Quantification of microbial DNA in laboratory environment during DNA extraction.

Tianda CHEN; Tingting ZHANG; Yanan YANG; Bowen ZHAO; Chongming WU

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Quantification of microbial DNA in laboratory environment during DNA extraction.

Author: Tianda CHEN ¹ ; Tingting ZHANG ¹ ; Yanan YANG ² ; Bowen ZHAO ¹ ; Chongming WU ²
Author Information

1. Quantihealth Co. Ltd., Beijing 100070, China.
2. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
Publication Type:Journal Article
Keywords: laboratory environment; microbiome; qPCR; skin sample; trace DNA quantification
MeSH: DNA; DNA, Bacterial/genetics*; Laboratories; Metagenomics; RNA, Ribosomal, 16S; Sequence Analysis, DNA
From: Chinese Journal of Biotechnology 2020;36(12):2541-2547
CountryChina
Language:Chinese
Abstract: Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.