Evaluating Methods for the Optimal Extraction of Microbial Nucleic Acids for Analysis of the Human Gut Microbiota

Five commonly used DNA extraction methods (Human Microbiome Project protocol, MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Stool Mini Kit, ZR Fecal DNA MiniPrep™, and one non-kit phenol:chloroform-based DNA isolation) were evaluated based on microbial community structure based on sequencing of the amplified V4 region of the bacterial and archaeal 16S rRNA gene. Three neurotypical female subjects in their mid-20s, with no dietary restrictions or recent antibiotic usage (>6 months), and located within Auckland, New Zealand, consented to supply three stool samples each. The results indicate that the largest source of variation can be attributed to intersubject variation, and that the DNA extraction method does influence interpretation of microbial community structure. This research contributes valuable insights to the current discussion regarding nucleic acids extraction methods which accurately represent human gut microbial structure.