Improving Human Identification Using the Human Skin Microbiome

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dc.contributor.advisorBudowle, Bruce
dc.contributor.committeeMemberLeudtke, Robert
dc.contributor.committeeMemberPhillips, Nicole R.
dc.creatorSherier, Allison J.
dc.date.accessioned2022-02-02T23:05:50Z
dc.date.available2022-02-02T23:05:50Z
dc.date.issued2021-12
dc.description.abstractThere are times when biological evidence has too low of quality or quantity of human DNA to provide enough information for human identification (HID). However, nucleic acids from the human skin microbiome are sources of genetic material that may be useful for HID. The studies in this dissertation 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. SNPs with high estimated FST were ascertained in three different ways to examine three distinct hypotheses. The hypotheses focused on testing whether a high FST, increased taxonomic abundance, and/or using a predetermined panel would be the most effective for HID. Classification accuracies ranged from 88 – 95%, and the method using the most taxa possible performed the best. Results from the study support that using genetic distance to select informative markers from the human skin microbiome for HID was viable. The predetermined panel only achieved an 88% accuracy, although it would be the most applicable of the tested method for forensic case work. 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% of the samples) which had FST estimates ≥ 0.1 were used with least absolute shrinkage and selection operator (LASSO) to select a list of informative SNPs for HID. The final list (i.e., hidSkinPlex+) contains 365 SNPs and achieved a 95% classification accuracy on 459 samples. The hidSkinPlex+ 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.
dc.format.mimetypeapplication/pdf
dc.identifier.urihttps://hdl.handle.net/20.500.12503/30796
dc.language.isoen
dc.subjectbacteria
dc.subjectskin microbiome
dc.subjecthuman identification
dc.subjectmicrobial forensics
dc.subjectforensic profiling
dc.subjectsupervised learning
dc.subjectmachine learning
dc.subjecttargeted massively parallel sequencing
dc.subjecthidSkinPlex
dc.subject.meshSkin / microbiology
dc.subject.meshMicrobiota
dc.subject.meshPolymorphism, Single Nucleotide
dc.subject.meshForensic Anthropology
dc.titleImproving Human Identification Using the Human Skin Microbiome
dc.typeThesis
dc.type.materialtext
thesis.degree.departmentGraduate School of Biomedical Sciences
thesis.degree.disciplineMicrobiology and Immunology
thesis.degree.grantorUniversity of North Texas Health Science Center at Fort Worth
thesis.degree.nameDoctor of Philosophy

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