Abstract
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 ecosystemsand 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 thefungal 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 typesand comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detectionand microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was foundto perform best. The PowerSoil Pro kit performed comparablybut with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Foodand Norgen Stool kits were included.
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