A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities

• DOI: 10.2144/btn-2022-0032
• Publication Date: 2022-06-17T12:43:03Z
• Authors: Justin P Shaffer; Carolina S Carpenter; Cameron Martino; Rodolfo A Salido; Jeremiah J Minich; MacKenzie Bryant; Karenina Sanders; Tara Schwartz; Gregory Humphrey; Austin D Swafford; Rob Knight
• Keywords: Shotgun; Amplicon; Pyrosequencing; Environmental DNA; Amplicon sequencing; Human Microbiome Project

Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems potentially members human microbiome, beyond those that can cause disease. To expand our analysis microbial to include data from fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against standardized protocol for archaea using 16S rRNA gene amplicon- shotgun metagenomics sequencing. The results presented considering diverse panel host-associated environmental sample types comparing cost, processing time, well-to-well contamination, yield, limit detection community composition among protocols. Across all criteria, MagMAX Microbiome kit was found perform best. PowerSoil Pro performed comparably but with increased cost per overall time. Zymo MagBead, NucleoMag Food Norgen Stool included.