What’s Wrong with the Gut of Children with Autism?

At its core, autism, with all its bizarre behaviors, poor language, social isolation and delays in development, might come down to an altered intestinal ecosystem.  That possibility was expressed by Professors Finegold and Borody [below] (and others) at the GI Think Tank at the Autism One conference in Chicago last month.

Borody and Finegold

I remain cautious about this perspective, but it has a fair chance of explaining some of the refractory and significant issues our children present us.  In a healthy gastrointestinal ecosystem there may be more than 5000 different species of bacteria present. That diverse ecosystem provides a stable foundation for the development of the child’s immune system (Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012 Jun 22;149(7):1578-93. Chung H, et al. Harvard Medical School, Boston, MA 02115, USA.). But it isn’t just the GI immune system -70% of the total human immune system is gut related.

Sadly, for most children, no probiotic or antibiotic intervention provides sustained healing of the gut ecosystem and this includes: specific carbohydrate diets, paleiodiets, raw camel milk, kefir, biofilm protocols or pounds of probiotics per year.

In contrast to a healthy gut, evidence from sophisticated DNA probes is telling us the autism ecosystem may be hanging around 300-500 species (a fraction of normal 5000 species). So it is biologically impoverished and with that species which would normal get a small piece of the metabolic impact of the gut, actually dominate the biochemistry and immunology. Therein lies the problem: altered ecosytem = altered biochemistry = altered immunology.

Now, more about probiotics and diet.  Many of you have spent $$$$ on special diets and probiotics and are largely where you started: poorly formed, foul smelling, weird colored bowel movements or stuck with chronic constipation.  After putting more thought into this, we shouldn’t be that surprised by the often poor results from both diet changes and probiotics.  The ecosystem of the gut is diverse and complex.  It is also specific to its anatomy.  Higher up in the mouth, esophagus, stomach and small intestine, species that can tolerate more oxygen in their environment are favored.  Lower down in the large bowel or colon, species that do not tolerate as much oxygen (anerobes or partial-anerobes) do better.

Probiotics are nearly exclusively aerobic (oxygen-liking) species. This simply means they would prefer to grow closer to the mouth, including the small intestines. Small intestinal bacterial overgrowth (SIBO) is a likely consequence of giving aerobic bacteria (probiotics) to a child, especially when we know sugars are more poorly digested in the autism gut.  (see: Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances. Williams BL, Hornig M, Buie T, Bauman ML, Cho Paik M, Wick I, Bennett A, Jabado O, Hirschberg DL, Lipkin WI.  PLoS One. 2011;6(9):e24585. Epub 2011 Sep 16.).

But at their best, probiotics, allow you to supplement just a few species: likely several thousand species less than the natural diversity of the human gut microbiome.  Without that broad ecological stability, the immune system gets pushed around far more than desirable.  The results are food allergies, irritable bowel (cramps, diarrhea and constipation), overgrowth of potentially toxic bacteria, and inflammation both in the gut and more widely in the body (eczema, asthma, and rhinitis). Further, the biochemistry of the gut microbiome, which is typically 50% of a person’s total metabolism, will shift dramatically.

All that is left is to explain how this ecological impoverishment of the autism microbiome, creates neurodevelopmental dysfunction. And this is where a whole bunch (nearly all) of psychologists, neurologist, and pediatricians struggle to see the connections. To be fair to their skepticism, the potential link between the gut microbiome and neuroimmune problems are just beginning to emerge in the medical literature.  (Immune and neuroimmune alterations in mood disorders and schizophrenia. Drexhage RC, Weigelt K, van Beveren N, Cohen D, Versnel MA, Nolen WA, Drexhage HA. Int Rev Neurobiol. 2011;101:169-201.) and (The mind-body-microbial continuum. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. Dialogues Clin Neurosci. 2011;13(1):55-62.).

However, even this eloquent model of human immunological development leaves out at least one critical step, which in my view separates autism from kids with food allergy, asthma and irritable bowels, but whom don’t have autism. This missing factor seems to be intrinsic immune activation in the brain of children with autism. 

The brain is very much like this castle. It has a barrier around it (the blood-brain barrier- BBB) just like the moat and drawbridge.  Each gate is design to only allow entrance to the king’s invited friends – in an ideal world that is the way our brain works – only allowing acceptable molecules access to the brain side of the BBB. 

Clearly the BBB is not as protective as it needs to be in autism, and it also appears the gate keepers (astrocytes and microglia) have even been bribed to work against the King (autoimmunity).  I still think this process of breaking down the castle/brain defenses is the work of a chronic pathogen (likely viral) residing in the endovascular compartment – which is the BBB.  This is where I think GcMAF is helping to correct the persistent issues (please see prior posts). 

But we need to get back to the gut ecosystem and explore what the medical literature is telling us about repairing that environment.

First, it is finally becoming more mainstream to think of fecal bacteriotherapy (FBT) or transplantation as the ONLY way to replace the missing good bacteria.  The shortcomings of traditional probiotics are clearly evident (ie, aerobic and few in diversity). FBT simply means giving health feces to an unhealthy person to make them healthy.  Sound ridiculous? It isn’t and it may be an inexpensive fix for a complex biological condition.

Finding a donor for providing an ideal ecosystem transplant is very challenging. Here are a few of the proposals for screening potential donors present in the medical literature.

The Australian CDD criteria:


Borody and Khoruts: Nat Rev Gastroenterol Hepatol. 2011 Dec 20;9(2):88-96.

Unfortunately, if you read the list of exclusion from Borody and Khoruts you will quickly realize there are few potential donors left within your family or circle of friends.  That is a a real problem.

Harvard proposed a somewhat easier protocol for screening the potential donors for acceptable criteria.


Pediatrics. Russell et al. 2010 Jul;126(1):e239-42. Epub 2010 Jun 14.

I tend to favor the Harvard protocol as it is more specific, and yet I do think we need to screen the donor’s gut history as well. 

This is the Harvard treatment protocol.



The Harvard protocol is fine if you have access to a hospital willing to work with you, or at a minimum, an out-patient center with x-ray and other equipment.  Others have suggested colonoscopy (surgical procedure), but again the risks benefits get harder to sort out.

Practically speaking – there is NO WAY this will be happening for autism: so I propose a modification of the current techniques being employed for FBT.

The Bradstreet Protocol for FBT in ASD :

1). The child’s family initiates screening of donors within the family and close friends. These individuals, if willing, will have more formal screening. First, however, the family should find donors who meet the following criteria:

a). Generally healthy with no known infectious diseases and with good bowel movements.

b). Limited use of antibiotics especially in last 6 months.

c). Stools are brown, formed and not foul.

d). No apparent abdominal pain patterns.

e). No obvious food allergies.

f). Not using heartburn medicine.

g). No significant food cravings: donor eats a diverse diet, including vegetables.

2). Once a list of potential donors is identified by the family, a short interview with the treating physician needs to take place to review history related to antibiotics, risky personal behaviors and medical issues.

3). Individual potential donors who are not excluded should then undergo medical screening to rule out:

a). Hepatitis A, B and C

b). HIV 1 and 2

c). Syphilis and Lyme disease

d). H. pylori

e). Fecal parasitology and culture or,

f). Comprehensive Stool Digestive Analysis 2.0 (Genova Disgnostics)

4). Once a healthy donor is identified, the process of preparing the child to receive the donation begins.

a). Prep the bowel just as required for colonoscopy (GoLYTELY®, Magnesium Citrate, X-prep®, enemas or other interventions to cleanse the bowel of existing feces.

b). Potential antibiotics (vancomycin, Xifaxan, etc), antifungals and anti-parasitics for the recipient.

c). Gather fresh feces from the donor and rapidly place 1 cup or less in plastic freezer bag with 250 -500 ml of sterile salt water (saline) and express excess air so as close to all air is removed as possible.

d). Mush the feces and water until it is a slurry or puree texture. Unlike Harvard I DO NOT RECOMMEND BLENDERS. They whip too much air into the donation and can change the microbiome.

e). Instill the slurry of fresh feces into the rectum via a retention enema and attempt to move the transplant to the right side of the colon. Massage the feces from the left lower abdomen up and to the right. Attempt to position the child in a knee chest – buttocks up – position and then after 5 minutes (if possible) move to a right down posture to gather the donor transplant to the right side.

f). Some children may require sedation. A bathtub may be a good location to attempt this. Consider a colon cleansing center for this procedure if you can get cooperation from them.

g). Leave the donor feces in place as long as possible before expulsion. 30 minutes is probably ideal but I realize this is unlikely. We can only do what we can do.

ALL of this requires physician supervision.

About Dr Bradstreet
Dr Bradstreet is a graduate of the University of South Florida College of Medicine and received his residency training at Wilford Hall USAF Medical Center. He is a Fellow of the American Academy of Family Physicians. He is an Adjunct Professor at the Southwest College of Naturopathic Medicine in Arizona. He is extensively published in the peer-reviewed literature on subjects of autism, oxidative stress, mitochondrial disorders, virology, hyperbaric oxygen, and toxicology (especially heavy metal chelation). He is trained in the the isolation and use of stem cells.

7 Responses to What’s Wrong with the Gut of Children with Autism?

  1. Eva says:

    Dr. Bradstreet, first of all thank you for all. I’m from Italy so excuse my bad English.
    I have a big doubt about FBT, I try to explain: You say that autistic kids have a biologically impoverished gut, with less than 10% species of a healthy gut. I suppose there might be lots of causes of this condition. When you do a FBT, I suppose you don’t remove these causes, or maybe according to the specific conditions you just can remove some of them. So, after FBT, that I consider like a “perfect mix of probiotic”, is there any chance that gut remain biologically healthy or like I presume, soon or after it will get poor again? FBT is a quite hard protocol anyway, it’s hardly to get it once a month…

  2. Cheryl says:

    unrelated question – a child you did not immunize that is now 12 years old (did not immunize due to an older sibling with Autism). what now? all the information about immunizations relates to small children. What do I do with my 12 year old? Do I start the process of immunization since she is developmentally fine. Do I only give her certain immunizations? I need help! I cannot find any information about this relating to an older child and there is no DAN doctor in my area.

  3. Melinda says:

    Hi Dr Bradstreet, I have asked about FBT for my 10 year old son but have been constantly told that it isn’t a procedure anyone will perform on a child? Are you aware of any clinics that do this? We are in Australia.

    • Professor Brody is one of the leading experts on FBT and he is in Australia. Whether he will treat a child is not something I know. I suggest you contact his team at http://www.cdd.com.au/pages/clinical_staff.html

      • Melinda says:

        Thanks, I have been In touch with his clinic, they do not treat children and will not see a child that is not presenting with a treatable gastrointestinal complaint first and foremost. I have been using a variety of protocols that are attributed to Dr Borody, yourself, Ray Peat and others that involve specific probiotics as well as supplements and we have seen an improvement in our son’s overall symptoms. For this reason I would be interested in FBT. I would be prepared to travel to a reputable clinic if there was one available, I just don’t know of anywhere that will treat a child for the presentation of autism. If this possibility is not an option, have you heard of any viable protocols that seem to be effective? I can’t get Learner’s Edge in Australia, I have to order it from overseas, are you aware of any clinical trials involving this product? Thanks for this page, it gives me the motivation to keep trying.

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