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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Autor principal:	Alan W. Walker
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	contamination microbiome sequencing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b9161e07949e4ce0af046491e3ecac6b
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id	oai: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
work_keys_str_mv	AT alanwwalker alotonyourplatewelltowellcontaminationasanadditionalconfounderinmicrobiomesequenceanalyses AT alanwwalker lotonyourplatewelltowellcontaminationasanadditionalconfounderinmicrobiomesequenceanalyses
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A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses

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