SNIC
SUPR
SNIC SUPR
Dental_calculus_metagenomics
Dnr:

SNIC 2017/1-382

Type:

SNAC Medium

Principal Investigator:

Katerina Guschanski

Affiliation:

Uppsala universitet

Start Date:

2017-10-10

End Date:

2018-11-01

Primary Classification:

10615: Evolutionary Biology

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Webpage:

Allocation

Abstract

Dental calculus, calcified dental plaque, is one of the few historical remains that captures animal interactions with the environment during life, by preserving DNA from the oral microbiome of the bacterial biofilm that comprises dental plaque, as well as respiratory pathogens and dietary biomolecules. It is often well preserved in museum collections and archaeological specimens, allowing characterisation of animal-environment interactions over time. However, to date DNA analyses of historical dental calculus have only been performed in humans. We will characterise the oral microbiome of wild Nordic animals from a temporal perspective, using dental calculus from museum specimens. We aim to investigate the effect of climate and human factors on microbial community structure, pathogen carriage and diet in ecologically and economically important species such as reindeer and brown bear. We intend to 1) perform exploratory metagenomics shotgun sequencing on a small set of samples to determine the best protocols and sampling methods, 2) characterise a larger set of samples with these optimised methods to investigate associations between ecological/temporal factors and oral microbiomes/dietary profiles, and 3) investigate a subset of samples further with deep metagenomics sequencing, with the aim to reconstruct metagenomes of ancient pathogenic and commensal oral microbes. The project will shed light on significant ecological events, such as reindeer survival over the Last Glacial Maximum and the effect of a population bottleneck on Scandinavian brown bears, thereby providing valuable insights for future conservation management strategies.