We all emit our own 'microbial cloud'

Every individual has a microbiome compiled of millions of bacteria, fungi, viruses, and other microorganisms that is unique for each one of us. Whenever we travel to a new location and sit down or touch something, we are spreading our microbiome to that new location. A lot of research has gone into this phenomenon and is called the microbiome of the built environment. A new study out of the University of Oregon has expanded on this understanding and has described what they call a “microbial cloud”.

The scientists found that individuals not only spread their microbiome to new locations through direct contact but the microorganisms on our body are also dispersed into the air making up this microbial cloud. To better understand this, the scientists had 11 individuals sit in an enclosed room for 4 hours and they analyzed the DNA from the bacteria in the air. They found that when each individual sat in the room, there were thousands of bacteria in the room and everyone’s was distinct. They were able to identify specific characteristics of the people such as if it was a man or a woman.

The bacterial combinations found in the room could be linked back to specific individuals even after the person inhabited the room for only 4 hours. There were specific groups of bacteria like Streptococcus, often found in the mouth, as well as Propionibacterium and Corynebacterium, often found on the skin, that were most useful in identifying the individuals. While these bacteria were found around all the study participants it was the combination of bacteria that was key to identifying the individuals.

This finding could have several important applications. One often-discussed application of the microbiome is its use in forensic applications. It may be possible to use this ability to identify people and know if they were in a room or not to see if someone committed a crime, though it is not clear if it will be possible to identify people in a crowd of other individuals. Other applications include understanding the spread of infectious disease between individuals and within buildings. This is an exciting new development and I am certain we will see more research looking at our microbial clouds in the future.

Your microbiome could be used to identify you

Scientists have long speculated that each individual’s microbiome may be unique and static enough so that it could be used for identification.  This becomes very important for forensic investigations, which we have written about before, and also raises many ethical concerns regarding privacy during microbiome sampling and donation.  Previously, most of the studies on this topic were not exhaustive enough to provide any firm conclusions.  Last week though, Curtis Huttenhower’s group from the Harvard School of public health published a powerful, and statistically robust method for tracing the a microbiome back to its host.  The study was published in the Proceedings of the National Academy of Sciences.

Using the Human Microbiome Project (HMP) database, the scientists used machine learning to construct a test for the most important conserved metagenomics traits after comparing individuals’ microbiomes over time.  The algorithm depended on both 16s rRNA sequences, as well as whole genome sequencing (in addition to derivatives of the whole genome sequencing).  The researchers note that the algorithm is not just looking for microbiome genes that are conserved over time, but rather microbiome genes that are conserved over time and unique amongst the population.  Overall, they found that after a year, their algorithm could accurately identify 86% of people based on their stool samples, with very few false positives.  Other sites on the body, like the skin, were less effective for identification, but it was feasible to use them.

This team definitively proved that a microbiome can be used to identify its host.  They admit that full sequencing if the microbiome is necessary, but regardless, it is possible.  This has all sorts of ethical and privacy concerns associated with it.  For example, microbiome data that is made publically available, though anonymized, could be traced back to its donors.  This could include information like STDs or other diseases.  Another obvious application of this would be in forensics, and it probably wont be long before a case hinges on microbiome evidence.

Could the microbiome help solve crimes?

Much of the residue on the skin that creates a finger print can be attributable to the microbiome.

We know the microbiome varies greatly between individuals, but is it unique enough, and static enough, to be traced back to an individual?  If it is, then it could theoretically be used to tie people back to the scene of a crime.  Unfortunately not everyone defecates during their crimes, and bacteria transferred from skin can degrade rapidly.  What about hair though?  Hair is commonly obtained as evidence in many crimes because it possibly contains human DNA, however the majority does not.  In these cases can the hair be analyzed for bacterial genomes, and then traced back to the perpetrator?  A team of scientists from Australia sought to answer that question in a newly published article from the journal of Investigative Genetics.

 Scalp and pubic hair was sampled from 42 individuals for the study.  The findings showed that while each of the people shared common bacteria, they also contained many unique bacteria.  Even with very little sampling depth, just identifying bacterial phyla, rather than genus or species, was enough to differentiate the people.  This was especially true with pubic hairs, which were much more individualized than the scalp hair.  In addition, the pubic hairs very clearly differentiated males and females based on the abundance of Lactobacillus, which are very abundant in female pubic hairs (as well as the vagina).  Finally, the results showed that the hairs, especially pubic hairs, were stable over a 5 month span.

Overall this study serves as proof of concept for the microbiome being used as forensic evidence.  This could especially be true for sexual assaults where there is no other physical evidence besides pubic hairs.  Interestingly, the study found differentiation between people without characterizing bacterial species or strains.  Higher resolution sequencing would almost certainly allow for higher discrimination in individuals.  So a warning for all the criminals who read this blog, you may want to consider shaving before committing any felonies.