[Quantification of microbial DNA in laboratory environment during DNA extraction]

Area of Science:

• Microbiology
• Genomics
• Environmental Science

Background:

• Metagenomic sequencing is vital for microbial research.
• Environmental microbial DNA contamination during extraction is a known issue.
• The impact on low-biomass samples remains unclear.

Purpose of the Study:

• To quantify environmental microbial DNA contamination during DNA extraction.
• To assess the effect of this contamination on metagenomic results from skin samples.
• To determine optimal conditions for analyzing low-biomass samples.

Main Methods:

• Collected environmental bacteria and quantified contaminant DNA using qPCR.
• Extracted DNA from pure water to identify airborne taxa.
• Performed metagenomic sequencing on skin samples extracted in open vs. aseptic environments.

Main Results:

• Open lab extraction yielded 28.9 pg of contaminant DNA, up to 30% of total DNA in skin samples.
• Dominant contaminants included Cutibacterium acnes and Escherichia coli.
• Contamination reduced the accuracy of metagenomic results by altering species abundance.

Conclusions:

• Environmental microbial DNA contamination poses a significant threat to metagenomic accuracy in low-biomass samples.
• Aseptic extraction environments are essential for reliable microbial profiling.
• Standard protocols may require modification for samples with minimal microbial load.