tribe in California, Dr. Anne Stone (Arizona State University), and Dr. Pedro da Gloria (Federal University of Para, Brazil).
In 2021, Dr. Cecil Lewis and I were awarded a grant from the National Science Foundation (NSF) to study how oral microbiome communities and oral pathogen genomes differ depending on host species, geographic location, time, and dietary lifestyle. Under the CHOMPER project, we have studied the oral microbiomes of Native American Ancestors in collaboration with their descendant or stakeholder communities. For example, our partnership with The Wichita and Affiliated Tribes in Oklahoma led to the recovery of oral microbiomes from their Ancestors dating back to more than 600 years ago (Honap et al. 2023). Another partnership with the Anson Street African Burial Ground Project, has led to the recovery of oral microbiomes from 17th - 18th century African descended individuals from Charleston, South Carolina (Fleskes et al. 2024).
Together, these oral microbiome data have helped elucidate the impact of European Contact and the changes brought about during the colonial era on the oral microbiome. Our research has shown that pre-European Native American populations carried oral microbial strains different from the ones carried by Europeans. The interactions between these strains led to different evolutionary outcomes for oral microbes. In case of the oral pathogen, Tannerella forsythia, the pre-contact era American strains were completely replaced by European strains, whereas for the oral commensal, Pseudoramibacter alactolyticus, the pre-contact era American strains continue to be prevalent today.
My research on this topic continues in collaboration with Dr. Keith Prufer (University of New Mexico) and Maya stakeholder communities in Belize, Dr. Cara Monroe (University of Oklahoma Health Science Center) and the Muwekma Ohlone Tribe in California, Dr. Anne Stone (Arizona State University), and Dr. Pedro da Gloria (Federal University of Para, Brazil).