This paper describes research on attributing an unknown microbiome sample to an individual, through the use of specific single nucleotide polymorphisms of selected human skin microorganisms.
This dissertation describes how nucleic acids from the human skin microbiome are sources of genetic material that may be useful for human identification (HID) when the quality or quantity of DNA in biological evidence does not provide enough information for HID. The two research studies described in this document test the hypothesis that specific single nucleotide polymorphisms (SNPs) of selected human skin microorganisms can be used to attribute an unknown microbiome sample to an individual. The first study investigated how Wright’s fixation index (Fst) can be used to select potentially informative SNPs for HID, and focused on testing which would be most effective for HID: a high Fst with increased taxonomic abundance and/or using a predetermined panel. Classification accuracies ranged from 88% to 95%. Results from the study supported that using genetic distance to select informative markers from the skin microbiome for HID was viable, and while the predetermined panel only achieved an 88% accuracy, it would be the most applicable of the tested methods for forensic casework. The second study focused on using Fst estimations to select SNPs abundant in 51 individuals sampled at three body-sites in triplicate for HID. The most common SNPs, present in 75% or more of the samples, which had Fst estimates less-than or equal-to 0.1 were used with least absolute shrinkage and selection operator (LASSO) to select a list of informative SNPs for HID. The final list, hidSkinPlex+, contains 365 SNPs and achieved a 95% classification accuracy on 459 samples and lays the foundation for a targeted sequencing panel that can be used to further study the stability and specificity of human skin microorganism SNPs for HID applications.