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.

Microbiota biofilms and colorectal cancer

Colorectal cancer is the 4th most deadly cancer in the world, and over 1 million people are diagnosed with it each year.  It has very few genetic indicators and it is rapidly growing in prevalence, thus researchers believe it is very likely associated with environmental causes.  An obvious environmental cause would be the microbiome, and researchers from John’s Hopkins helped establish this link with their recent publication in PNAS.  In their article they show that biofilm formation in the colon is tightly correlated with colorectal cancer.

The researchers studied a cohort of people that had colorectal cancer along with healthy people as controls.  In those people with tumors they studied the microbiome of the tumors themselves along with other, distal parts of their colons.  They discovered that the majority of people with tumors, whether benign or malignant, had thick biofilms growing on and even in the tumor.  What’s more, is that the researchers noticed that biofilms were forming all along the colon, even in the distal parts.  Biofilms were not seen in healthy patients, and in some of the patients with tumors. 

Interestingly, the bacteria in the biofilms between different patients did not necessarily correlate, and so it appeared the presence of biofilms, rather than the composition of the biofilm was critical.  Moreover, the biofilms studied decreased the gut permeability, leading to ‘leaky guts’, which we have covered on this blog before.

A normal colon has a mucous layer to prevent any bacteria from infiltrating the underlying epithelial cells.  It is possible that people with decreased mucosal integrity are at risk for bacteria to invade and form these biofilms which may eventually lead to cancer.  In fact, according to this small study, people with biofilm formation in their colon have a 5-fold increase in their likelihood to get colorectal cancer, much higher than any other known indicator.  More research on a larger scale still needs to be performed.  Still though, biofilm detection could be a useful diagnostic for colorectal cancer, and biofilm management could be a target for drugs or probiotics.