Microbiome

Environmental DNA

Shotgun

16S ribosomal RNA

Bacteria

Ribosomal RNA

Microbial population biology

Amplicon

Biology

Shotgun sequencing

Gene

Biodiversity

Metagenomics

Pyrosequencing

Internal transcribed spacer

Human Microbiome Project

Ecology

DNA sequencing

Archaea

Microbial ecology

Computational biology

DNA extraction

Amplicon sequencing

Polymerase chain reaction

Genetics

BioTechniques

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

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