Reducing microbial and human contamination in DNA extractions from ancient bones and teeth

Area of Science:

• Paleogenomics
• Molecular Biology
• Ancient DNA Analysis

Background:

• Generating DNA sequences from ancient samples faces significant challenges from microbial and modern human DNA contamination.
• High contamination levels limit the feasibility of ancient DNA analyses, impacting genomic insights.

Purpose of the Study:

• To evaluate DNA decontamination procedures for ancient bones and teeth before DNA library preparation and high-throughput sequencing.
• To assess the efficacy of phosphate buffer and sodium hypochlorite treatments in reducing contamination and increasing endogenous DNA yield.

Main Methods:

• Investigated DNA decontamination using phosphate buffer to release surface-bound DNA.
• Applied sodium hypochlorite treatment to remove DNA contaminants from ancient bone and tooth samples.
• Quantified microbial and endogenous DNA levels before and after treatments.

Main Results:

• Phosphate buffer treatment removed an average of 64% microbial DNA while retaining 37% endogenous DNA, doubling informative sequences.
• Sodium hypochlorite treatment increased informative sequences 4.6-fold on average (up to 24-fold) but degraded 63% of endogenous DNA.
• Both methods significantly reduced microbial DNA, lowering genome sequencing costs.

Conclusions:

• Phosphate buffer and sodium hypochlorite treatments are effective in reducing microbial DNA contamination in ancient samples.
• These methods enhance the efficiency and reduce the cost of ancient DNA sequencing.
• Efficient removal of modern human DNA contamination from ancient samples remains a significant challenge.