Using Skin Microbiomes for Forensic Human Identification
Can scientists tell people apart by their microbiomes? While microbiome composition can be influenced by factors such as who you live with, your diet, and your environment, the skin microbiome is relatively stable over time, making it a good candidate for differentiating individual people. Technologies like whole-genome sequencing (WGS) differentiate to the single nucleotide level and allow scientists to differentiate one strain from another, but what are the most stable species for interrogation? A longitudinal study now published in Applied and Environmental Microbiology looks at the potential of Propionibacterium acnes, a gram-positive bacterium and member of the skin microbiome, to provide a robust and reproducible marker panel.
PCA analysis shows similarity between microbiome samples (left) or 27 P. acnes genetic markers (right) from cheek samples taken over 3 years. Source.
To assess P. acnes differences, the scientists looked both at the presence or absence of genetic features as well as nucleotide diversity of shared clade-specific markers. These latter sequences are necessary to capture nucleotide-level details of genetic variation that contribute to their use for accurate identification. Samples from the same individual have little variance when looking at the microbiome, and using a set of 27 P. acnes genetic markers decreases variance (see right), increasing predictive values.
Algorithms using microbial markers on the chest and, surprisingly, the palm were the most accurate in identifying individuals. Finding palms to be highly correlative was unexpected because our palms are constantly exposed to numerous microbes, which may themselves colonize the hand and influence microbial composition. These sites were among 14 body sites on 12 individuals assessed at 3 separate times during a nearly 3-year period by the three scientists involved in the study, Sarah Schmedes, August Woerner, and Bruce Budowle.
Using the microbiome in forensics has been previously suggested, and met with both enthusiasm and skepticism within the scientific community. One of the sources of skepticism has been the dynamic nature of microbiomes based on environmental influences. This study demonstrates that a systematic search for the most stable locations of different microbial species may lead to a marker panel for practical applications one day. However, the scientists clearly state that use of microbiome forensic testing is still a nascent field with many validating studies yet necessary.