Farrer, Andrew G, Wright, Sterling L, Skelly, Emily, Eisenhofer, Raphael, Dobney, Keith 
ORCID: 0000-0001-9036-4681 and Weyrich, Laura S
(2021)
Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus.
SCIENTIFIC REPORTS, 11 (1).
7456-.
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Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus.pdf - Published version Download (2MB) | Preview |
Abstract
Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Mouth, Dental Calculus, Humans, RNA, Ribosomal, 16S, Environment, Biodiversity, Decontamination, Phylogeny, Species Specificity, Principal Component Analysis, Metagenomics, DNA, Ancient |
| Divisions: | Faculty of Humanities and Social Sciences > School of Histories, Languages and Cultures |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 04 Jun 2021 13:56 |
| Last Modified: | 18 Jan 2023 22:36 |
| DOI: | 10.1038/s41598-021-86100-w |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3125126 |
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