Determining Informative Microbial Single Nucleotide Polymorphisms for Human Identification

The skin microbiome is a highly abundant and relatively stable source of DNA that may be utilized for human identification (HID). In this study, a set of single nucleotide polymorphisms (SNPs) with a high mean estimated Wright's fixation index (FST) (.0.1) and widespread abundance (found in $75% of samples compared) were selected from a diverse set of markers in the hidSkinPlex panel. The least absolute shrinkage and selection operator (LASSO) was used in a novel machine learning framework to generate a SNP panel and predict the human host from skin microbiome samples collected from the hand, manubrium, and foot. The framework was devised to emulate a new unknown person introduced to the algorithm and to match samples from that person against a population database. Unknown samples were classified with 96% accuracy (Matthews correlation coefficient [MCC], 0.954) in the test (n = 225 samples) data set. A final panel of informative SNPs was determined for HID (hidSkinPlex1) using all 51 individuals sampled at three body sites in triplicate. The hidSkinPlex1 panel comprises 365 SNPs and yielded prediction accuracy for the correct host of 95% (MCC = 0.949). The accuracy of the hidSkinPlex1 panel may be somewhat overestimated due to using 26 individuals from the training data set for the selection of the final panel. However, this accuracy still provides an indication of performance when tested on new samples.