Reagent and laboratory contamination can critically impact sequence based microbiome analyses. Kit contamination

Background: The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. Results: In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Conclusions: Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.

研究背景：近年来，16S rRNA基因测序（16S rRNA gene sequencing）、宏基因组学（metagenomics）等非培养分析技术的广泛应用，极大地革新了微生物群落研究领域。此类基于测序的研究方法存在一项潜在混杂因素：DNA提取试剂盒及其他实验室试剂中存在污染DNA。
研究结果：本研究证实，常用DNA提取试剂盒中普遍存在污染DNA，且不同试剂盒及试剂盒批次间的污染组成差异显著；此类污染会对低微生物生物量样本的测序结果产生关键性影响。
研究结论：污染会同时影响基于PCR的16S rRNA基因测序研究与鸟枪宏基因组学（shotgun metagenomics）。上述结果提示，在将基于测序的技术应用于低生物量环境中微生物群落的研究时，需格外谨慎。本研究提供了一份涵盖大量潜在污染菌属的详尽清单，并给出了缓解污染影响的相关指南，同时强烈建议对阴性对照样本进行并行测序。