A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses

ABSTRACT DNA sequence-based microbiome studies can be impacted by a range of different methodological artefacts. Contamination originating from laboratory kits and reagents can lead to erroneous results, particularly in samples containing a low microbial biomass. Minich and colleagues (mSystems 4:e0...

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Main Author: Alan W. Walker
Format: article
Language:EN
Published: American Society for Microbiology 2019
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Online Access:https://doaj.org/article/b9161e07949e4ce0af046491e3ecac6b
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spelling oai:doaj.org-article:b9161e07949e4ce0af046491e3ecac6b2021-12-02T18:25:16ZA Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses10.1128/mSystems.00362-192379-5077https://doaj.org/article/b9161e07949e4ce0af046491e3ecac6b2019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00362-19https://doaj.org/toc/2379-5077ABSTRACT DNA sequence-based microbiome studies can be impacted by a range of different methodological artefacts. Contamination originating from laboratory kits and reagents can lead to erroneous results, particularly in samples containing a low microbial biomass. Minich and colleagues (mSystems 4:e00186-19, 2019, https://doi.org/10.1128/mSystems.00186-19) report on a different form of contamination, cross-contamination between samples that are processed together. They find that transfer of material between samples in 96-well plates is a common occurrence. The DNA extraction step, particularly when carried out automatedly, is identified as the major source of this contamination type. Well-to-well contamination distorts diversity measures, with low-biomass samples particularly affected. This report has important implications for attempts to decontaminate microbiome sequencing results. As contamination is derived from both external sources and crossover between samples, it is not appropriate to simply remove sequence variants that are detected in negative-control blanks, and more-nuanced decontamination approaches may be required.Alan W. WalkerAmerican Society for MicrobiologyarticlecontaminationmicrobiomesequencingMicrobiologyQR1-502ENmSystems, Vol 4, Iss 4 (2019)
institution DOAJ
collection DOAJ
language EN
topic contamination
microbiome
sequencing
Microbiology
QR1-502
spellingShingle contamination
microbiome
sequencing
Microbiology
QR1-502
Alan W. Walker
A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses
description ABSTRACT DNA sequence-based microbiome studies can be impacted by a range of different methodological artefacts. Contamination originating from laboratory kits and reagents can lead to erroneous results, particularly in samples containing a low microbial biomass. Minich and colleagues (mSystems 4:e00186-19, 2019, https://doi.org/10.1128/mSystems.00186-19) report on a different form of contamination, cross-contamination between samples that are processed together. They find that transfer of material between samples in 96-well plates is a common occurrence. The DNA extraction step, particularly when carried out automatedly, is identified as the major source of this contamination type. Well-to-well contamination distorts diversity measures, with low-biomass samples particularly affected. This report has important implications for attempts to decontaminate microbiome sequencing results. As contamination is derived from both external sources and crossover between samples, it is not appropriate to simply remove sequence variants that are detected in negative-control blanks, and more-nuanced decontamination approaches may be required.
format article
author Alan W. Walker
author_facet Alan W. Walker
author_sort Alan W. Walker
title A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses
title_short A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses
title_full A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses
title_fullStr A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses
title_full_unstemmed A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses
title_sort lot on your plate? well-to-well contamination as an additional confounder in microbiome sequence analyses
publisher American Society for Microbiology
publishDate 2019
url https://doaj.org/article/b9161e07949e4ce0af046491e3ecac6b
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