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

Friday Apr 13 | BY |
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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:

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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:

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  1. Beverly says:

    Wow sounds like we have depleted our bodies too like we have the earth I take adult stem cell nutrition has helped me God Bless

  2. Ugo says:

    Is it not arrogant and self-delusional to walk so far out-of-step with Mother Earth’s natural rhythms and rules and still expect to remain negatively affected?

    It can be no mere coincidence that the damage to our health and quality of life is but the echo from the injurious cacophony we’ve shouted at Mother Earth.

  3. Sarah says:

    Donna Gates seeems to get pretty good results with her Body Ecology approach: include fermented vegetables as a major part of your diet in order to replenish your own healthy gut flora. It’s a different approach, rather than picking some conbination of other species out there, she encourages rebuildig your own gut flora which are unique to you.

  4. Xavier says:

    Awesome information! Which foods are high in fiber?

  5. Maia Alpern says:

    Interesting. As someone with Celiac disease I found the article to be eye opening with respect to the figures he quoted for the population that reacts to gluten in some way. As a health coach specializing in gluten-free lifestyle management, I know many people have a sensitivity but didn’t realize it may go as high as 70%.

    The only problem I had with this article is his recommendation to stop eating gluten and then get tested. That might be ok if not much time has elapsed but to get an accurate test you must still be consuming gluten at the time you are tested. If you go gluten-free, start the healing process before the tests, you may get false negative test results. In addition, when gluten is reintroduced, often the reactions are much worse than when you were consuming it regularly.

    If you, or someone you know, might have issues with gluten, please go to for my free 5 step program to get information regarding symptoms, suggested medical tests, educational video on the difference between celiac and gluten sensitivity, and more.

    Maia Alpern
    Founder of

  6. Maia Alpern says:

    OOPS, posted on the wrong article. I had just read Dr. Williams’ article on Celiac disease that is listed in the Related Articles section above and must have hit the back button and posted my comment here. Sorry for any confusion.

    Maia Alpern
    Founder of

  7. Velda says:

    This is very interesting. I have read a little about fecal implants before. Interesting concept, to say the least. I think I would first go with Donna Gates’ suggestion to eat fermented foods. In fact, I have your book, Kevin, “Cultured”, and want to someday finish it (real soon, I hope) and start fermenting my own food, from my own farmette.

    Thanks for all the interesting things you bring to us, Kevin. You are so consciencious, thoughtful and concerned. I’m glad that my friend suggested I start subscribing to your articles, several years ago now.

  8. Though this article at first seems weird, I tend to agree that our western diets are unhealthy for our stomachs.

    After spending 9 months in New Zealand, 4 months in Southeast Asia, 6 weeks in India, and 5 months in Europe, I returned to the states.

    During 2 years of travel, I had two major stomach issues, but was otherwise fine.

    Within the first 2 months of returning to the states, I had stomach problems on three separate occasions.

    I returned over the holidays, and thought I could eat whatever I wanted, because that’s what I had done during travels around the world. My fault.

    But when I was sick in the states in November and December, it honestly felt like all the good stuff in me (which I now think was this “gut flora”) was being killed off and pushed out.

    I’m now much more aware that I have to read the labels on everything I’m eating in the US, and I am eating more of a plant-based diet… which is somewhat difficult when the society is based on eating meat and heavily processed milk and starches, and doing so in large quantities.

    But awareness is definitely key, so thank-you for posting this article.


  9. elizabeth says:

    I am about to do a colonic hydrotherapy but one of the issues discussed was that good bacterias in the gut will be “killed” and therefore have to establish the colonies again after the treatment. It is recommended that the therapy be done on a monthly basis for at least six months.

    I am a bit worried about the frequency as there may not be enough time between treatments to get the good bacterias going as they are being “killed” each treatment.

    Have not asked the clinic yet as to what was included in the water enema that is to be used.

    Once I found out, I’ll post it.


  10. Linda says:

    Thanks Kevin for great information. Wondered
    why my gut won’t heal now I know why. Guess I
    need to work harder on healing and taking
    probiotics daily and maybe look
    in to fecal implants…

    Again thank you so much,

  11. Meri says:

    Thanks again Kevin for all the information you provide.

  12. Maggie says:

    I have had tremendous issues with the intestine and food intolerances being intolerant to most everything and elergic to rice. Since eating fermented foods I have made huge improvements and will not eat nor lunch or dinner without a fermented food. I do eat a lot of super foods from David Wolfe, Kevin and other and am a vegan although I am a type O blood and a protein type. I find that eating the super foods that are high plant protein I feel great at the age of 6. Its a matter of experimenting and seeing what’s right for you and the ambient. I don’t eat foods with gluten and quite honestly think that nobody should. I do great with quinoa, buckwheat, and amaranth and loads of salads and veggies. Nutrition has become a hobby for me and I make it fun.

  13. Maggie says:

    I am 63 not 6

  14. Anna21 says:

    Excellent information. I follow Dr. Williams’ recommendations.

    In addition, I started eating unwashed produce (veggies, fruit) from my organic garden as they have populations of good bacteria. Haven’t gotten sick yet : )

    But don’t try that with veggies & fruits from the supermarket which are handled by scores of people with filthy hands.

  15. Bryan says:

    Thanks for the reminder Anna21. It does not matter where you go, there are people who are just unconscious about what they are touching. I try to stick with the pour type bulk bins at stores as the scoop type just leave too many options for touching, spilling, dropping stuff in.

    It seems like more and more, the challenge is to find health professionals that once can get tested by and have results coached over.

    I have done the Master Cleanse over the years and wonder about the saline flush in the mornings and if one might get more ‘live’ concentrated probiotics into the GI Tract this way as the fluid passes through much more quickly than food.

  16. RACHEL says:

    While I agree with the author/doctor, I cannot help but think how impractical his advice is. Do you know how crazy my doctor would think I am if I told her I want a fecal implant? If I wanted one, then the heck would I even find a facility that does those?

  17. Stephanie says:

    The internet has loads of info on fecal implants… desperate people who are sick with ulcerative colitis, crohns, and c-difficil… very deadly is said to kill at least 300 people a day in the US. They are starting to do implants for these people… check YouTube!

  18. Richard F says:

    Fecal implanting is totally new to me, but it sure makes sense. However, I believe the first step in making the whole digestive system healthy is to make sure that the stomach can produce strong enough acid. This is required for the digestion of protein and the absorption of minerals and much more. Once the acid is up to snuff probiotics won’t get through this wonderful acid barrier and must be taken through the rectum.

    My guess is that once the stomach is functioning properly with a good strong acid, proper food will feed good bacteria in the lower intestine and bowel and they will kill off the bad guys. Fecal implanting would certainly speed up the healing process.

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