Over the past decade microbial forensics has shifted from solely biosecurity applications to include human identification (HID). Studies have shown that the human skin microbiome could potentially serve as an adjunct to traditional DNA evidence, especially when the human DNA is low quantity. Recently, a custom targeted panel for the human skin microbiome has been developed. The panel leverages loci specific to key microbes that are highly abundant and stable on human skin.
In her presentation at ISHI 32, Allison Sherier, will present a study where skin swabs from the non-dominant hand of 51 individuals were collected in triplicate and were analyzed for HID purposes. High FST SNPs were selected using three different methods to determine if the number of taxa and/or SNPs had an impact on HID accuracies. The SNPs were then input into a support vector machine (SVM) to classify unknown samples to the individual from which they most resembled.
We chatted with Allison to learn what makes microbial forensics advantageous, how ancestry informative SNPs aid microbial forensics use, and advice for those starting a graduate program in forensics.
How has microbial forensics traditionally been employed? What makes microbial forensics so advantageous for human identification purposes?
Traditionally microbial forensics was applied to characterizing microorganisms to investigate biological terrorist attacks, biocrimes, or an accidental release of a biological agent. However, with the advancements in massive parallel sequencing and bioinformatics, the applications of microorganism analyses have substantially expanded. The human microbiome has approximately the same number of microorganisms as the human body has nucleated cells. These microbial cells provide an abundant amount of information that may potentially be used for human identification.
Without giving too much away, can you describe the custom targeted panel for the human skin microbiome that you’ll be presenting at ISHI?
Schmedes et al. (2018) designed the hidSkinPlex to contain common, abundant, and stable microorganisms for the skin microbiome based on publicly available human microbiome data. One goal of this project is to reduce and refine the markers of the hidSkinPlex to potentially make a more sensitive and robust panel.
Schmedes SE, Woerner AE, Novroski NMM, Wendt FR, King JL, Stephens KM, Budowle B. 2018. Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification. Forensic Sci Int Genet 32:50-61.
How do ancestry informative SNPs aid microbial forensics use?
Ancestry informative markers (AIM) regularly used in human bio-ancestry studies commonly have high FST estimates, wherein a few high FST markers are first mined from genomes and then used to predict population group affinity(ies). FST can be estimated by evaluating orthologous SNPs in two different skin microbiome populations (i.e., skin microbiome samples from different individuals). FST estimates could provide insight into whether the alleles of a marker observed between microbial populations are identical by descent, allowing for better discrimination between microbial populations. This approach in turn may improve the accuracy of associating a skin microbiome sample with its respective human host.
Were there any surprises that arose in your research?
No surprises occurred in the core findings of my project. However, the large amount of data produced during the calculation of FST estimates and the support vector machine classification was a bit surprising. Currently, for this limited sample size of skin microbiome hand samples, I have generated about 400 GB of raw data. Learning how to ‘wrangle’ the data and several new coding languages, it has taken me some time to manage this amount of data.
What tips would you give to someone who is just starting a graduate program in forensics, or what is the best advice you’ve received?
Graduate school is always a big decision. The best advice I suggest is to treat it like a job. Make yourself deadlines and goals and stick to them. The typical week should be working on your classes, research, and writing from 8 am to 5 pm Monday through Friday. Focusing on graduate school as a job meant that I had time for myself and my family. This approach also helped me prevent burnout early on in my program.
Has there been anything good that came out of the pandemic that you’ll continue doing going forward?
The pandemic changed many things, but it did force me to be more intentional about time for myself. Working from home allows me to have extra time (not commuting), but I quickly realized I was working a ton of extra hours. I finally had to start scheduling my day a little more closely and adding specific time to go work out or take walking breaks. I hope to keep up this extra separate time as I start to work full time on campus.
What is your favorite Disney character and why, or which Disney character do you most relate to and why?
Alice in Wonderland has always been a favorite of mine. Alice is just a young girl trying to work through her life and the world around her. She meets a bunch of super unusual characters that shape her experiences and guide her. A very close second is the Cheshire cat.
If you could have one superpower, what would it be and why?
I am an animal lover. So above all else, the ability to talk to animals would be my pick.
What’s one thing that others may not know about you?
I used to show Brahman cattle in high school and managed a show cattle ranch in Oklahoma for a year during my bachelor’s degree. For the people not familiar with show cattle, you raise a heifer (female) or steer (altered male) and show them at county fairs or stock shows. The heifers are typically shown at multiple shows until they have their first calf, and steers are generally shown at one big show. While managing the show cattle farm, at 19 years old, I oversaw halter breaking heifers and steers from a few months of age up to 2 years. I also managed their daily needs and did essential work to prepare them for shows.
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