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Research Article
Laura Weyrich
Pennsylvania State University
Corresponding Author
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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 bleach immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are efficient, no one has systematically compared them. Here, we compare untreated dental calculus samples to four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite (bleach) immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% bleach immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing to ancient calculus samples from a single site. We identify ancient oral microbiota, as well as soil and skin contaminants. Overall, both the EDTA and UVB treatments are effective at reducing the proportion of environmental taxa while increasing oral taxa in relation to untreated samples.
Keywords
Ancient DNA analysis, calculus, human health, paleodemography, ethylenediaminetetraacetic acid (EDTA)
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CURRENT STATUS: Published
View the published article at Scientific Reports.
Version 1
Posted 31 Dec, 2020
No community comments so far
Editorial decision: Major revision
On 05 Feb, 2021
Reviews received
Received 24 Jan, 2021
Reviewers agreed
On 11 Jan, 2021
Reviewers agreed
On 10 Jan, 2021
Reviewers invited
Invitations sent on 06 Jan, 2021
Editor assigned
On 06 Jan, 2021
Editor invited
On 30 Dec, 2020
Submission checks complete
On 30 Dec, 2020
First submitted
On 27 Dec, 2020
Metrics
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Subject Areas
Dentistry
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A new preprint design is coming!
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See the published version of this preprint at Scientific Reports.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Laura Weyrich
Pennsylvania State University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at Scientific Reports.
Version 1
Posted 31 Dec, 2020
No community comments so far
Editorial decision: Major revision
On 05 Feb, 2021
Reviews received
Received 24 Jan, 2021
Reviewers agreed
On 11 Jan, 2021
Reviewers agreed
On 10 Jan, 2021
Reviewers invited
Invitations sent on 06 Jan, 2021
Editor assigned
On 06 Jan, 2021
Editor invited
On 30 Dec, 2020
Submission checks complete
On 30 Dec, 2020
First submitted
On 27 Dec, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Dentistry
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at Scientific Reports.
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 bleach immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are efficient, no one has systematically compared them. Here, we compare untreated dental calculus samples to four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite (bleach) immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% bleach immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing to ancient calculus samples from a single site. We identify ancient oral microbiota, as well as soil and skin contaminants. Overall, both the EDTA and UVB treatments are effective at reducing the proportion of environmental taxa while increasing oral taxa in relation to untreated samples.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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