It’s a microbe’s world…we’re just living and dying in it

Our last post explored the significance of what is becoming something of a buzzword in today’s science news: the microbiome.  For those of you who missed it, here is the abridged version.  The human microbiome consists of vast communities of bacteria, fungi, and viruses living in and on the body.  Yes, you live to serve trillions of microbes, who in turn live to serve you.  With the advent of sequencing technologies, scientists are now beginning to identify them and suspect that possessing a wide variety is key to staying healthy.  Some researchers have even suggested a link between a loss in microbial diversity and the recent astronomic rise in food allergies, diabetes, obesity, and autism.

But the microbiome may not simply offer insight into our physical and mental well-being.  With increasing accuracy, it can reveal a great deal about who we are as individuals — the people with whom we interact, the spaces we occupy, and even our ethnicity, says Dr. Jack Gilbert, a microbial ecologist at Argonne National Laboratory.

“…[W]e can match you up to your computer keyboard and mouse, to your doorknobs, light switches and floor, and even to your dog by the microbes you share,” adds Dr. Rob Knight, a world authority on the human microbiome at the University of California at San Diego.


How does this work exactly?  Well, each one of us leaves behind traces of our bacterial selves or what Knight and Gilbert call microbial signatures.  “The skin microbiome is our primary interface with the world and the interface we most readily leave behind when we interact with a space,” says Gilbert.  It therefore reveals many aspects of who we are and how we live our lives.

In August, both Knight and Gilbert were involved in a study on the microbiome of families.  And the analysis of the six week project indicated that the microbes found populating a home were distinct to its occupants, and if they took up residence elsewhere, their microbiota traveled with them.  The findings of this study clearly have wider implications.  Frequent travelers, for instance, may take comfort in knowing that it is in fact their cooties — not those of previous guests — colonizing the hotel room.  Within just 24 hours, the microbiota of the new guest have nearly replaced those of the former occupant, said Gilbert when speaking to the Washington Post.

So, if we’re leaving bacterial traces on keyboards, doorknobs, and all over even the most adorable B&B, one may sensibly deduce that we are leaving them elsewhere, which is the general notion driving microbial forensics forward.  In this vein, researchers at Murdoch University in Australia examined bacterial species populating human hair, finding that these microbes are incredibly distinctive from one individual to the next.  Forensic biologist Silvana Tridico, who oversaw the project, hopes that the discovery may be useful in sexual assault cases, especially when there is no DNA evidence to link the perpetrator to the victim.

But what if the victim is already dead?  Could this field of inquiry still offer clues?  Gilbert believes so and quite firmly.  In the same interview with the Washington Post, he reported that scientists could examine the deceased’s bacterial colonies in an attempt to determine who last had contact with the body.  “An actual fingerprint is rarely left on a body, but a microbial fingerprint certainly is,” said Gilbert.

At this point, it bears mentioning that when a person dies — by trauma or natural causes — the microbiome changes and so significantly that experts in the field have accorded it its own name: the necrobiome.  Naturally, one of the best ways of understanding this transition from micro to necro is examining human decomposition — an undoubtedly grim occupation, but for Dr. Daniel Wescott of Texas State University, its importance cannot be understated.

Wescott oversees the Forensic Anthropology Research Facility, one of only a handful of body farms in the U.S.  For those of you scratching your head, I strongly advise against Google searching “body farm.”  In lieu of what are sure to be graphic, nightmare-inducing images, I’ll share a hopefully more sleep-friendly definition.  At said locations, researchers like Wescott study how the human body decays under a variety of conditions, and it is through close examination of this process that the mysteries of the necrobiome begin to unravel.  For starters, Wescott and his team may have unlocked a more accurate method for determining a person’s time of death.

But how?  What makes these “death” microbes so revealing?  To the untrained eye, a dead animal looks like little more than a messy buffet for insects and opportunistic scavengers.  And when I ask Gilbert, he concedes that there is indeed a great deal of chaos taking place, especially on the microbial level.  “A living body manages its microbiome like a farmer would their crops,” says Gilbert, and “[w]hen the body dies, this control disappears, and the microbiome runs wild…”  That being said, scientists are beginning to track patterns in how this chaos unfolds, and it is these patterns that intrigue biologists like Jessica Metcalf at the University of Colorado, Boulder.


“Microbial communities in and on an individual change dramatically during decomposition, but in a very predictable way,” says Metcalf.  And so predictable is the process that scientists often compare it to a clock.

Knight clarifies, “The patterns of different kinds of microbes that colonize a decaying body at different stages can be used as a clock that tells you how long it has been since death.”  But this is just one kind of microbial clock, he goes on to say.  Others may indicate age or the last time a person ingested antibiotics.  Knight continues, “Understanding how faithfully our microbes record events in our lives and even associated with our deaths is a major focus of ongoing research in my laboratory and others.”

In the months and years to come, Knight’s research, as well as that of many others in this burgeoning field, will likely continue to revolutionize how we understand the multitude of microbes we host.  But the study of how they impact both our lives and deaths is very much in its infancy, Gilbert cautions.  Larger data sets contingent on costly technology will be critical in the advancement of the field.  Nevertheless, at this current juncture, I think we can all agree on one thing: you are what you eat and most certainly, whatever eats you.  And the beat goes on.