Benchmarking DNA Isolation Methods for Marine Metagenomics Studies

Abstract

Metagenomics is widely applied to study marine microbial communities. High quality DNA samples is critical for metagenomic projects success. In this work, we systematically evaluated the performance of eight widely used commercial DNA purification kits (Stool; Microbiome; PowerFecal; Blood and Tissue, and PowerSoil (all from Qiagen), PureLink Microbiome (Invitrogen), Monarch HMW DNA (NEB), and Soil Genomic DNA Isolation (LSBio)) with three types of samples: water, sea floor sediments, and digestive tract of a model invertebrate Pacific oyster Magallana gigas. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a kitome e.g., a set of contaminating taxa inherent for each type of DNA purification kit used. Each kit was ranked according to its performance. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.