It is often important to focus on what is missing to correct an unhealthy ecosystem.


Many of you are aware of the many beneficial bacterial species located within the Lactobacillus and Bifidobacterium genera. Fewer of you, however, are aware that there are also beneficial yeasts that inhabit our gastrointestinal tract. While much remains to be discovered about gut bacteria, we know even less about beneficial yeasts, although one such yeast, Saccharomyces boulardii (S. boulardii) has been extensively studied. (1) (2)

I’ve stated formerly that doctors would have a higher success rate treating small intestinal bacterial overgrowth (SIBO) and other gastrointestinal ailments if they understood how yeast often plays a part in these diseases. The high relapse rate experienced by those treated for SIBO using just antibiotics might very well be chalked up to this oversight.

Many of you have intimate knowledge of how an overgrowth of Candida albicans (C. albicans) can wreak havoc in your life. I too battled a yeast overgrowth during my bout of dysbiosis that often left my tongue coated in a yellowish-white gunk, my sinuses constantly clogged and my nether regions in perpetual itch.

Healthy colonies of beneficial bacteria and yeast keep naturally occurring opportunistic fungi—including C. albicans—from colonizing the digestive tract.

However, when I’ve spoken with some about their gut dysbiosis, I’ve often noted skepticism about the necessity of reintroducing, augmenting or feeding beneficial gut organisms for any lasting cure. Some of this hesitancy is no doubt owed to many trying ineffective probiotics that failed to deliver any results.

Another reason may be the often uncomfortable reactions many have when they do try an effective probiotic. Some report exacerbation of symptoms, failing to realize that this is to be expected when an already overburdened liver and immune system strains to cope with a flood of newly displaced pathogens.

But I suspect there’s another reason people resist the idea of replenishing gut flora. It’s human nature to focus on the pathogen or pathogens that might be causing their discomfort in contrast to what might be missing.

A healthy gut is populated with communities of commensal and competing organisms that together lead to an environment that is diverse and promotes good health. But when, for whatever reason, changes occur that reduce or eliminate key gut organisms, ecological shifts within the digestive tract reach a tipping point.

What was diverse and healthy, becomes dominated by a few invasive species and unhealthy. What was once neutral, or perhaps even beneficial, becomes pathogenic. When that happens, many of the symptoms I outlined in the Inflammatory-Cortisol Ballet come surging to the foreground.

As a way of illustrating this point, I want to recount an experience I lived through.

I used to live in a semi-rural part of Orange County, California. I say used to because developers during the last housing bubble have since eradicated much of that natural environment.

My experience happened in the mid 1990s when a very large tract of undeveloped land was cleared behind us to build several planned communities. This project also included building a four lane divided road to link our neighborhood and the ones being built with a major freeway to the North.

This construction project caused the disappearance of some large native animals: mainly deer, bobcats and coyotes. For neighbors who had lost pets to the latter, this turn of events was initially greeted as good news. No longer did they have to worry about Fluffy or Sparky becoming coyote food.

However, whatever initial relief existed, soon morphed into a growing realization that our environment was no longer familiar to us.

The first time I became aware of this was when I pulled into my driveway and saw a colony of rabbits happily feasting away on my lawn in the bright Southern California sunshine. Even honking my horn didn’t scare the little buggers away.

Up to then, I could count on one hand the number of rabbits I’d ever seen. But now we were overrun by a veritable plaque of these long-eared critters because coyotes, their foremost predator, were nowhere to be found.

However, it just wasn’t my lawn that was paying the price. I vividly recall one Saturday afternoon spent planting fourteen flats of marigolds in our front flowerbed. For you non-gardeners out there, a flat has sixteen plants when in four-inch containers. If you do the math, that comes out to 224 freaking marigolds!

And yes, I was sore as hell the next morning after that much gardening. Nevertheless, I fully expected to be greeted by a vibrant display of color for the next few months whenever I walked outside my front door.

So you can imagine my utter dismay when retrieving my newspaper the next morning I was greeted not with a colorful spray of orange and yellow flowers, but with green stalks gnawed almost entirely to the ground by what must have been an evil, red-eyed coven of ravenous bunnies. I spontaneously developed warm empathy for Elmer Fudd.

As if being overrun by rabbits wasn’t bad enough, being besieged by field mice and rats really made me pine for our absent wild canines. It was not unusual to see rodents climbing tree trunks, entering attic crawl spaces, burrowing through dryer air vents, raiding bird feeders or scurrying around the yard at all hours of the day. Lucky for us, our Siberian Husky slept outside and enjoyed killing them for sport. We were usually greeted with one or two dead rats on his bed every morning.

Gopher holes began to pop up everywhere. Pest-control trucks became a common sight around the neighborhood.

The increase in field mice, rats, gophers and rabbits attracted hawks and other winged predators. This helped keep things in check, but meant we were constantly dodging bird crap when we walked outside. Leaving a clean car on the driveway or street became impossible.

A whole family of owls took up residence in a tree in the front yard. I fondly remember their staring back at me every time I went to get the mail. What I don’t lovingly recall were the half-eaten mouse carcases and owl poop littering my path to the mailbox.

Pools, hot tubs, fountains, bird baths and ponds were soon filling with dead rodents. You see, many people could no longer deal with the infestation so they starting putting out poison, or having the county do the same. But a poisoned mouse or rat is a very thirsty animal, so many ended up drowning in any water they found to quench their insatiable thirst. Sadly, several pets were sickened or died during this period from accidentally ingesting the same poison.

After almost a year and a half of constant construction, the houses and road were completed. The coyotes and other displaced animals slowly returned, and ecological balance was again restored, or as best as could be expected in a now built-up suburban community. What had been a nuisance became as innocuous as a butterfly.

Now, what I just described should be understandable to all of you, not because you lived through it or something similar, but because of the narrative. It’s clear from my story that the environmental disturbances I described resulted from displacement of key animals, in particular coyotes, because of a major construction project.

But what if you hadn’t been told any of this? What if all you knew was that there was an increase in the number of rabbits, mice, rats, gophers and birds? What if you were given no historical context or understood how absent predators can lead to ecological imbalance?

Would any of you have guessed that the real cause of this phenomenon resulted from what was missing? Or would you have focused instead on the visible outcome? My guess is that many people, including their doctors, would do the latter.

Displacement of key gut organisms causes these same types of ecological disturbances within us, but they do so at the cost of our health. Antibacterials and antifungals, whether pharmaceutical or herbal, serve the same role as poison to control for infestations of unwanted organisms. They are very effective—in the short-term. However, their continued use can also cause unintended consequences like the buildup of antibiotic-resistant strains, not to mention collateral damage to remaining beneficial gut flora. But more importantly, they fail to replace what is missing.

It is the height of wishful thinking to believe that any pharmaceutical or over-the-counter non-probiotic or non-prebiotic supplement will ever be developed to fill the role of gut flora in human health. And it’s also folly to believe that gut dysbiosis can be prevented or cured without these organisms.

Whether by taking effective probiotics, or eating fermented food, or supplementing with prebiotic fiber, or eating resistant starch, or undergoing a fecal transplant, or all the above, key species of a normal and healthy gut ecosystem must be augmented or re-introduced and given the substrates they need to flourish and promote intestinal biodiversity. Otherwise, a person risks never becoming healthy.

Focusing on the intestinal equivalent of rabbits, mice, rats and gophers is often necessary to begin healing. But in the end, only restoration of our internal coyotes guarantees lasting gastrointestinal health.



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