Optimization of microbial DNA extraction from human skin samples for CRISPR typing

Abstract

The human skin microbiome, a complex microbial community harbored by the human skin surface, has been proposed as a new forensic genetic marker for human identification to complement short tandem repeat typing. A recent study utilized Streptococcus clustered regularly interspaced short palindromic repeat (CRISPR) polymorphism of the skin microbiome to characterize individuality of the skin microbiome; however, further validation is required for forensic purposes. Optimization of the DNA extraction protocol is critical for both forensic human DNA and microbiome analyses. Previous reports have demonstrated that DNA extraction protocols may alter the results of microbiome analysis, suggesting careful selection of DNA extraction protocols. In this study, we evaluated protocols for DNA extraction from skin swab samples by comparing two DNA extraction protocols, EZ1 DNA Investigator Kit and DNeasy PowerSoil Kit, in order to optimize the metagenomic CRISPR typing method. Quantification of 16S rRNA gene copy numbers and qualification of CRISPR diversities suggested that microbial DNA yield and composition of the CRISPRs were not altered by the two DNA extraction methods. Furthermore, the accuracy of the individual prediction models built using each sample set was comparable. Thus, our results support that the EZ1 platform, an automated DNA extraction protocol used in forensic laboratories, can also be used for metagenomic CRISPR typing intended for forensic human identification.