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Probiotics: Helpful and Harmful

Probiotics: Helpful and Harmful
January 23, 2017 Patrick Nemechek, D.O.

Probiotics: Helpful and Harmful

The use of probiotics is becoming extremely commonplace with a growing number of products being supplemented with a growing number of bacteria that are touted as health promoting.
It is apparent consumers do not fully understand what they are, or what they can do, because the same people who use anti-bacterial wipes or gels will purchase a probiotic which is full of bacteria and swallow it without question.
A probiotic is a supplement that contains bacteria that are capable of secreting mild acids once they reach the intestinal tract.
Consumers are unaware that they also interact with the immune, nervous, hormonal and intestinal systems in potentially harmful ways.
Probiotics are often sold as a “healthy” blend of “natural bacteria” that will restore or replenish your intestinal flora. These products are vastly overstating anyone’s understanding of intestinal bacteria.
With modern technologies, we can sequence the DNA of the thousands of different bacteria that live within the intestinal tract. But most require such unusual factors for survival that scientists are unable to grow approximately 80% of the bacteria detected.
Without being able to grow them, researchers can only guess at basic aspects of their function and behavior.
If the researchers are guessing, then the sellers cannot fully understand what they are selling, and have no scientific basis to offer assurances of safety as they do.
But despite this lack of understanding, many people have discovered that probiotics relieved some of their digestive issues. This is a very important clue because it means they have an overgrowth of (lower) colonic bacteria within the (upper) small intestinal tract.
This bacterial overgrowth is called SIBO, Small Intestine Bacterial Overgrowth. This occurs when colonic bacteria migrate too high into the wrong section of the intestines.
This may occur after taking antibiotics or antacids or when something alters the speed of the digestive tract such as anesthesia, vaccines, or brain injury resulting in Autonomic Nervous System Dysfunction (Dysautonomia).
SIBO affects a large portion of the population and as many as 20% of people with SIBO report no intestinal symptoms. Others with SIBO experience intestinal distress (diarrhea, constipation, eat-and-must-go to the bathroom ASAP, excessive bloating), food sensitivities/intolerance, night sweats, morning nausea, sour stomach or “low blood sugar” between meals, skin problems (rashes, hives, eczema), and recurrent strep and bladder infections.
Our intestinal tract is around 40 feet long. It works like a conveyor belt, moving food and waste products forward that our brain controls through our Autonomic Nervous System (“Autonomics”).
The Autonomics are the brain’s master control mechanism for the organs, hormones, and immune system. The Parasympathetic branch of the Autonomics control our “rest and digest” brain commands and inflammation.
SIBO may start after we experience an injury to our Autonomic Nervous System which alters the movement of our intestinal tract.
The Autonomic injury may be a direct physical injury (concussion, car wreck), an indirect injury (emotional trauma), a metabolic injury (pregnancy, drug reaction, chemo/radiation), or an inflammatory injury (excessive vaccine reaction, antibiotics, anesthesia, surgery, reaction to allergy testing).
Our bacteria have learned the first rule in real estate; location is everything.
The colonic bacteria move up to a much better neighborhood (small intestine) where nutrients help them replicate and survive.
The invading bacteria digest the nutrients and then release gases, toxins, and waste products that give us symptoms.
The bacteria are smart and they will work to stay in their new location. They have learned to send signals to the brain via the Autonomic Nervous System’s main nerve, the Vagus Nerve. These bacterial signals further alter our Autonomics and slows down our digestion even more.
Bacteria from the colon do not like an acidic environment and supplementing with probiotics creates an increase in acids in the small intestine. More acid production, means less colonic bacteria overgrowth, and the person may feel less symptoms.
The relief in symptoms from increased acid is also probably why apple cider vinegar makes some people feel better.
But probiotics do not fix the underlying neurological Autonomic problem, and people may lose the benefits once the bacteria can replicate and continue their migration upward.
Probiotics may also cause health problems in other ways. I have seen children and adult patients become more nauseated, depressed, anxious, and even develop arthritic symptoms when they started supplementing with probiotics.
And a word of caution, just because you do not feel an obvious ill effect does not mean the probiotic is not adding to your systemic inflammation level that triggers a wide variety of illness.
So instead of adding living bacteria to the intestinal tract, I recommend a prebiotic fiber called inulin. Inulin is a fiber that can only be eaten by the healthy bacteria that normally inhabit the small intestine, not the invading bacteria from the colon.
As the normal small intestine inhabitants grow in numbers, they excrete mild acids that the colon bacteria do not like and recede. It gently rebalances the intestine’s natural bacteria without the influence the unknown bacteria found in probiotics.
Some have SIBO to the extent that inulin is not enough to control the colonic bacteria and they need a short course of antibiotics to knock down the bacterial overgrowth plus Autonomic Nervous System treatment for their brains to regain neurological control over the movement of their digestive tract.
There are five stages in Autonomic Dysfunction and the first two stages do not have noticeable symptoms. It is only in the third stage of Autonomic Dysfunction that people start to experience symptoms that affect their daily life GI trouble.
Autonomic Dysfunction does not appear on an MRI, CT scans, and it is not detected in yearly bloodwork. For over 10 years I have tested the Autonomics using spectral analysis to pinpoint the tone and balance of each of the Autonomic Nervous System’s two main branches. I also use Heart Rate Variability (HRV) testing as a marker for Autonomic function and recovery.
I have found to maintain healthier bacteria one must also restore neurological (Autonomic) control over the intestinal tract. We must repair and maintain both the intestinal tract as well as repair and maintain Autonomic function.
SIBO and Autonomic treatment often involves short-term medications to restore a better bacterial blend, core nutritional changes to support neurological repair and stem cell production, Vagal Nerve Stimulation, and long-term dietary changes.
I have discovered a multifaceted formula for Autonomic restoration that is so unique and effective that in 2016 I filed a patent application for “The Nemechek Protocol for Autonomic Recovery” (Patent Pending).
Controlling SIBO and maintaining Autonomic Nervous System balance is not easy, but it is also not impossible. The process takes work and a marathoner’s mindset; each day your efforts, foods, and medications either support or endanger your recovery and health.
Fixing the brain, to fix the body, takes persistent effort by the patient but I have seen recovery years or decades after the person’s Autonomic injury or onset of SIBO.
I am a classically trained internal medicine physician (D.O.) from UCLA and my Internal Medicine and Autonomic practice is in the Phoenix area. My research background has been focused on the Autonomic Nervous System, brain metabolism, and metabolic inflammation.
I use all available scientific and medical tools to induce the nervous system and organs to repair themselves by normalizing inflammation control mechanisms, inducing natural stem cell production, and re-activating innate restorative mechanisms.
For more information, call my office at 623-208-4226.
© 2016. Dr. Patrick M. Nemechek and Jean R. Nemechek. All Rights Reserved. Patent Pending.


  1. Author
    Patrick Nemechek, D.O. 2 months ago

    Traditionally fermented foods are safe to consume with my protocol.

  2. Zahra 2 months ago


    I have recently started my 4.5 year old son on your protocol. I read your book but I have a question that I am still confused about. My son likes to eat yogurt with his lunch and if I don’t give him yogurt he doesn’t eat his lunch. I am still doing your protocol completely but I can’t remove yogurt from his diet. Will the protocol still work ? Thanks in advance for your reply.

  3. Shilpa 2 months ago

    Thanks for your response Dr.

  4. Author
    Patrick Nemechek, D.O. 2 months ago

    Everyone normally has candida within their stool as well as within theri mouths and on their skin.

    Finding it does not indicate that it needs to be treated.

  5. Shilpa 2 months ago

    Hello Dr. Nemechek,
    Thanks so much for the protocol and for supporting people in such a genuine way. My 13 yr old son started it (with Rifaximin course) and is already showing positive changes. No side effects experienced so far.
    We (parents) have been diagnosed with Candida with proper stool test. I am wondering if we can benefit from your protocol to heal our gut? I have read that Rifaximin can worse the Candida. Any advice based on your expertise would be very helpful.

    Thanks so much.

  6. Author
    Patrick Nemechek, D.O. 2 months ago

    As I’ve said before, there is no scientific evidence that yeast (candida) contributes to the features of autism or developmental problems.

    Most of us have candida in our intestinal track so the culture proves nothing.

  7. Anonymous 2 months ago

    Hello Dr. Nemechek,

    I started my 13 yr old son on your protocol with Rifaximin a month back. We have started seeing lot of progress already. Thank you so much for the protocol itself and for being supportive to your readers through these posts. I have read your book which suggests that there is no point taking inulin after the Rifaximin. I hope there is no regression since his system did not develop as steadily like with inulin. However, he experienced no side effects so far. Only good.

    Do you think we adults can also benefit from the protocol? We have been officially diagnosed with Candida using stool test from Genova. However, I feel the protocol may benefit general gut health. Would Rifaximin increase the Candida issue? Prior advise has been to flood the system with healthy probiotics / Saccharomyces boulardii. Any thoughts?
    Thanks and appreciate your response sincerely

  8. Anonymous 3 months ago

    For parents trying to navigate the often confusing and contradictory advice around autism being able to ask a question and get a straightforward answer is truly refreshing. Thank you so much for taking the time to respond.

  9. Author
    Patrick Nemechek, D.O. 3 months ago

    I recommend my patients remain on all the protocol elements while they take antibiotics.

  10. Anonymous 3 months ago

    Hello Dr. Nemechek, my 4.5 year old daughter started your protocol 2 weeks ago but she was just prescribed amoxicillin for a urinary tract infection. While she is on antibiotics would you advise continuing with the inulin? Also, I know probiotics are not to be given while on your protocol, is that still true if one is taking antibiotics? Thank you.

  11. Author
    Patrick Nemechek, D.O. 4 months ago

    I have a variety of youTube video posted. One discussed the difference between the use of one over the other.

  12. Shilpa 4 months ago

    Dr. Nemechek Thanks for your prompt response! Truly appreciate it. I plan to implement your protocol after completing the book shortly. For a 13 yr old, should i start with Inulin first or Rifaximin? Have heard such encouraging stories from people that hoping and praying this will solve the challenges we have been facing!

  13. Author
    Patrick Nemechek, D.O. 4 months ago

    The majority of what is often referred to as “leaky gut from Candida” is actually a process referred to in the medical sciences as “bacterial translocation”.

    The reason is that we now understand that most of the intestinal issues observed in patients (and in response to the variety of medicines and homeopathic remedies) is actually from bacteria not yeast, fungi or Candida.

    So my protocol will often help with the symptoms you are seeing because they are from bacteria and not Candida (yeast).

  14. Shilpa 4 months ago

    Dr. Nemechek. Thanks for educating us on SIBO and your protocol that can help those who suffer. I have started reading your book to learn more. One question – Does the protocol work in case of Candida? I have a 13 yr old who has Candida symptoms and also ADD symptoms. Is Inulin /Rifaximin proffered in case of Candida? Thanks for your advice.

  15. Author
    Patrick Nemechek, D.O. 4 months ago

    You’re welcome.

  16. Sandhya 4 months ago

    Dr Nemechek, thank you so much for your response.

  17. Author
    Patrick Nemechek, D.O. 4 months ago

    I would not think so.

  18. Author
    Patrick Nemechek, D.O. 4 months ago

    I am unfamiliar with the fungal issue you are describing.

  19. Author
    Patrick Nemechek, D.O. 4 months ago

    Atopic dermatitis can behave similarly to what you describe, and the fluctuations in skin color are from fluctuations in inflammation.

    The level of inflammation in children is reduced overtime with my protocol and will predictably improve the skin as well.

  20. Sandhya 4 months ago

    Hi Dr. Nemechek. I’m among a group of parents in India who are following your protocol and are seeing lots of gains. I had a question regarding atopic dermatitis. My son is 8 years old and on inulin and the oils. Would he need Rifaximin for his atopic dermatitis ?

  21. Anonymous 4 months ago

    My 8 year old son was diagnosed with mild autism when he was 2.5 years old. Ever since he was 2 years old i have noticed darkening on the inside of his joints which would worsen when he was sick. A couple of dermatologists said it was atopic dermatitis but I’m not sure. Probiotics were the only thing which cleared up the darkening and also his easy excitability. He had stopped flapping and making sounds while on probiotics. Since being on the protocol i have witnessed awakening in terms of more awareness, more questions, and better understanding. Unfortunately the darkening on the inside of his joints and his easy excitability is back. He is on a diet but unfortunately he ate some chocolate at school and his above symptoms have worsened. My question is, what causes the skin darkening and will it be cured with the protocol ?

  22. Olivia 4 months ago

    Dr. Nemechek,
    I have been giving my daughter (age 6) probiotics, fish oil and EVOO for the past 4 months to control a fungal infection. She is not developmentally delayed. My son (age 8) is on the protocol. My daughter has an intestinal fungal infection. Her symptoms are stomach upset and yellowed teeth and her blood work shows the cause. The histamine-degrading probiotics have helped her. I recently switched her to inulin and her teeth are again yellowing. Is this protocol not for those with only fungal infections or do I need to keep upping the inulin to see the affect in her?

  23. Author
    Patrick Nemechek, D.O. 5 months ago

    Inulin would increase the concentration of Bifidobacteria.

  24. Jennifer Testerman 5 months ago

    Will inulin still be effective in a system with very little Bifidobacteria? I am a non-secretor, FUT2 +/+, and suffer from Collagenous Colitis, SIBO, and several of the other symptoms I have noted in your videos/blog posts. I am so grateful to hear you speak against probiotics— they made me very ill.

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