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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 I was granted a patent (Methods of Reversing Autonomic Nervous System Damage, Paten No. 10,335,396).
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. Kelly 1 year ago

    What about “food-based” probiotics? In otherwords: Raw SauerKraut or the “gut shots” that are basically fermented kimchi juice? Can we keep eating these as long as we’re not taking a “probiotic pill”?

    • Author
      Patrick Nemechek, D.O. 1 year ago

      Traditionally prepared fermented foods are OK.

      The concept of a gut shot sounds like an attempt to make a natural medicine.

  2. Heather 1 year ago

    Dr. Nemechek, thank you for your important and timely book. My 10 yr.-old son was diagnosed with ADHD and an anxiety disorder and has had an IEP in place since kindergarten. He has been seeing a functional neurologist since his diagnosis, but your protocol seems to be the missing piece in his healing. I have given him insulin for the last six months (up to 1 tsp twice a day), but he is still not having a daily bowel movement. He usually has one every four or five days. I do give him a magnesium supplement every night, and he does not eat gluten , or really many grains other than rice and quinoa. His overall health has improved immensely, but unfortunately he just came down with strep throat and is now on amoxicillin. Are these antibiotics going to be a step backwards for us? And how do I help him further with his bowel issues? Thank you.

    • Author
      Patrick Nemechek, D.O. 1 year ago

      Don’t overfocus on the bowel issues, they will ultimately improve with further improvement of autonomic function.

  3. Valerie 1 year ago

    my 9yo with ADHD, delays, and learning disabilities also has severe chronic idiopathic constipation. He is on lactulose 40 ml/BID, which is the upper limit the GI doctor will dose him (he’s ~85#). Now he’s being sent to a motility specialist (again) because that dose doesn’t give the stooling pattern the GI wants . I don’t know what to do about lactulose; I know it’s also a prebiotic, but idk if it’s weaker/stronger then inulin.. I cannot take him off lactulose without a replacement without risking additional outpatient procedures to clear blockages, and my son cannot (Miralax, mag products at high doses don’t work and some triggered reflux) or will not (MoM, etc) take the other constipation remedies mentioned in your book. He will take ex-lax with no problem. Would that be harmful to replace lactulose?
    I started the protocol 2 months ago and just continued his lactulose dose with the NP supplements, thinking it would be better than not doing it at all. The GI dr doesn’t know what to advise about lactulose and the NP. Any thoughts on his lactulose with inulin? He’s taking 2 gummies/day with his 40ml BID lactulose plus other NP supplements as recommended.

    • Author
      Patrick Nemechek, D.O. 1 year ago

      I’ve seen several kids do worse after lactulose was used for constipation.

      Inulin is more predictable and will support recovery.

  4. Julie 1 year ago

    Hello! I just finished your book and will be starting my almost 5 year old son on the protocol. He is not officially diagnosed, but the neurologist believes it is ADHD. I stopped probiotics a little over a week ago, but am waiting for the inulin to arrive before starting the protocol. Since stopping the probiotic, my son has been more aggressive and bounces between hyper, angry, and sad dozens of times throughout the day. He’s having meltdowns the way he did when he was younger (coincidentally, like the meltdowns before introducing probiotics). Could these behaviors be due to stopping the probiotics, which masked these symptoms the whole time? Thank you for giving so many people hope and results. Praying this works for my little guy!

    • Author
      Patrick Nemechek, D.O. 1 year ago

      Its often hard to link this change in behavior with this change in regimen especially when gut bacteria are involved.

      There is a chance that the probiotics increased his propionic acid levels and you’re experiencing an awakening by stopping them.

    • Julie 1 year ago

      Thank you!

  5. Swarna Vemuri 1 year ago

    Hello Dr. Nemechek,
    I have a 7 year old (turning in May) boy who has speech, behavioral issues. (on spectrum)
    He has been on 1/2 capsule in water of the probiotics in rotation (Bifidobacterium, Bulgaricum and Superdophilus stored in refrigerator) prescribed by his Ayurvedic Practitioner. It has been only two months on it but he had two rounds streps and antibiotics (with diarrhea). If I start him on Inulin should I stop these probiotics?
    I only ask because of the particular strains am not sure they prebiotics or probiotics.
    Thanks in Advance

    • Author
      Patrick Nemechek, D.O. 1 year ago

      If you are asking me about probiotics you haven’t read the book nor understand the principles behind my approach.

  6. N. Panayotova 1 year ago

    Hello, dr Nemechek! My daughter has often diarrhea with undigested food in stool. Her pediatrician recommended Enterol, which is traditional remedy against Clostridium difficile in my country. It include Saccharomyces boulardii. Also we often use brewer’s yeast (Saccharomyces cerevisiae) for this purpose. Should we avoid them? Thank you in advance!

    • Author
      Patrick Nemechek, D.O. 1 year ago

      I generally recommend the avoidance of all probiotics while using my protocol.

      The inulin I recommend often has the same beneficial effect on diarrhea.

  7. Jenn 2 years ago

    Dear Dr Nemechek,
    Thank you for your protocol and helping so many families! Before starting the protocol, I was giving my 4 y/o probiotics as this is what many practitioners recommend. Every time I would give her a probiotic (tried 3 formulations) or even a multivitamin, she would become very dysregulated and have a worsening of her symptoms. I don’t fully understand why this happens, but it’s not a coincidence. I very much agree with your comments on probiotics. We now are following just your protocol and I have clearly seen gains in my daughter’s regulation and even expanded social play. Thank you!

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Thank you for sharing your real world experience.

      Probiotics may have a place in the future but at present, the varieties of species and strains sold to the general public in no way represent some of the few positive findings coming out in the literature.

      We frequently have parents sharing horror stories about how their child was injured with probiotics.

  8. Jessica 2 years ago

    Hi Dr Nemechek . I finished your book and will be starting my 2.5 year old, diagnosed with ASD, on your protocol. She has been on a probiotic (HMF Neuro) since November per our Neuroptahic Doctor as well as fish oil. I understand that your protocol states NO Probiotic so I will be ending that ASAP. Should I wait a couple of weeks or any time frame to “clear” her system of the probiotic before she starts the Inulin? Also, should we avoid any and all snack foods that list soybean oil, sunflower oil etc as well as all yogurts? I guess I’m asking do we simply need to reduce the Omega 6 intake or completely remove the Omega 6 intake from the diet? Only asking bc she’s picky and I’ll need to find some new snack foods! I want to do this right! Thank you in advance. This is the first book/diet that I feel confident about based on your expertise and explanations. Wish us luck!

    • Author
      Patrick Nemechek, D.O. 2 years ago

      You need no more than a week to stop one protocol and start mine.

  9. Beth Oehlhof 2 years ago

    I have your book and am going to start the protocol. My doctor won’t prescribe the Rifaximin. Is there any other way to balance the bacteria? Can I still benefit from high doses of fish oil now until I find a Dr. who will prescribe the Rifaximin? I want to do the protocol with my 10 year old and 15 year old. I’ll do the insulin for the younger one. Same question, will my 15 year old benefit from the fish oil without the prescription? Thanks!

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Many c hildren in the teens will still benefit from inulin its just that the older they get the more likely the inulin will not be effective and the rifaximin is required.

  10. Anonymous 2 years ago

    Can we give homeopathy medicine with ur protocol

    • Author
      Patrick Nemechek, D.O. 2 years ago

      I do not recommend it.

  11. Charlene 2 years ago

    Hello Dr. N, thank you for giving us hope and results! My daughter is 5 years old mild ASD and we have just started your protocol. She takes Montelukast granules (anti histamines) for respiratory allergies, should I stop giving her the granules? Thank you in advance

    • Author
      Patrick Nemechek, D.O. 2 years ago

      I do not believe any prescription medications prescribed by your physician need to be stopped in order to start the protocol.

  12. Brittany Lopez 2 years ago

    Your information has been very interesting to me. My son is currently battling a yeast overgrowth that got much worse after a week of antibiotics. How would the inulin interact or affect his yeast issues?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Inulin does not interact with yeast.

  13. Abu D 2 years ago

    Hi Dr,

    Your protocol seems to have worked with many people, particularly parents with delayed children. I have a child with SPD and I was wondering if your protocol would work for him. My particular question is about a colonizing probiotic, Reuteri which I was planning on giving him before putting him on your protocol. Is Reuteri harmful or cooperative with your pre-biotic protocol.


    • Author
      Patrick Nemechek, D.O. 2 years ago

      I strongly advise against the use of probiotics in all my patients.

      Don’t think simplely throwing some bacteria down your child’s throat will help improve their gut balance.

      It is far more complicated than that.

    • Author
      Patrick Nemechek, D.O. 2 years ago

      I strongly advise against the use of probiotics in all my patients.

      Don’t think simply throwing some bacteria down your child’s throat will help improve their gut balance.

      It is far more complicated than that.

  14. Anonymous 2 years ago

    My 4 year old son is following the protocol and I must say that things are improving slowly. However he is still such a picky eater. Last year , when we weren’t following the protocol I tried the manuca honey. I gave him a tsp per day and after two days we started consuming the manuca , he started eating everything and being hungry all the time. However this only lasted a month. Lately when I researched on the benefits of Manuca Honey I found that it helps with SIBO. What is your opinion regarding the above? Can we give Manuca Honey with the protocol? Thanks in advance and thanks for everything

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Frequent hunger is not normal nor would I take that as a positive thing.

  15. Jim 2 years ago

    Dr N thanks for all your effort and for giving us hope. I have one question, my boy is on protocol, but he has explossive diarrhea, normally in my family, when someone had diarrhea, we took bacillus claussei, it’s ok for the protocol?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      No do not take the probiotic.

      If protocol is causing diarrhea, a common issue is giving to much oil at one time.

      Try separating the amount of oils given at any one time.

  16. Zahra 2 years 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.

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Traditionally fermented foods are safe to consume with my protocol.

  17. Shilpa 2 years ago

    Thanks for your response Dr.

  18. Shilpa 2 years 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.

    • Author
      Patrick Nemechek, D.O. 2 years 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.

  19. Anonymous 2 years 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

    • Author
      Patrick Nemechek, D.O. 2 years 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.

  20. Anonymous 2 years 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.

  21. Anonymous 2 years 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.

    • Author
      Patrick Nemechek, D.O. 2 years ago

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

  22. Shilpa 2 years 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!

    • Author
      Patrick Nemechek, D.O. 2 years ago

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

  23. Shilpa 2 years 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.

    • Author
      Patrick Nemechek, D.O. 2 years 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).

  24. Sandhya 2 years ago

    Dr Nemechek, thank you so much for your response.

    • Author
      Patrick Nemechek, D.O. 2 years ago

      You’re welcome.

  25. Sandhya 2 years 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 ?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      I would not think so.

  26. Anonymous 2 years 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 ?

    • Author
      Patrick Nemechek, D.O. 2 years 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.

  27. Olivia 2 years 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?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      I am unfamiliar with the fungal issue you are describing.

  28. Jennifer Testerman 2 years 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.

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Inulin would increase the concentration of Bifidobacteria.

  29. Ellen 3 years ago

    How do you feel about Houston Enzymes that digest in the stomach not intestines. And I also have to question on the oils. Every time my son takes oil of any kind he burps and regurgitates. ..any suggestions and should I just give it to him even though he does this. Thank you for your help!

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Don’t recommend any probiotics or digestives of any kind.

  30. Anonymous 3 years ago

    Dear Dr Nemechek, I read your book and thought it was amazing! My son just turned 16 and is Apraxic and Autistic non-verbal. We do drink 5 oz Keifer a day which seems to make his chronic constipation worse. I take the Kiefer and it makes me feel so good I am thinking he should take it to… Any thoughts on this? Milk also stuffs him up. Could this be the SIBO? I also had a question about behaviors because my son is so sensitive. Every time I do any kind of different protocol I end up stopping because of off the wall behavior. I’m not sure if it’s teeth coming in or headaches but he gets what appears to be really bad pains and he grabs his teeth and tries to bend his hands and cannot calm down until I give him Tylenol and calm magnesium. What kind of negative reactions should I expect and should I start him out with the kids Dose first? Just an afterthought… I have been giving him bananas and flax oil and see some changes. Thank you for any help and thank you helping these kids!

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Reading my protocol will answer most of the questions but more importantly put them into perspective of the process you child will travel through during the recovery process.

  31. Heather 3 years ago

    Dr. Nemechek, I have a confirmed yeast allergy (from IgG and igE) so haven’t been taking any kindof probiotic/fermented food. What should I do to get the good bacterias in me? Thanks so much for any help.

    • Author
      Patrick Nemechek, D.O. 3 years ago

      There is no way to rebuild our missing gut bacteria at present other than FMT in those with very low diversity counts.

  32. Monica baker 3 years ago

    Hello Dr Nemchek. First of all thank you so much for making this information available and taking the time to respond to everyone. It’s rare to see a doctor that takes the time to think outside the box and has such a big heart to truly help.people without concern for his bottom line. We have spent thousands of dollars we didn’t have in the last few years on doctors that were not able to help is much. I will be buying your book tonight and I have started the boys on the inulin 1/4 tsp today. They have been on Pro EPA fish oil for the last week or so and I will be ordering your recommended brand and the olive oil. A quick overview, my 4 yo has speech apraxia I believe might have been caused by infant torticollis and ecephaloplagia (I think it was called, flat head). He had a lot of other issues, was unable to digest food, and emotional control problems, but they have been resolved, except for the apraxia. My 7 yo has developed ADHD in the last year. He has global hypotonia and global nutritional deficiencies. We were gluten free for a year and he was doing better alsthougb still not absorbing nutrients from food properly. Then we went heavy einkorn wheat for about a year and that’s when ADHD symptoms developed. His stools are very mushy and poorly digested. The youngest often has pale stools. Both their OAT tests show markers for liver or kidney problems. I don’t know if they have SIBO but The stop analysis test showed mild dysbiosis in the 4 yo and severe dysbiosis In the 7 yo. They are each missing one whole class of good bacteria, one has no lactobacillus, the other no bifidobacterium (7 yo). Would such findings warrant probiotic use? We are doing raw milk yogur and kefir and homemade sauerkraut. I have removed all gluten and most of the things they are daily that they could have developed a sensitivity to, and my 7’a adhd has improved greatly. He still has some hyperactivity and impulse control issues but his concentration and focus are incredible now. It seems to me like they could benefit from the vagal stimulation protocol. What are your recommendations? We live in SC. Are there any other practitioners that can do this closer to us? Would it be worth to travel to see you, and if so how long would we have to be there and how much would it cost? Thank you SO much for your help! I have been
    recommending your protocol to all the desperate mommies in the natural ADHD healing group I’m in

    • Author
      Patrick Nemechek, D.O. 3 years ago

      If you are asking about using probiotics or my thoughts on vagus stimulation, you need to take a serious look at the protocol.

      There is an great deal you need to understand to take your child through this process to it’s maximum potential.

  33. Jesica La Rue 3 years ago

    Aloha. We purchased your book and started the protocol a few ago for our 8 yr old, TBI , Autism and Febrile seizures . Dosage for Inulin was 1/4 tsp but we reduced to 1/8 tsp due to him breaking out in hives. The hives are red and intense on his ears, face and neck. Is this an allergic reaction or a part of the process?? Thank you for your time

    • Author
      Patrick Nemechek, D.O. 3 years ago

      No hives from inulin would be a very rare reaction since inulin is contained in a wide variety of plants commonly eaten.

      Look for something else such as a probiotic in another product or if the brand is not one of the preferred brands.

  34. Tiffany 3 years ago

    We have recently started your protocol and have seen great gains.
    I am curious, we have a history of CDiff and HPylori. Recently someone close to us was diagnosed with HPylori (different source). As a preventative measure I’d like to stick my child on Saccharomyces Boulardii as we spend a deal of time with this person now however do not want to cause other issues.

    Please advise.

    • Author
      Patrick Nemechek, D.O. 3 years ago

      As I’ve said many times, adding this probiotic will greatly increase your chances of relapse and will not lessen the likelihood of contracting H. pylori, there is no evidence this will help

  35. Jade Perkins 3 years ago

    Hi, I want to put my children and myself on your Protocol but my naturopath states that the inulin will worsen our strep issues. Is she right?

    Thank you.

    • Author
      Patrick Nemechek, D.O. 3 years ago

      I believe your naturopath is mistaken. Studies have shown prebiotics decrease susceptibility to strept infections.

  36. Debbie 3 years ago

    Dr. I fear my daughter may have autonomic issues due to lyme and thus may have PANDAS. Then a couple of days later I discovered she has an inguinal hernia and read this will require surgery. I am fearful of the danger of anesthesia. Do u have any advice or concerns I should address if she does require surgery? Thank u so much in advance.

    • Author
      Patrick Nemechek, D.O. 3 years ago

      If you are on my protocol, I discuss the issue of relapse in 2 separate chapters in my book.

      I suggest you read those over, and they may give you some insight into your daughter’s situation.

  37. Shannon Petrovic 3 years ago

    Dr. Nemechek,
    I have a 14 y/o girl dx’D with POTS two years ago. Hers started overnight with extreme dizziness. No gut issues. Those symptoms, upset stomach, nausea, stomach pain, are fairly recent (last 4 months or so). I’ve only just been introduced to your protocol and I’m trying to cram it all in. Is it possible that this has been SIBO all along, but gastro issues wouldn’t present until much later? She did start a probiotic in January and I finally took her off in September along with many other supplements b/c nothing seemed to be helping and she was tired of swallowing pills. It hadn’t occurred to me that the probiotic could have hurt her until running into information about this protocol. My question, wouldn’t she have had gut trouble all along if SIBO was the cause of her orthostatic intolerance /postural HR increase and will the protocol just resolve SIBO if SIBO was just a recent development (is it only a recent development or is SIBO something that takes years to feel the symptoms)? If, in fact, it isn’t SIBO, will the protocol be harmful to try?

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Some studies indicate that about 20% of adults with SIBO have no obvious intestinal symptoms (diarrhea, constipation, GERD or cramping). I have seen data on kids but I suspect its about the same.

      I’ve successfully treated many kids and adults with POTS but can only do so if I address SIBO with my protocol.

      BTW, We’ve just posted a new article on POTS.

  38. Jodie 3 years ago

    Dr Nemechek,

    What is the process of probiotics causing arthritic symptoms? You’re the first doctor I’ve seen to acknowledge this. I’ve tried a lot of different probiotic brands and each I’ve had to stop due to severe neck, upper back and rib/sternum pain. Some of the pain even still lingers now. My doctors have no explanation for it and think it can’t possibly be from probiotics.



    • Author
      Patrick Nemechek, D.O. 3 years ago


      Our body was designed through evolution to protect us from foreign and potentially dangerous organisms such as bacteria, fungi and parasites. Our skin and immune system are on constant guard for invaders and respond with a vigorous immune response should our defenses become breached. The immune system reaction to these organism releases pro-inflammatory cytokines that can add to our fatigue, joint and muscle pain, diarrhea, brain fog and fever.

      Studies indicate a large proportion of the population has dysbiosis of the intestinal track with many having bacterial overgrowth (SIBO) in particular. Those with SIBO have a 10,000-100,000-fold increase in the number of bacteria within the small intestine. This massive increase of intestinal bacteria breaches the protective barrier and results in bacterial translocation otherwise known as leaky gut.

      Leaky gut allows fragments of proteins, fatty molecules, sugars, viruses, protozoans and bacteria to seep into the tissue immediately surrounding the small intestine. This area around the small intestine is the home of 80% of all of our white blood cells (80% of your entire immune system). The leakage is similar to tossing kindling right into the immunological fire.

      To make matters worse, doctors recommend patients swallow additional foreign bacteria. These doctors pretend like they know what these bacteria will and will not do when in fact the most experienced researchers in this field cannot accurately predict the behavior of bacterial strains within the human body. It is well known that bacteria that behave in a seemingly harmless manner in a petri dish or a laboratory mouse can act in a very harmful manner inside the human body, especially one with impaired defenses from bacterial overgrowth.

      Probiotics are being sold with misleading labeling suggesting that a particular brand contains the precise species of bacteria for this or that condition when in fact no one really knows. Its misleading because the field of experts in intestinal bacteriology have no idea which species are needed. It’s mainly about recurrent sales.

      Our culture is confusing to me. People are so paranoid of simple germs they are constantly wiping their hands with antiseptic gels or avoiding someone with a sneeze or a runny nose yet every morning the same person may purposefully swallow capsules full of “germs” simple because someone suggested it might be useful.

      Stay away from probiotics. I have never found a situation where they are helpful, and daily hear of stories such as yours where children or adults are harmed by them.

  39. Anne Marie 3 years ago

    My son is 11 and carries and Autism diagnosis since age 3. He was also diagnosed with Hereditary Fructose Intolerance at age 9. It is a rare genetic disorder affecting 1:20,000. He can’t eat any foods containing fructose, sucrose or sorbitol. Hence, most plants. Does inulin contain fructose? if so, what other options are there for acceptable prebiotic dietary fiber for him?
    thank you

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Inulin is common in many foods (high concentrations in onions and garlic for instance) and does not contain the sugars you mention.

      I would ask you geneticist if use of inulin is approved.

  40. Anonymous 3 years ago

    Hi Dr Nemechek
    Please could you tell me your thoughts on using KIB500 in place of antibiotics for a 12 year old with ASD who is FODMAP sensitive (causes a lot of burping) and burps a lot with carbohydrates also. I have suspected SIBO for a long time and it was made worse by 9 month PPI treatment to heal an ulcer.

    • Author
      Patrick Nemechek, D.O. 3 years ago

      I am unfamiliar with KIB500.

  41. Ruth 3 years ago

    Dr. Nemecheck,

    Can your protocol be used in a 6 year old child with symptoms of heartburn, and gassy. Non Autistic child but in the past had speech delay and some sensory issues. He was doing great and took antibiotics due to ear infection and shortly after that he showed symptoms of heartburn and loss of focus. ( maybe ADHD?)

    Thank you

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Yes, my protocol is effective for non-autistic children who may be demonstrated only developmental delay, signs of early or developing ADD/ADHD,, headaches, intestinal issues (heartburn, constipation, abdominal pain), and emotional issues (anxiety, aggression or depression).

      This wide variety of symptoms are all due to 1 or 2 issues, impaired neuronal pruning or impaired brain injury repair because of underlying inflammation.

  42. Anonymous 3 years ago

    Dr. Nemecheck,
    Are digestive enzyme products helpful or harmful with your protocol?
    My 8 year old son has autism and has been on MB12 shots daily and Kirkman EnZym-Complete/DPP-IV 11 w/Isogest for the past 16 months.
    Many thanks,

  43. Sangeeta jain. 3 years ago

    my son eatsca lot.
    frequent urination

  44. Kelsey Emuss 3 years ago

    Dr Nemechek,
    Could a Chiropractor understand (be enlisted) to work on the Vagal nerve stimulation?
    I am binge reading everything on your blog so I may pop up in a few spots 🙂

    • Author
      Patrick Nemechek, D.O. 3 years ago

      I think so. We are preparing material to help other health professionals properly utilize The Nemechek Protocol.

    • Alisa 2 years ago

      Hello Dr. Nemechek,
      I was going to ask the same about acupuncture and acupressure: could either be useful for those of us unable obtain the electronic VNS?

    • Author
      Patrick Nemechek, D.O. 2 years ago

      Electro acupuncture can be a form VNS as long as the vagus nerve is stimulated and the electricity is dosed properly

    • Alisa 2 years ago

      Learn something new everyday… Thank you!

  45. Anonymous 3 years ago

    With your Autism protocol Dr. Nemechek, what are your thoughts on BRAVO yogurt?

    • Author
      Patrick Nemechek, D.O. 3 years ago

      BRAVO is the kind of product I worry about. It is a probiotic supplement in the form of a yogurt, not a yogurt produced by traditional methods.

  46. Kara 3 years ago

    What are you thoughts on probiotic rich foods (i.e. sauerkraut, etc.)? Would those types of foods not be good to use on this protocol?

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Natural, historically made foods such as kefir, kimchi and sauerkraut are fine.

  47. lilia 3 years ago

    i just want to tell you about the biofilm; i testify to have seen the biofilm in the fecal matiere of my child, it ‘s like gelatine candies ; this biofilm hide developpement of microorganismes and also parasites and i have found even Tenia and oxyres
    the health of the child approuve when there is an evacuation of biofilm
    and the big approuvement was when there is evacuation in matiere fecal of like blach worm (it looks like!!!!!)
    do you have any information about that !!
    for the diet; for the time i did not breaks the diet ;how can i be sure that there is not now a gluten and caseino intolerance

    • Author
      Patrick Nemechek, D.O. 3 years ago

      I too trained as a microbiologist and admit there is a great amount to be learned about biofilms, microbiota and there impact in autism.

      But as a clinician, I am a pragmatist. My protocol has a significant impact in a large proportion of autistic children, and is simple, inexpensive and does not require the permission of the healthcare system to use.

      Most food intolerance resolves with use of inulin, and I encourage the parents to start at a low dose, slowly increase and only change 1 variable as a time as they move through the process of instituting the protocol, eliminating less effective supplements and expanding the diet.

      Good luck and thank you for your comments.

  48. lilia 3 years ago

    thank you for the answer
    i’m an algerian microbiologist and my son was diagnosticated as autist in age of 2.5 years(sever degree) and after my research i made a protocol using only a diet (gluten and casein and sugar free) with a large consommation of olive oil extra virgin and with garlic (prebiotic) and curcuma and also a large consommation af green vegetable
    for my son after the begining of the therapy there was a priod of diarhéé and when i do some simple bacteriologic examination i found a big profileration of candida!
    now my chil is 6 years old he is total recovery he speaks arabic and also little french he practice sport and he is very social

    • Author
      Patrick Nemechek, D.O. 3 years ago

      That’s great to hear. Congratulations to you and your son.

  49. lilia 3 years ago

    what about candida spp developement and also formation of mycelium , it can cause permeability syndrome (caseiomorphine and glutenomorphin)

    • Author
      Patrick Nemechek, D.O. 3 years ago

      As I’ve said previously, more recent and precise studies are demonstrating that there seems to be no Candida (yeast) overgrowth in autistic children compared to non-austic kids.

  50. Eric B. 3 years ago

    Will inulin help this situation.
    Expected/Beneficial flora
    4+ Bacteroides fragilis group
    NG Escherichia coli
    4+ Bifidobacterium spp.
    4+ Lactobacillus spp.
    3+ Enterococcus spp.
    1+ Clostridium spp.

    Commensal (Imbalanced) flora
    4+ Enterobacter cloacae complex,isolate 2
    4+ Gamma hemolytic strep
    3+ Hemolytic Escherichia coli
    3+ Lactococcus lactis

    Dysbiotic flora
    3+ Enterobacter cloacae complex

    • Author
      Patrick Nemechek, D.O. 3 years ago

      Inulin helps rebalance the intestinal flora in the small intestine. This is where the excess production of propionic acid due to bacterial overgrowth occurs

      Test results such as this represent the mixture of flora in the distal colon so I can not say if this result would change with the use of inulin.

  51. Anonymous 3 years ago

    Hello – how much Inulin for a 60lb child? The powdered inulin?

    • Author
      Patrick Nemechek, D.O. 3 years ago

      I recommend reading my Autism article as it discussing inulin in more detail.

  52. Mónica Flores 3 years ago

    Hi doctor, What dosis you use for rifaximin , for a boy with autism and 60 lb Weight.



    • Author
      Patrick Nemechek, D.O. 3 years ago

      Specific doses of medications are best determined by your local physician

  53. Tim 3 years ago

    Thanks for clarifying.

    Less of a comment, more of a request – I’d be curious to hear your thoughts and wisdom in a blog post on food sensitivities and food sensitivity testing (such as the ones offered by Cyrex labs).

    • Author
      Patrick Nemechek, D.O. 3 years ago


      Good question.
      With the exception of severe allergic reactions that are life threatening (e.g., peanuts, walnuts, etc), most “food sensitivities” go away after reversal of bacterial overgrowth, especially after using Rifaximin (Xifaxan).

      While some individuals clearly are lactose intolerant because they’ve lost the ability to digest milk sugar (lactose), a significant portion of “milk intolerance” also seems to be from overgrowth and likewise improves with rifaximin.

      Inulin can greatly improve a wide variety of food intolerances but not as consistently or completely as Rifaximin.

      Gluten intolerance (not Celiac Disease) most likely is from an abnormal inflammatory reaction to gluten within the tissues surrounding the small intestine. This seems to be related to an impaired vagus inflammatory reflex because it quickly resolve within a few weeks of vagus stimulation. I have more on gluten in my post on the topic.

      Dr. N

  54. Tim 3 years ago

    This is a really interesting blog post.

    Just curious – what is the reason for inulin only feeding the right kind of bacteria? Shouldn’t it feed bacteria indiscriminately? (when you mention “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”)

    • Author
      Patrick Nemechek, D.O. 3 years ago

      The bacterial familes that predominantly colonize the colon vs the small intestine are very diffeerent in many aspects. One is their capability of digesting different fibers.

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