The Future of Microbiome Forensics

bacteriaEverywhere we go we leave microscopic traces of ourselves, and we collect microscopic traces of others. Microscopic DNA left at the scene of a crime is commonly used to identify criminals and substantiate evidence against them. What about other microscopic traces humans leave behind or even collect, can we be identified or tracked based solely on the bacteria that inhabit our body?


Everyone’s skin is covered in bacteria, it is all over you and the surfaces you interact with. Scientists call each community of bacteria a microbiome. Until the past few years this knowledge was little more than a curiosity as Scientists attempted to understand if this population of bacteria on our bodies affected us in any way. Then some studies came around which suggested that bacteria influence things like mammalian circadian clocks and appetites. Some others attempted to quantify the types and amounts of bacteria on our skin, inside our body, and in our environments. From all of this, Scientists began to see that both the microbiome of our environments and our bodies have unique qualities.

The traces of DNA we leave around are much different than bacteria because the bacteria are alive and so can colonize and replicate. A criminal can say, wash their hands to remove blood or DNA traces from their skin but if they have interacted with someone for a period of time their microbiome could be altered. These bacteria can then transfer to their home or others they have interacted with, leaving a unique trace that cannot be easily erased.

I became interested in the idea of tracking people using bacteria back in 2012 when I was in graduate school at the University of Chicago. I wanted to see if  bacteria on the sole of my shoe would stick around. So I planted some bacteria and walked around for a day and then tried to isolate and identify that bacteria.


Bacteria planted on the sole of my shoe

My idea was that banks, convenience stores, or other places could purposefully plant rare species of bacteria on their premises and thus provide innocuous tracking of individuals in case of crimes (there are a lot of robberies on the South Side of Chicago). Though the scope of this work was very limited and the results inconclusive, it led me to explore more into the realm of biological surveillance and forensics. I came to understand that the question of “How can we be tracked?” needs to be explored alongside the question of “How can people prevent their own tracking?”, whether it is for honest or nefarious purposes.

Now in 2015, tracking people through microbiomes has been tested through forensic analysis of phones and shoes. Sean Gibbons, a Ph.D. student in Biophysics at The University of Chicago and co-author on the study told me that they could differentiate between two people with 97% accuracy when using phones and 99% when using shoes! They could even track what surfaces shoes had been walking over. Before that, another study found that in a group of hundreds of people an individual could be uniquely identified with ~80% accuracy up to a year later by using their fecal microbiome (a little more invasive than shoes, I know). Sean told me, “As far as these methods being ready for today’s courtroom, I’m not sure. You’d have to be very skeptical. The error rate is a bit too high for comfort, but less reliable methods could perhaps be combined with other tried-and-true forensic evidence to help build a case.”

Sean believes the bacteria are all there, they just needed better datasets to help with identification. “We are covered in microbes that live in our sebum (skin oils), and whenever we touch a surface we deposit some of these microbe-infused oils (i.e., a fingerprint). Therefore, if you touch anything at all, you instantaneously deposit a few hundred/thousand microbes. In that sense, a person only has to come into brief physical contact with a space or object to leave a microbial trace.”

How can we avoid this tracking? Can we control our microbiome if we want to? Research shows that microbiomes are strongly affected by the environments we are in and the people we interact with. People who live together share a microbiome with their homes and roommates, even if they are not intimately involved.

Are antibiotics then, going to be a new weapon against forensic analysis?

The problem is that some of the surfaces in the home contain the microbiome of the inhabitants, which means that just changing your own microbiome wouldn’t be enough! It’s a cycle, the bacteria that colonize us are the ones that we disperse through our lives and the ones we disperse through our lives are the ones that colonize us. Your clothes, your bed, your shower, all contain traces of bacteria that tell something about your daily routine. Maybe your friend is a Gammaproteobacteria accumulator and your favorite bar, a Firmicutes haven.

Editing our microbiome may be as easy as cleaning our house, downing some antibiotics and moving in with a friend for a few days or maybe not? Though some work shows that antibiotics can effect our microbiome(obvi), antibiotic use can probably be identified by looking for common bacterial species missing. What about microbiome transplants? Fecal microbiome transplants have been occurring for a while now, maybe I can just ask my friends to collect some bacterial samples from their body and put them in a spray bottle?

I don’t know because none of this has really been tested!

One thing is for sure, Bio-Forensic analysis will eventual move beyond DNA samples, the question is just, When?


This entry was posted in DNA, forensics on by .

Josiah Zayner

About Josiah Zayner

Dr. Josiah Zayner (yeah I know pretty pretentious right?) received his Ph.D. in Molecular Biophysics from the University of Chicago and currently works as a Research Fellow at NASA where he engineers bacteria for in situ resource utilization and sustainability for long-term space exploration and colonization. He has a number of Scientific publications and awards for his work on protein engineering and is also recipient of Art awards for creating Speculative Science works including the Chromochord, the first ever bioelectronic musical instrument. His Art looks to the future of humanity to challenge the boundaries of what Science and Art may be. Josiah (this third person stuff is weird) is also the creator of The ILIAD project, a citizen Science search for natural antibiotics and the Founder and CEO of The Open Discovery Institute(ODIN), DIY Science's first store. He enjoys Whiskey and Red Bull, sometimes together. His work has been featured in Scientific American, Popular Science, Businessweek and NPR, among others.

Leave a Reply