There is growing scientific evidence that an imbalance of intestinal bacteria called SIBO (Small Intestinal Bacterial Overgrowth) along with excessive inflammation within the brain are responsible for the features associated with Autism as well as ADD/ADHD, mood disorders, and developmental delay in children.

Bacterial overgrowth occurs when large numbers of bacterial that predominantly live in the colon migrate upwards, and increase the number of bacteria within the small intestine by 10,000 to 100,000-fold. This added bacterial load in the small intestine has two consequences that contribute to Autism.

First, the bacteria often tend to be of a clostridium species which can produce propionic acid in massive amounts. Propionic acid is a short chain fatty acid that is normally produced in small amounts within the intestine but the higher concentrations are being linked to some of the behavioral aspects of autism.

In animal studies, high propionic acid leads to the development of antisocial behaviors, increased sensitivity to sound, light, and touch, as well as gait abnormalities. In human studies, children with autism have very high concentrations of propionic acid within their tissues.

Secondly, the increased concentration of bacteria within the small intestine causes leakage of pieces of bacteria into the large concentration of immune cells that surround the small intestine and triggers the inflammatory reaction referred to as leaky gut.

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Leaky gut causes an increase in peripheral pro-inflammatory cytokine levels and allows for the inflammatory priming of a specialized form of white blood cell known as microglia within the central nervous system.

The combined production of inflammatory cytokines and activated microglia are primarily responsible for the developmental issues, seizures, sensory issues, mood and attention disorders commonly associated with autism.

A child is born with approximately 100 billion neurons and over the ensuing 18 years, needs to prune these neurons down to 50 billion in a process referred to a synaptic pruning. Excess inflammation from leaky gut, microglia priming and omega 3:6 imbalances prevents otherwise healthy microglia from pruning fast enough, and results in developmental delay.

The priming effect from the bacterial overgrowth causes many microglia to shift into the M1-phenotype, and results in the brain being less able to fully repair itself from commonplace physical (falls and bumps to the head), emotional (fear, abuse, neglect) and inflammatory (surgery, infections, vaccines) brain injuries.

A small residual amount of damage will remain after each injury, and each new injury leaves residual damage upon the prior injury in a process referred to as cumulative brain injury. The abnormal neurological functioning from cumulative brain injury can occur slowly over time and or rapidly depending on the intensity of the brain injury. Damage to different portions of the brain will result in different outward symptoms such as ADHD, chronic anxiety or gait abnormalities.

The elevated inflammatory cytokines are also able to turn on certain genes that are linked with autism and may be responsible for certain features or more severe forms of Autism.

And finally, the excessive inflammatory environment in the brain reduces the seizure threshold and make seizures more likely to occur. The drop in the seizure threshold from inflammation is seen when young children without Autism develop febrile seizures with the fever and inflammatory reaction that occurs with simple upper respiratory viral infections or middle ear infections.

My understanding of the bacterial and inflammatory features in Autism have opened the door for me to provide groundbreaking treatment. The bacterial overgrowth increases propionic acid levels that cause kid’s brains to function differently, almost like a chemical impairment or slight intoxication, and at the same time the inflammation prevents normal neuron pruning and development as well as inhibits normal brain injury repair.

My approach to reverse the key components in Autism is straightforward. To provide the brain with a healthy, non-inflammatory environment to function more normally and to allow microglia to correctly prune and repair the brain, we need to reverse bacterial overgrowth and suppress the production of inflammation cytokines that are produced from a variety of sources.

By applying a logical understanding of science, I have focused application of The Nemechek Protocol™ medical consultation and treatment services on Autism, and have reversed the key features of Autism in many children.

The Nemechek Protocol for Autism uses a prebiotic fiber called inulin to reverse and control bacterial overgrowth, and high doses of omega-3 fatty acids to normalize microglial function and normalize the inflammatory state within the brain.

Cooking with domestic extra virgin olive oil also helps reduce brain inflammation resulting from linoleic acid, an omega-6 fatty acid found in in high concentration in cooking oils and processed foods. Inulin is a natural fiber found in onions, garlic, artichokes, agave, chicory root and many other plants.

When buying powdered inulin, I avoid ones that also contain probiotics or digestive enzymes as these ingredients can makes some aspects of Autism worse. (See my post on probiotics for more info on this topic.)

I find that 2-4 inulin gummies or 1/2 to 1 teaspoon of powdered inulin daily can reverse bacterial overgrowth enough to allow an autistic child (2-8 years of age) to become much more aware and interactive with their environment within a few weeks. And depending on the amount of underlying developmental delay, children will often start speaking within a few weeks to a few months.

Remember this is a simple plant fiber found in foods we eat every day, and is safe in children. If children get a little gassy or bloated, I recommend cutting back on the dose. Inulin is heat-tolerant and can be mixed or sprinkled over any form of liquid or food.

To help reduce the inflammation within the brain and normalize the behavior of microglia, my autistic patients are placed on omega-3 fatty acids (EPA and DHA) from fish. A recommended starting dose for small childrens is about 600 mg of omega-3 (the total of EPA plus DHA) per day. DHA is particularly important as it is the main omega-3 in the brain. (Read this post for more information on DHA as brain food.) Omega-3 fatty acids may be given in the forms of simple fish oil mixed in their food or drinks.

I don’t recommend fermented fish oil. And when dosing I tend to increase the dose of omega-3 is the children are older (specific dose for varying ages of children can be found in The Nemechek Protocol for Autism and Developmental Disorders) When in doubt, I favor a high dose.

If children have difficulty with diarrhea or prior problems with fish oil causing diarrhea, I have the kids start inulin fiber alone for 2-3 weeks in order to let the gut bacteria balance out, and then slowly increase the dose of fish oil and usually the tolerance is much better.

Whether the parents use Nordic Fishies or or another brand of liquid fish oil, I recommend they buy a high-quality brand as there is a very high level of fraud in the supplement industry.

All families are asked to cook their foods in domestic extra virgin olive oil (EVOO). EVOO contains 70% oleic acid, and oleic acid reverses the underlying inflammation coming from excessive linoleic acid toxicity. (Watch my screencast for more information on the benefit of olive oil.)

Linoleic acid is most commonly found in the unnatural vegetable oils added to the foods we purchased. (See my other post about omega-3/omega-6 rebalancing for more information on this topic.)

The bigger, older children with autism require more effort and higher doses of inulin. To gain better control of SIBO in older children I often treat with a 10-day course of Rifaximin (Xifaxan in U.S.). Rifaximin is a non-absorbable antibiotic that is only used for other bacterial overgrowth conditions (hepatic encephalopathy and IBS with diarrhea).

Follow-up use of inulin after Rifaximin is sometimes used if intestinal symptoms are still present. If inulin does not make any significant difference as a follow-up therapy, I stop it. I never add probiotics after resetting with Rifaximin because probiotics can easily make things worse even if they helped prior to the use of Rifaximin.

The reversal of bacterial overgrowth with inulin results in a drop of propionic acid and can result in a sudden improvement in function within a few weeks. But many children do not fully return to normal because they still have underlying developmental delay (some quite severe) as well as ADD, ADHD, sensory issues, seizures, as well as chronic depression, anxiety or aggressive behaviors. ( Watch my screencast about how leakage of LPS from bacterial overgrowth prevents the brain from fully recovering from injuries.)

These remaining conditions take longer but week by week things can slowly improve. If there is no significant improvement within 2 months, I generally increase the dosage of omega-3 fatty acids. If things still do not improve or seem to plateau after a couple months, I now add bioelectric Vagus Nerve stimulation to the Nemechek Protocol with good results. (See my screencast about vagus nerve stimulation.)

The brains of older kids that have experienced prolonged bacterial overgrowth and inflammation as well as more brain injuries that occur over time, generally take longer to show improvement but I have seen significant progress in older kids as well.

I care for 2 teenage non-verbal autistic boys (14 and 16 years of age), and although they showed signs of continual improvement, they took about 4-5 months to begin speaking.

More recent is a remarkable case of a 23-year-old non-verbal autistic girl with frequent seizures. Within 8 months her seizures had reduced from 5-7 per day to 2-3 per week, and she can now write her name and converse in both Spanish and English (she lives in a dual language family).

For autistic children, the Nemechek Protocol will need to be daily and possibly forever but the benefits are life changing. Inulin fiber, omega-3 fatty acids and olive oil are from natural sources, are commonly consumed by most of us every day, and are available without prescription.

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.

March 23, 2017 – An Addendum on Recovery

My Experience with Autism Recovery:

Uniformly all the kids under my care (50-60 to date) seem to be improving in significant ways.

In terms of speech, some younger kids start speaking within a few weeks while kids in the teens might take 4-6 months. Our 23-year-old patient didn’t start speaking until after 8-9 months of treatment.

Importantly, even the most severe cases have a noticeable improvement in their awareness of their surroundings within a week or 2. I interpret this as a decline in the toxic effect of the propionic acids on their brains. Parents report more eye contact, awareness or acknowledgement others have entered the room. They also seem more tolerant of being touched or held, or are more willing to approach someone and be physically close to them.

After the first few weeks, recovery rates are highly variable, and I believe this is due to the degree of developmental delay underlying the toxic state. If the inflammatory cytokine process has been going on since birth, there can be so much developmental delay as to be labeled mentally retarded. But if the developmental delay is simply mild, kids may seem very functional quickly.

The important point to remember is that your child’s brain and an enormous capacity to continue the path of development once the inflammation is controlled. Neuronal/synaptic pruning will re-initiate, and according to the developmental delay literature, they can catch-up about 2-3 months of development for every 1 calendar month. In my estimation, it seems to advance this fast if not faster.

The underlying wild card is what gene has been activated by the inflammation and what might it do to the neurological impairment of your child’s brain. The inflammatory environment that prevents normal synaptic pruning and recovery from brain injury also triggers the litany of genes being found in autism.

Inflammatory cytokines abnormally produced by the mother are affecting the child’s nervous system within the womb, and then the imbalance of intestinal bacteria of the child as well as high omega-6 food sources continue to fuel the inflammatory process within the child after birth.

These inflammatory cytokines are the primary process through which the genes within the DNA that had been dormant for 1,000’s of years in the child’s ancestors are finally activated, begin altering how cells function, and contribute to the overall variety of neurological, behavioral characteristics that manifest in autism.

Here’s the potential for recovery in the autistic brain. A 23-year old non-verbal autistic female (Lennox-Gastaut Syndrome), was having 6-8 seizures per day and had never held her parents gaze for her entire life. She did not like to be held, could not color or write, and sat curled up in a chair most of the day rocking.

Within 2 months’ of starting our protocol (rifaximin, high dose omega-3 fatty acids, and mother cooking with California olive oil), her seizures had dropped to 1-2 a day, she would sit upright in a chair and she slept through the night.

At month 4 she started looking her parents in the eyes and holding their gaze, and was more able to be touched and hugged.

At her month 6 office visit, she started smile at me, her seizures had reduced to 1-2 per week, she could now write her name (although she had never been shown previously) and could draw objects that were recognizable.

At 8 months, she began speaking rudimentary Spanish and English (dual language household) but emotionally is behaving as if she is 3 years old.

At 18 months, she speaks very clearly in full sentences, her seizures have declined to 1-2 per month (despite discontinuation of 2 seizure medications), and her emotional maturity has risen to about that of a 4-5-year-old.

But don’t despair. No matter how badly the developmental delay has slowed brain maturation, the potential for an unbelievable recovery is present. We are beginning to understand that once human genes are turned on by inflammation, they can ultimately be shut back off again once the inflammatory environment within the body is significantly reduced.

Do your best to be patient and give this approach a chance. Because the path to recovery over all things medical is 3 steps forward, and 1-2 back, compare today’s behavior to last month’s, not yesterday’s. The neurons within the human brain, like your hair, can only grow and change only so fast.

Every month, your child’s brain has the ability to “catch-up” 2-3 months in development. That means every calendar year, they may catch-up 2-3 years. I believe once the inflammation is suppressed, all that is required for recovery is a good solid inflammation suppressing regimen and patience.

May 26, 2017 – Addendum on The Misconception of Feeding Bad Bacteria and Yeast

The conclusion that increased stemming, less sleeping or increased anxiety is from inulin feeding “bad” bacteria such as Klebsiella has been a concern of several commenters.

I’m not saying this is impossible but I do not believe that to be the case, and have never seen such a reaction in the many children I’ve worked with. There are several reasons for this.

First, inulin’s main effect is within the lumen of the small intestine where bacteria digest inulin through a process referred to as fermentation. The primary effect is the production of the healthy short chain fatty acid known as butyric acid. Only small amounts pass through to the colon.

Secondly, a significant increase in pathogenic bacteria, or overgrowth bacteria would almost certainly cause an increase in diarrhea, stool frequency, abdominal cramping, reflux and eczema. We do not see this, and in fact there in general a reversal of these symptoms with the use of symptoms with the use of inulin. If the intestinal ( not neurological or behavioral) symptoms were to worsen on inulin, I would suggest the inulin be discontinued and would suggest using Rifaximin.

The development of constipation with the use of inulin is a sign of underlying autonomic dysfunction from developmental and cumulative injury that eventually reverse after a few months of fish oil.

Thirdly, propionic acid has a sedating effect on children, almost as if the children had been taking Valium or Xanax. Therefore, once inulin reverses the bacterial overgrowth and the propionic acid levels decline, the children will come out of their stupor. There behavior at this point is predicated but their pre-existing developmental abnormalities and cumulative brain injuries and not some toxic effect of inulin.

A fourth point is that the detection of pathogenic bacteria such as Klebsiella in the stool by no means suggests these bacteria are present within the small intestine where inulin has it’s main effect. Detection of pathogenic bacteria such as <em>Klebsiella pneuomiae</em> or <em>Clostridium difficle</em> are commonly in asymptomatic patients and are essentially harmless. Their growth is kept in check by a healthy balance of other bacteria which is further bolstered with inulin.

And finally, some parents are worried about overgrowth of candida. I agree that candida and other yeasts/fungi inhabit the intestinal tract but more detailed studies demonstrate yeast/fungal overgrowth does not occur in autism. And while the observations of clinical improvement about reduction of sugars and etc. are correct (think GF/CF, FODMAPS, GAPS), they were misattributed to yeast instead of the bacterial overgrowth for which we have mounting evidence.

Because of this, I believe the use of potent anti-fungal drugs is unwarranted in the specific treatment of autism.

Hope this helps.

© 2017. Dr. Patrick M. Nemechek and Jean R. Nemechek. All Rights Reserved. Patent Pending.