The Biodiversity Crisis Happening Inside of You

Human gut microbe

Bacteria in the human gut | Image credit: Centers for Disease Control and Prevention (CDC)

Many of us are troubled by stories of how the biodiversity crisis is changing the planet, but what about the biodiversity crisis raging on inside our guts?  As habitat loss, pollution, and global warming drive the disappearance of species and in the worst cases, the collapse of entire ecosystems, on an infinitesimally smaller scale, a similar phenomenon is unfolding in our bodies or more technically, our microbiome — that is, the trillions of microbes living in and on each and every one of us.  And the costs of losing this microbial diversity?  Perhaps equally ruinous to our health.

“Global warming is what human activity is doing inadvertently to the macro-environment.  Our missing microbes and loss of diversity are based on what we are doing inadvertently to our micro-environment,” explains the director of the Human Microbiome Program at NYU, Dr. Martin Blaser, who sees a close relationship between the state of the human microbiome and the marked increase in diseases like asthma, food allergies, diabetes, obesity, and even autism.

The climb in these wide-ranging and often debilitating diseases certainly accounts for growing public interest, as well as a burgeoning probiotic industry that may be said to be literally feeding off of the former. 

But what explains these apparently devastating changes to our microbiome?  A number of scientists, including Blaser, point to poorer diets, cleaner living conditions, and the overuse of antibiotics in the Western world.


When speaking with NPR’s Terry Gross, Blaser noted that farm animals have been given antibiotics for roughly 70 years, and perhaps equally troubling, here in the U.S. most children have ingested on average a startling four courses of antibiotics by their third birthday.  As broad spectrum drugs, these antibiotics are indiscriminately killing off bacteria — both good and bad — at what Blaser considers a critical stage in the development of a child’s microbiome.

While scientists agree that maintaining bacterial diversity is important, they are only beginning to understand the complexity of our microbial makeup.  So, not unlike WoRMS, an initiative seeking to document the biodiversity of our oceans before certain species disappear, research programs are well underway to study the diversity of the human microbiome.  Peoples living in remote parts of southern Africa and South America are of particular interest, as their microbiome offers a glimpse into how our own may have once looked prior to changes in diet and the introduction of modern medicine.

It would stand to reason that identifying which microbes are missing may be the secret to improving our health, and Dr. Blaser agrees.  Blaser said on NPR, “I think that’s going to be part of the future of medicine, that we’re going to understand the science of the microbiome well enough so that we can look at a sample from a child and say this child is lacking such-and-such an organism…”

But until then, what can we do?  When I suggest store-bought probiotics as a possible remedy, Dr. Blaser advises caution, explaining that “studies show that if you take a ‘probiotic’ today, by tomorrow, it no longer can be found in the body.”  He has described the business of probiotics, a largely unregulated industry, as the Wild West.  And when we spoke, he clarified that “[n]early all the products are untested for their efficacy in controlled trials.” 

So, if store-bought probiotics aren’t the answer, how can we restore the health of our microbiome?  Well, so far the most effective proven alternative to health shop options likewise consists of probiotics, but its source may be far too off-putting even for the most desperate treatment seeker — its source being human excrement.


At this point, I imagine I’ve lost roughly half of our readership, but for those who can stomach it (pun intended), read on, as fecal microbiota transplantation — or FMT for short — is indeed being hailed as one of the latest and greatest medical innovations by the Cleveland Clinic.  And for good reason.  FMT has proven to be incredibly effective in combating C. diff, a dangerous infection which is often resistant to antibiotics.  Quite remarkably, patients suffering from the infection may recover within a day of receiving treatment.  In a controlled trial conducted at the Academic Medical Center in Amsterdam, 13 of 16 patients felt better after a single fecal transplant.  As they say, the proof is in the pudding — the last of my puns, I promise.

FMT is a fairly simple procedure, which involves taking a stool sample from a healthy individual and transplanting it into the colon of an afflicted one. In addition to treating C. diff, fecal transplants are being employed under clinical trials for irritable bowel syndrome, ulcerative colitis, Crohn’s, and HIV.  What makes FMT so effective, particularly in the case of C. diff, is that the new healthier bacteria “have little effective competition” and more easily take root, explains Dr. Blaser.

It is these seemingly miraculous recoveries, combined with relatively limited access to FMT, fueling a dangerous DIY movement in which sufferers are performing their own fecal transplants.  And some are even taking instruction from popular how-to videos on YouTube.  “[T]he procedure itself is simple enough to do yourself at home,” explains Carolyn Edelstein, Director of Global Partnerships at OpenBiome, a nonprofit that supplies stool to hospitals, where FMT’s are performed.  But the process of finding a suitable donor is as tricky as the procedure is easy.  “Only 4% of people pass our full clinical assessment,” adds Edelstein.

“FMT is the transfer of biological materials — it is no safer than a blood transfusion, and probably less; this needs to be carefully controlled so serious mishaps do not occur,” explains Dr. Blaser, echoing Edelstein’s concern.

To address issues of safety and perhaps no less important, the stigma of employing human excrement for treatment, the Massachusetts General Hospital in Boston has developed a pill that could eventually replace the need for transplants.  And at OpenBiome, Edelstein says a synthetic bacteria could substitute stool altogether in the next few years.  As for Blaser, he sees promise in both Western medicine and what modernity hasn’t yet altered.

At the end of the day, a fisherman in the wilds of Borneo could hold the key to salvation for an IBS sufferer in Queens.  As Blaser points out, it will be the peoples relatively untouched by this human biodiversity crisis who “may ultimately be the source of restoration for us.”