Probiotics: Helpful and Harmful

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 ‚Äúhealthy‚ÄĚ blend of ‚Äúnatural bacteria‚ÄĚ that will restore or replenish your intestinal flora. These products are vastly overstating anyone‚Äôs 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 (‚ÄúAutonomics‚ÄĚ).
The Autonomics are the brain‚Äôs master control mechanism for the organs, hormones, and immune system. The Parasympathetic branch of the Autonomics control our ‚Äúrest and digest‚ÄĚ 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.
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July 4, 2019 4:50 am

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”?

May 12, 2019 10:56 am

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… Read more »

April 27, 2019 6:20 pm

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… Read more »

April 12, 2019 3:04 am

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… Read more »

April 14, 2019 6:27 pm

Thank you!

Swarna Vemuri
Swarna Vemuri
April 10, 2019 1:58 pm

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

N. Panayotova
N. Panayotova
March 11, 2019 12:54 pm

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!

February 3, 2019 5:08 pm

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… Read more »

January 25, 2019 2:50 am

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 ‚Äúclear‚ÄĚ 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?… Read more »

Beth Oehlhof
Beth Oehlhof
January 1, 2019 3:31 am

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!

December 30, 2018 5:49 pm

Can we give homeopathy medicine with ur protocol

December 15, 2018 9:04 am

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

Brittany Lopez
Brittany Lopez
November 23, 2018 5:33 am

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?

Abu D
Abu D
November 3, 2018 9:07 pm

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.


October 16, 2018 7:50 am

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… Read more »

September 7, 2018 6:13 pm

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?

May 24, 2018 3:48 pm


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.

May 18, 2018 5:27 am

Thanks for your response Dr.

May 16, 2018 12:30 am

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.

May 16, 2018 12:08 am

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… Read more »

April 26, 2018 4:51 am

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.

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