Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/119784
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Type: Journal article
Title: Assessing alignment-based taxonomic classification of ancient microbial DNA
Author: Eisenhofer, R.
Weyrich, L.
Citation: PeerJ, 2019; 7(3):1-24
Publisher: PEERJ Inc.
Issue Date: 2019
ISSN: 2167-8359
2167-8359
Statement of
Responsibility: 
Raphael Eisenhofer and Laura Susan Weyrich
Abstract: The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
Keywords: Microbiome; palaeomicrobiology; ancient DNA; bioinformatics; alignment; taxonomic classification; shotgun metagenomics; microbiology
Rights: © 2019 Eisenhofer and Weyrich. Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
RMID: 0030111717
DOI: 10.7717/peerj.6594
Grant ID: http://purl.org/au-research/grants/arc/DE150101574
http://purl.org/au-research/grants/arc/CE170100015
Appears in Collections:Australian Centre for Ancient DNA publications

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