Get Used to Fun(gal) Company

Like many people, I have become more aware in recent years of the microbiome and its impact on our health, but I'd been unaware of the mycobiome, its fungal subset.  That changed when I read an in-depth story in The New York Times on a drug resistant fungus named Candida auris.

It reported on a man who recently died in a U.S. hospital from it, and here's the scariest part of the story:

"Everything was positive — the walls, the bed, the doors, the curtains, the phones, the sink, the whiteboard, the poles, the pump,” said Dr. Scott Lorin, the hospital’s president. “The mattress, the bed rails, the canister holes, the window shades, the ceiling, everything in the room was positive."

The story went on to explain: "Over the last five years, it has hit a neonatal unit in Venezuela, swept through a hospital in Spain, forced a prestigious British medical center to shut down its intensive care unit, and taken root in India, Pakistan and South Africa."   Dr. Tom Chiller, who heads C.D.C.'s fungal branch (who knew!) said: "It is a creature from the black lagoon.  It bubbled up and now it is everywhere."

Spread of Candida auris.  Credit: The New York Times. Image from Kazuo Satoh et al., Microbiology and Immunology

Some would argue that, as bad as it sounds, your chances of contracting Candida auris is actually very small, but my feeling is: ignore the mycobiome at your own risk.

If you're squeamish, the situation is worse.  A separate Times story points out that "you're covered in fungi," with fungi present both on the inside and the outside.  There's fungi at the bottom of the ocean, there's fungi at the top of mountains, and there's fungi in Antarctica.  One biologist says they are "on every grain of sand, in every gram of soil from the Arctic to the tropics." 

If all that makes you consider fleeing the Earth to escape it, a new study  has found that even the International Space Station is full of both bacteria and fungi.  The bacteria populations tend to ebb and flow, while the fungal communities are more stable over time.  

Stubborn little life forms, aren't they?  

Batrachochytrium dendrobatidis.  Credit: CSIRO

As Candida auris illustrates, fungi can be killers.  Science reports that a fungus named Batrachochytrium dendrobatidis (Bd) "has wiped out more species than any other disease," causing 91 species to go extinct and another 491 species to decline, especially among frogs.   That's why fungi like Candida auris that are resistant to current antifungals are scary.  We've started to recognize the problem of drug resistant bacteria, but, as a recent research paper declared: "Worldwide emergence of resistance to antifungal drugs challenges human health and food security."

Well, then, the solution is clear, right?  Find more of those antifungals and kill them all, right?  Not so fast.  As we've started to learn about the microbiome, the "right" mycobiome is essential to our health.  Fungi have been connected with, among others, Crohn's disease, ulcerative colitis, hepatitis B, asthma, prostate cancer, obesity, and graft versus host disease (GVHD).  We don't know when the problem is too much of them, too little, or too many of the "wrong" kind.  

And, yet, we're only starting to pay attention.  A 2016 report found that "only 269 of more than 6,000 Web of Science search results for the term “microbiome” even mention “fungus,” and the scientific search engine returns only 55 papers pertaining to the “mycobiome.”'   Studies about the microbiome generally are still a small minority of all medical research papers, and studies about the mycobiome are a tiny minority of that minority.

The author urged:

The scientific community must adopt an all-inclusive characterization of the human microbiome going forward; studies that focus solely on bacteria are myopic and doomed to failure, and they squander precious research funds.

We are literally swimming in our mycobiome, and having it swim within us, but we are just barely beginning to understand its importance.   "Myopic and doomed to failure" is an apt description of our current focuses.

Credit: Ghannoum and Tang, The Scientist

One expert, Dr. J. Curtis Nickel of Queen's College (Canada), told the Times:

I personally suspect that it’s an interaction of all the different bacteria, fungi and viruses.  An unhealthy population of these organisms exacerbates disease and perhaps even — this is the next step — causes it. But boy, we’re not there yet."

Boy, we are not. 

We tend to view healthcare as a fight.  We declare war on diseases.  We battle our maladies.  We have antibiotics, antivirals, and antifungals.  We beat illnesses.  Dying is a loss.  It all makes for a very colorful metaphor, and positions our clinicians and healthcare organizations as noble warriors, but it is a flawed metaphor.

Our health is not "our."  We think of ourselves as this collection of cells that share the same DNA, but it's not that simple.  Few of us live in a bubble; "we" includes the many other organisms that accumulate, starting at birth and continuing throughout our lives.  We can't avoid them, nor have we evolved to ignore them.  Our health lies in our co-existence with them -- whatever that means.

The problem is that, for the most part, we don't know what that means.

Brute force approaches like antibiotics have, no doubt, saved countless lives, but at an untold cost.  We're only starting to understand how these "anti" efforts have altered our microbiome and mycobiome, for how long, and to what effect.  We have yet to have our penicillin moment with the microbiome and mycobiome.

In many ways, 20th century medicine can be viewed as the era of antibiotics.  For all the good they've done, I think someday we'll look back at some of our current "anti" efforts as fighting a losing battle against things that should be our best allies.

My belief is that 21st century medicine will become viewed as the era of coexistence with our microbiota, when we recognize that the health of our microbiome and mycobiome is the same as "our" health. 

Many of may think of our health as a garden, that we must tend carefully -- planting the right things, giving them enough food and water, weeding constantly, and pruning as necessary.  But that's another flawed metaphor: we are not the gardener, we are the garden.