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

Alan W. Walker* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalComment/debatepeer-review

9 Citations (Scopus)
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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.
Original languageEnglish
Article numbere00362-19
Number of pages3
Issue number4
Early online date25 Jun 2019
Publication statusPublished - 31 Jul 2019

Bibliographical note

A.W.W. receives core research funding from the Scottish Government’s Rural and Environment Science and Analytical Services (RESAS) division.

I thank Paul Scott, Wellcome Sanger Institute, for his title suggestions for this commentary.


  • contamination
  • microbiome
  • sequencing
  • Sequencing
  • Contamination
  • Microbiome


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