Your Gut — As Damaged as the Earth’s Environment? : Exclusive Article by J. E. Williams

Friday Apr 13 | BY |
| Comments (18)

Are probiotics the answer to your indigestion?

When I first started practicing three decades ago, we had only yogurt and kefir for gut repair. Things have changed a lot since then.

The trillions of bacteria that live in our gut—the colon or lower intestine, as well as the small intestine and higher up the gastrointestinal tract, to some degree, in the stomach and esophagus—are as damaged as the environment of the planet.

Gut ecology of modern people; it’s a disaster. Generations of refined food, pasteurized milk, lots of refined sugar, and antibiotic overuse, have ruined our gut flora. The link between dysbiosis, disrupted gut ecology, and health is looking stark.

Over the course of my practice, I’ve seen ever increasing incidences of cancer, autoimmune diseases, thyroid and adrenal glandular conditions, autism, Alzheimer’s and other progressive neurodegenerative diseases, gastrointestinal diseases, mood disorders, and obesity. We blame meat eating, viruses, stress, and weak adrenals. But, clinically, none of these, unless taken to the extreme, hold up as underlying causes. Rather, they appear to be tag-along conditions. Is the gut the missing link?

Experimenting with Probiotics
By the early 1990s, increasing scientific and clinical evidence suggested that this was the case. The fix, we thought, was easy: prescribe probiotics. Probiotics are live microorganisms, which when administered in adequate amounts, confer a health benefit on the host. In practice, however, it wasn’t that easy.

Laboratories had a hard time keeping bacteria alive, or “viable” as it was called. Then, the acid bath of the stomach knocked them dead on arrival. How many friendly microorganisms made up the right dosage? How many times a day? To take with or without food became the naturopath’s dilemma. Nobody really knew the right answer.

Stool testing got better, so we could measure at least a few probiotic species in the gut. Things didn’t look good. Even when taking probiotics, the results didn’t add up. Laboratories got smarter, and made available more choices of probiotics with greater viability. We already knew about fiber and gut health, so we made sure our patients got at least 25 grams daily in their diet or included a fiber supplement.

Fiber helps friendly bacteria stay alive. We learned about prebiotics: fiber and carbohydrates—like Jerusalem artichoke flour, which probiotics feed on to help colonies thrive. The synergistic combination of prebiotics with fiber and probiotics was termed “symbiotics.”

Our Guts are Permanently Damaged
Stool test results still didn’t add up. People ate more vegetables, took probiotics daily, added functional foods and medical beverages swarming with probiotics, got colonics, used probiotic infused enemas, and still their populations of friendly microorganisms were dismal. Clearly the therapy wasn’t working. So, laboratories found a way to get more bacteria into every capsule. I used to tell my patients to take 5 billion active organisms daily. Now, I recommend 25 to 50 billion several times daily. Even that hasn’t done well enough.

I started to read more, attend probiotic conferences, listen to recordings of scientific proceedings, and try different probiotic formulas. Always on the look out for the best medicine, I critically reviewed products from various labs. Though my patients stool test results improved, however, the major breakthrough I was looking for didn’t come. The problem, it seems, is no longer the product, or my program, but that gut ecology has become permanently damaged to such as degree that getting it to flourish again is a monumental task.

Where Do We Go from Here?
One option is fecal implants, using stool from healthy people with robust natural flora. One of my patients from Europe with an extremely rare, crippling autoimmune disorder traveled to India and got two fecal implants. Though they didn’t cure his condition, his stool tests improved dramatically, and his elevated inflammation markers when down. It seemed to work. But no one knows how many implants are needed to restore health to a damaged gut.

Another option is to repopulate the depleted gut using ancestral feces. Ancient bacteria may hold the clue. Martin Blaser at New York University analyzed fossilized feces and found them not only richer in bacteria than in the intestines of modern people, but also with more variety. Dr. Blaser found that modern Western gut microbiome is vastly different from the bacterial DNA of our ancestors. It seems that rural African children have gut microbiomes closer to our ancestors.

We have to learn respect for the ancient bacteria that live with us, and in many ways, “are” us. Each of us has a unique mixture of bacteria. Healthy populations of friendly bacteria are associated with robust health. Restoring health requires effective therapy for repairing the gut.

Best Medicine Today
In all chronic diseases, consider restoring gut ecology.

  • Get a stool test to evaluate your microbiome.
  • Start with a plant-based, high fiber diet.
  • Add medical grade probiotics up to 50 billion units daily, taken with meals.
  • Add a prebiotic supplement.
  • Retest your levels of bacteria in six months. If no improvement, change probiotics and keep going.

It can take two-to-four years to make a dent in gut restoration. If there’s still no improvement, or you want to jump-start your gut restoration program, consider fecal implants. I wouldn’t be surprise if some enterprising individual took these clues seriously. Perhaps we’ll soon have a home kit to recolonize our guts with ancient African bacteria.

For more information including guidelines for prebiotic and probiotic supplementation:

* * *

Picture courtesy bellypowell via

Dr. J. E. Williams


Dr. Williams is a pioneer in integrative and functional medicine, the author of six books, and a practicing clinician with over 100,000 patient visits. His areas of interest include longevity and viral immunity. Formerly from San Diego, he now resides in Sarasota, Florida and practices at the Florida Integrative Medical Center. He teaches at NOVA Southeastern University and Emperor’s College of Oriental Medicine.

Visit Dr. Williams’ Website:

And Follow on Facebook:


Comments are closed.