Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

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 endogenou...

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Autores principales:	Andrew G. Farrer, Sterling L. Wright, Emily Skelly, Raphael Eisenhofer, Keith Dobney, Laura S. Weyrich
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/efa3973aa9004faa9fab4547c7fc5e25
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spelling	oai:doaj.org-article:efa3973aa9004faa9fab4547c7fc5e252021-12-02T18:17:41ZEffectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus10.1038/s41598-021-86100-w2045-2322https://doaj.org/article/efa3973aa9004faa9fab4547c7fc5e252021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86100-whttps://doaj.org/toc/2045-2322Abstract 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.Andrew G. FarrerSterling L. WrightEmily SkellyRaphael EisenhoferKeith DobneyLaura S. WeyrichNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Andrew G. Farrer Sterling L. Wright Emily Skelly Raphael Eisenhofer Keith Dobney Laura S. Weyrich Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
description	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.
format	article
author	Andrew G. Farrer Sterling L. Wright Emily Skelly Raphael Eisenhofer Keith Dobney Laura S. Weyrich
author_facet	Andrew G. Farrer Sterling L. Wright Emily Skelly Raphael Eisenhofer Keith Dobney Laura S. Weyrich
author_sort	Andrew G. Farrer
title	Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
title_short	Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
title_full	Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
title_fullStr	Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
title_full_unstemmed	Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
title_sort	effectiveness of decontamination protocols when analyzing ancient dna preserved in dental calculus
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/efa3973aa9004faa9fab4547c7fc5e25
work_keys_str_mv	AT andrewgfarrer effectivenessofdecontaminationprotocolswhenanalyzingancientdnapreservedindentalcalculus AT sterlinglwright effectivenessofdecontaminationprotocolswhenanalyzingancientdnapreservedindentalcalculus AT emilyskelly effectivenessofdecontaminationprotocolswhenanalyzingancientdnapreservedindentalcalculus AT raphaeleisenhofer effectivenessofdecontaminationprotocolswhenanalyzingancientdnapreservedindentalcalculus AT keithdobney effectivenessofdecontaminationprotocolswhenanalyzingancientdnapreservedindentalcalculus AT laurasweyrich effectivenessofdecontaminationprotocolswhenanalyzingancientdnapreservedindentalcalculus
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Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

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