PhD Studentship in Ancient Metagenomics

Updated: 25 days ago
Job Type: FullTime
Deadline: 01 May 2021

Title: Tracking the history of human disease using ancient oral microbiome data.

Project Description:

Food has long been a crucial component of human sociality and health. More and more, we are finding that there is a delicate balance between what we eat, the microbes that live within us and our general health and susceptibility to infectious disease. Ancient dental calculus, a calcified biofilm from teeth, is a valuable resource containing ancient microbial, host and dietary biomolecules; however, the methodologies used in analysing this complex data are still in the developmental stage and the full scope of how this data can be used to study human health has yet to be determined. This doctoral research project will generate whole-genome metagenomic libraries from ancient dental calculus samples and analyse this data in the context of ancient proteins and human (host) DNA to better understand how shifts in culture have affected human health.

The main objective of the project is to assess the impact of cultural differences on the quantitative and qualitative structure of the oral microbiome within sets of European populations. There are three main components: the Bronze Age transition, urban vs. rural and tobacco-use vs. non-use. The first component of the project will assess differences between the Neolithic and Bronze Age populations in Italy. The Bronze Age transition brought both demographic and cultural change as well as a shift in the prevalence of pathology in the archaeological record. This component will assess if these shifts in ancestry, diet, pathology and culture correlate with shifts in the oral microbiome as part of the ERC Advanced Grant, Making Ancestors: The Politics of Death in Prehistoric Europe . The second component will assess differences in oral microbiome between urban and rural populations in medieval Estonia as part of the interdisciplinary medieval Estonia project headed by Dr. Kristiina Tambets. The final component will compare oral microbiomes of pre-Tobacco populations in Western Europe with known smokers as part of the Tobacco Health and History project . You will collaborate with Dr. Sarah Inksip at the University of Leicester who has post-doctoral researchers generating novel metabolomic data identifying psychoactive substances (e.g. tobacco) and health markers for these populations. Both of these data sources will be combined with the host and pathogen (e.g. Mycobacterium tuberculosis) genomes to better understand the impact of the introduction of tobacco smoking on the health of European populations after 1492. There will be opportunities to travel for collaborative interaction and conferences.

About us

The ancient DNA research group at the Estonian Biocentre, Institute of Genomics is a friendly, growing group focused on producing exemplary research in the fields of ancient human population genetics, pathogen genomics and the emerging field of ancient meta-genome/proteomics. The lab is headed by Dr. Scheib (Associate Professor of Ancient DNA) and includes Dr. Tambets (Associate Professor of Population Genetics), post-docs, PhD students, Master’s students and two laboratory technicians. You can check out our lab on Research Gate and the official UT website .

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