Cargando…

Assessing alignment-based taxonomic classification of ancient microbial DNA

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Eisenhofer, Raphael, Weyrich, Laura Susan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420809/
https://www.ncbi.nlm.nih.gov/pubmed/30886779
http://dx.doi.org/10.7717/peerj.6594
_version_ 1783404144167485440
author Eisenhofer, Raphael
Weyrich, Laura Susan
author_facet Eisenhofer, Raphael
Weyrich, Laura Susan
author_sort Eisenhofer, Raphael
collection PubMed
description 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.
format Online
Article
Text
id pubmed-6420809
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher PeerJ Inc.
record_format MEDLINE/PubMed
spelling pubmed-64208092019-03-18 Assessing alignment-based taxonomic classification of ancient microbial DNA Eisenhofer, Raphael Weyrich, Laura Susan PeerJ Bioinformatics 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. PeerJ Inc. 2019-03-13 /pmc/articles/PMC6420809/ /pubmed/30886779 http://dx.doi.org/10.7717/peerj.6594 Text en © 2019 Eisenhofer and Weyrich http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , 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.
spellingShingle Bioinformatics
Eisenhofer, Raphael
Weyrich, Laura Susan
Assessing alignment-based taxonomic classification of ancient microbial DNA
title Assessing alignment-based taxonomic classification of ancient microbial DNA
title_full Assessing alignment-based taxonomic classification of ancient microbial DNA
title_fullStr Assessing alignment-based taxonomic classification of ancient microbial DNA
title_full_unstemmed Assessing alignment-based taxonomic classification of ancient microbial DNA
title_short Assessing alignment-based taxonomic classification of ancient microbial DNA
title_sort assessing alignment-based taxonomic classification of ancient microbial dna
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420809/
https://www.ncbi.nlm.nih.gov/pubmed/30886779
http://dx.doi.org/10.7717/peerj.6594
work_keys_str_mv AT eisenhoferraphael assessingalignmentbasedtaxonomicclassificationofancientmicrobialdna
AT weyrichlaurasusan assessingalignmentbasedtaxonomicclassificationofancientmicrobialdna