| Literature DB >> 35713407 |
Justin P Shaffer1, Carolina S Carpenter2,3, Cameron Martino1,3,4, Rodolfo A Salido1,5, Jeremiah J Minich6, MacKenzie Bryant1, Karenina Sanders1, Tara Schwartz1, Gregory Humphrey1, Austin D Swafford3,7, Rob Knight1,3,8,9.
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 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.Entities:
Keywords: Earth Microbiome Project (EMP); Katharoseq; Macherey-Nagel; MagAttract PowerSoil; high-throughput sequencing; mock community; mycobiome; rRNA; whole genome sequencing
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Year: 2022 PMID： 35713407 PMCID： PMC9361692 DOI： 10.2144/btn-2022-0032
Source DB: PubMed Journal: Biotechniques ISSN： 0736-6205 Impact factor: 2.746