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Assessing alignment-based taxonomic classification of ancient microbial DNA

Eisenhofer, Raphael, Weyrich, Laura Susan·2019·PeerJ
DOI 10.7717/peerj.6594PMC PMC6420809
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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.

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  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

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Metadata

Authors
Eisenhofer, R., & Weyrich, L. S.
Affiliations
Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia
ORCID
Eisenhofer, Raphael
Venue
PeerJ
Publisher
PeerJ
Published
2019-03-13
Volume
7
Pages
e6594
ISSN
2167-8359
DOI
10.7717/peerj.6594
PMC
PMC6420809
Cited by
39
References
8
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)
Funders
  • Australian Research Council (DECRA: DE150101574)
  • ARC Centre of Excellence CABAH (CE170100015)

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