Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• DNA extraction significantly impacts gut microbial research outcomes.
• Advancements in research scale and technology require evaluation of new extraction methods.
• Reliable microbial community profiling is essential for accurate biological interpretations.

Purpose of the Study:

• To systematically evaluate eight common DNA extraction methods for gut microbiome analysis.
• To assess method performance using a microbial mock community and human fecal samples.
• To identify optimal extraction methods for large-scale gut metagenomic studies.

Main Methods:

• Evaluation of eight DNA extraction kits using a microbial mock community and human fecal samples.
• Performance metrics included nucleic acid yield, quality, and microbial profile assessment.
• Shotgun metagenomics was employed for in-depth microbial community profiling.

Main Results:

• All tested methods yielded sufficient DNA for shotgun metagenomic sequencing.
• QIAamp PowerFecal pro (PF) and DNeasy PowerSoil HTP (PS) kits showed higher accuracy and lower variability in mock communities.
• Extraction method explained 21.4% of microbiome variation in fecal samples, impacting 32% of species abundances; PF and PS methods enhanced microbial diversity, especially for Gram-positive bacteria.

Conclusions:

• Mechanical lysis with small beads, as used in PF and PS kits, improves DNA extraction efficiency and microbial diversity.
• PF and PS methods are simple, automation-friendly, and cost-effective for large-scale gut metagenomic research.
• Consistent DNA extraction method selection is vital for reliable comparative metagenomic analyses.