microDecon: a highly accurate read‐subtraction tool for the post‐sequencing removal of contamination in metabarcoding studies

McKnight, Donald T., Huerlimann, Roger, Bower, Deborah S., Schwarzkopf, Lin, Alford, Ross A., and Zenger, Kyall R. (2019) microDecon: a highly accurate read‐subtraction tool for the post‐sequencing removal of contamination in metabarcoding studies. Environmental DNA, 1 (1). pp. 14-25.

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Abstract

Contamination is a ubiquitous problem in microbiome research and can skew results, especially when small amounts of target DNA are available. Nevertheless, no clear solution has emerged for removing microbial contamination. To address this problem, we developed the R package microDecon (https://github.com/donaldtmcknight/microDecon), which uses the proportions of contaminant operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) in blank samples to systematically identify and remove contaminant reads from metabarcoding data sets. We rigorously tested microDecon using a series of computer simulations and a sequencing experiment. We also compared it to the common practice of simply removing all contaminant OTUs/ASVs and other methods for removing contamination. Both the computer simulations and our sequencing data confirmed the utility of microDecon. In our largest simulation (100,000 samples), using microDecon improved the results in 98.1% of samples. Additionally, in the sequencing data and in simulations involving groups, it enabled accurate clustering of groups as well as the detection of previously obscured patterns. It also produced more accurate results than the existing methods for identifying and removing contamination. These results demonstrate that microDecon effectively removes contamination across a broad range of situations. It should, therefore, be widely applicable to microbiome studies, as well as to metabarcoding studies in general.

Item ID: 62435
Item Type: Article (Research - C1)
ISSN: 2637-4943
Keywords: 16S; bacteria; bioinformatics; controls; decontaminate; microbiome
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Copyright Information: © 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Additional Information:

A version of this publication was included as Chapter 6 of the following PhD thesis: McKnight, Donald T. (2019) Life finds a way: the recovery of frog populations from a chytridiomycosis outbreak. PhD thesis, James Cook University, which is available Open Access in ResearchOnline@JCU. Please see the Related URLs for access.

Funders: Australian Wildlife Society, Skyrail Rainforest Foundation, Australian Society of Herpetologists, Holsworth Wildlife Research Endowment
Date Deposited: 08 Mar 2020 22:34
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 100%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960899 Flora, Fauna and Biodiversity of Environments not elsewhere classified @ 100%
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